Vol. 17 No. 2, October 2016

Accredited by the Indonesian Institute of

Sciences No. 818/E/2015

Editorial Board

Editor-in-Chief

Markus Anda Mineralogy and Soil Classification (Scopus ID : 23024287000 / h-Index: 6)

Indonesian Center for Agricultural Land Resources Research and Development,

Indonesia

International Editorial Board

Supriadi Plant Pathology, Indonesian Spice and Medicinal Crops Research Institute,

Indonesia

Budi Tangendjaja Animal Feed and Nutrition, (Scopus ID: 6508321607 / h-Index : 6) Indonesian

Center for Animal Research and Development, Indonesia

Dewa Ketut Sadra Swastika Socioeconomics, Indonesian Center for Agricultural Socio Economic and Policy

Studies, Indonesia

Randy Alan Dahlgren Soil Science and Biogeochemistry, (Scopus ID: 7005899511 / h-Index : 45)

University of California, Davis, United States

Bunyamin Tar'an Plant Biotechnology, (Scopus ID: 56181765200 / h-Index : 17) University of

Saskatchewan, Canada

Soon-Wook Kwan Plant Breeding and Molecular Breeding, (Scopus ID : 55782595000 / h-Index

: 9) Pusan National University, Republic of Korea

Sri Yuliani Postharvest Technology, (Scopus ID : 9844293200 / h-Index : 6) Indonesian

Center for Agricultural Postharvest Research and Development, Indonesia

I Made Tasma Plant Breeding and Molecular Biology, (Scopus ID : 6507936762 / h-Index : 6)Indonesian Center for Agricultural Biotechnology and Genetic Resources

Research and Development, Indonesia

Puji Lestari Molecular Biology, (Scopus ID : 6507413576 / h-Index : 6) Indonesian

Center for Agricultural Biotechnology and Genetic Resources Research and

Development, Indonesia

Md. Babul Akter Crop Physiology and Molecular Breeding, Bangladesh Institute of Nuclear

Agriculture (BINA), Bangladesh

Assistant Editor

Endang Setyorini Indonesian Center for Agricultural Library and Technology Dissemination,

Indonesia

Slamet Sutriswanto Indonesian Center for Agricultural Library and Technology Dissemination,

Indonesia

Layout Editor

Ujang Sahali Indonesian Center for Agricultural Library and Technology Dissemination,

Indonesia

All inquiries and manuscripts should be sent to the:

The editorial office

Indonesian Center for Agricultural Library and Technology Dissemination

Jalan Ir. H. Juanda No. 20

Bogor 16122, Indonesia

Telephone : +62 251 8321746

Fax : +62 251 8326561

E-mail : pustaka@litbang.pertanian.go.id

Website : http://pustaka.litbang.pertanian.go.id; http://ejurnal.litbang.pertanian.go.id/index.php/ijas

Printed in Indonesia

2016, Indonesian Agency for Agricultural Research and Development, Jakarta, Indonesia

ISSN 1411-982X

E-ISSN 2354-8509

SCIENCE

Indonesian Journal of

AGRICULTURAL

International Peer-Reviewer

Kularb Laosatit Genetic and Molecular Biology, (Scopus ID : 36872678000 / h-Index : 3), Faculty

of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen,

Nakhon Pathom, 73140, Thailand

Ahmad Kurnain Soil Science, (Scopus ID : 56515310300 / h-Index: -), Lambung Mangkurat

University, Banjarmasin, Indonesia

Purwiyatno Hariyadi Postharvest, (Scopus ID : 16156219500 / h-Index : 6) Bogor Agricultural

University, Indonesia

Ika Mariska Plant Physiology and Biotechnology, (Scopus ID : 6507460259 / h Index : 4)

Indonesian Center for Agricultural Biotechnology and Genetic

Resources Research and Development, Indonesia

Backki Kim Biochemistry, Genetics and Molecular Biology, (Scopus ID : 56042253700 /

h-Index : 3), Texas A&M University, College Station, TX 77843, United States

Sutoro Agronomy, Indonesian Center for Agricultural Biotechnology and Genetic

Resources Research and Development, Indonesia

Production and quality enhancement of mango using fan jet

sprayer irrigation technique

Nani Heryani, Budi Kartiwa, Yayan Apriyana and Haris Syahbuddin 41–48

Agrobacterium tumefaciens-mediated in-planta transformation

of Indonesian maize using plG121Hm-Cs plasmid containing nptII

and hpt genes

Edy Listanto, Eny Ida Riyanti and Sustiprijatno 49–56

Genomic variation of five Indonesian cacao (Theobroma cacao L.)

varieties based on analysis using next generation sequencing

I Made Tasma, Dani Satyawan, Habib Rijzaani, Ida Rosdianti,

Puji Lestari and Rubiyo 57–64

The potential use of SSR markers to support the morphological

identification of Indonesian mungbean varieties

Reflinur, Puji Lestari and Suk-Ha Lee 65–74

Capillary water rise in peat soil as affected by various

groundwater levels

Muhammad Imam Nugraha, Wahida Annisa, Lailan Syaufina

and Syaiful Anwar 75–83

Indonesian Journal of Agricultural Science is previously published as Indonesian Journal of Crop Science (1985 - 1999). This

journal is published in one volume of two issues per year by the Indonesian Agency for Agricultural Research and Development.

It is available online at: ejurnal.litbang.pertanian.go.id/index.php/ijas

The journal publishes primary research articles from any source if they make a significant original contribution to the experimental

or theoretical understanding of some aspect of agricultural science in Indonesia. The definition of agricultural science is kept as

wide as possible to allow the broadest coverage in the journal.

ISSN 1411-982X

E-ISSN 2354-8509

Vol. 17 No. 2, October 2016

SCIENCE

Indonesian Journal of

AGRICULTURAL

CONTENTS

UDC: 631.87

Wahida Annisa and Dedi Nursyamsi (Indonesian Swampland

Agricultural Research Institute, Banjarbaru)

Iron Dynamics and Its Relation to Soil Redox Potential and

Plant Growth in Acid Sulphate Soil of South Kalimantan,

Indonesia (Orig. Eng.)

IJAS, April 2016, vol. 17 no. 1, p. 1–8, 1 tab., 8 ill., 27 ref.

Organic matter has a function to maintain reductive

conditions and to chelate toxic elements in acid sulphate soils.

The study aimed to assess the dynamics of ferrous iron (Fe2+)

in acid sulphate soil and its correlation with soil redox

potential (Eh) and plant growth. The experiment was arranged

in two factorial randomized block design with three

replications. The first factor was two types of organic matter:

(1) control (without organic matter), (2) rice straw and (3)

rush weed (Eleocharis dulcis). The second factor was time of

decomposition of organic matter: I1 = 2 weeks, I

2 = 4 weeks, I

3

= 8 weeks, and I4

= 12 weeks (farmer practice). The results

showed that concentration of ferrous iron in the soil ranged

from 782 to 1308 mg kg-1 during the rice growing season. The

highest constant rate of iron reduction (k F2+) was observed on

application of rice straw and rush weed with decomposition

time of 8 weeks with the k Fe2+ value of 0.016 and 0.011 per

day, respectively, while the ferrous iron formation without

organic matter had the k Fe2+ value of 0.077 per day. The

ferric iron (Fe3+) reduction served as a function of soil Eh as

indicated by the negative correlation of ferrous iron and Eh (r

= -0.856*). Organic matter decreased exchangeable iron due

to chelating reaction. Iron concentration in roots was

negatively correlated with soil soluble iron (r = -0.62*).

Application of rice straw decomposed for 8 weeks increased

the height of rice plant up to 105.67 cm. The score of Fe2+

toxicity at 8 weeks after planting ranged from 2 to 3, so rice

crop did not show iron toxicity symptoms.

(Author)

Keywords: Ferrous iron, redox potential, plant growth, acid

sulphate soil

————————————————————————UDC: 634.471.1-18

Yosi Zendra Jonia, Riry Prihatinia, Darda Efendib and Ika

Roostikac (aIndonesian Tropical Fruit Research Institute,

Solok, bDepartment of Agronomy and Horticulture, Bogor

Agricultural University, Bogor, cIndonesian Center for

Agricultural Biotechnology and Genetic Resources Research

and Development, Bogor)

Effect of Different Sources of Plant Growth Regulator on The

Induction and Development of Mangosteen Somatic Embryos

(Orig. Eng.)

IJAS, April 2016, vol. 17 no. 1, p. 9–16, 1 tab., 9 ill., 26 ref.

Somatic embryogenesis is a technique for regenerating

embryos derived from somatic cells of various plant species.

This technique along with the utilization of plant growth

regulator (PGR) might benefit for mass propagation and

improvement of plant species through biotechnological tools.

The study aimed to determine the effect of different plant

growth regu-lators, namely 6-benzyladenine (BA) and

thidiazuron (TDZ) on the embryogenic callus induction as well

as casein hydrolysate and malt extract on the somatic embryo

development of mangosteen. The explants used were in vitro

young stems of mangosteen clone Leuwiliang. This study

consisted of two experiments, namely induction of

embryogenic callus and formation of somatic embryo. The

first experiment was arranged as factorial in a completely

randomized design with BA (0 and 0.7 mg l-1) as the first factor

and TDZ (0, 0.1, 0.5 and 1.0 mg l -1) as the second factor. The

second experiment consisted of four treatments, i.e. casein

hydrolysate and malt extract at the rate of 500 and 1,000 mg

l-1. The results showed that the best medium for embryogenic

callus induction was MS supplemented with 0.1 mg l-1 TDZ,

which resulted semifriable calli. Casein hydrolysate and malt

extract could not induce the formation of somatic embryos.

After two times subcultures on the same MS medium

supplemented with 0.5 mg l-1 TDZ and 0.7 mg l-1 BA, a total of

33.8 somatic embryos per explant was induced. The successful

somatic embryogenesis would support mangosteen breeding

and in vitro mass propagation program.

(Author)

Keywords: Garcinia mangostana, plant growth regulator,

callus induction, somatic embryo

————————————————————————UDC: 635.356-152

Nur Kholilatul Izzaha, Reflinurb and Tae-Jin Yangc (aIndonesian

Industrial and Beverage Crops Research Institute, Pakuwon,

Sukabumi, bIndonesian Center of Agricultural Biotechnology

and Genetic Resources Research and Development, Bogor,cDepartment of Plant Science and Research Institute for

Agriculture and Life Sciences, Seoul National University

Seoul)

Development of EST-SSR Markers to Assess Genetic Diversity

of Broccoli and Its Related Species (Orig. Eng.)

IJAS, April 2016, vol. 17 no. 1, p. 17–26, 5 tab., 4 ill., 31 ref.

Development of Expressed Sequence Tag-Simple Sequence

Repeat (EST-SSR) markers derived from public database is

known to be more efficient, faster and low cost. The objective

of this study was to generate a new set of EST-SSR markers for

broccoli and its related species and their usefulness for

assessing their genetic diversity. A total of 202 Brassica

oleracea ESTs were retrieved from NCBI and then assembled

into 172 unigenes by means of CAP3 program. Identification

INDONESIAN JOURNAL OF AGRICULTURAL SCIENCE

ISSN 1411-982X (printed version) Volume 17, 2016

E-ISSN 2354-8509 (electronic version)

The descriptons given are free terms. This abstract sheets may be reproduced without permission or charge.

of SSRs was carried out using web-based tool, RepeatMasker

software. Afterwards, EST-SSR markers were developed using

Primer3 program. Among the identified SSRs, trinucleotide

repeats were the most common repeat types, which accounted

for about 50%. A total of eight primer pairs were successfully

designed and yielded amplification products. Among them, five

markers were polymorphic and displayed a total of 30 alleles

with an average number of six alleles per locus. The

polymorphic markers were subsequently used for analyzing

genetic diversity of 36 B. oleracea cultivars including 22

broccoli, five cauliflower and nine kohlrabi cultivars based on

genetic similarity matrix as implemented in NTSYS program.

At similarity coefficient of 61%, a UPGMA clustering

dendrogram effectively separated 36 genotypes into three

main groups, where 30 out of 36 genotypes were clearly

discriminated. The result obtained in the present study would

help breeders in selecting parental lines for crossing.

Moreover, the novel EST-SSR markers developed in the study

could be a valuable tool for differentiating cultivars of broccoli

and related species.

(Author)

Keywords: Broccoli, cauliflower, kohlrabi, EST-SSR markers,

genetic diversity

————————————————————————UDC: 634.773+635.965.274

Riry Prihatinia and Norihan Mohamad Salehb (aIndonesian

Tropical Fruit Research Institute, Solok, bDepartment Cell and

Molecular Biology, Faculty of Biotechnology and

Biomolecular Sciences, Universiti Putra Malaysia 43400 UPM

Serdang Selangor DE)

Sensitivity of Pigment Content of Banana and Orchid Tissue

Culture Exposed to Extremely Low Frequency

Electromagnetic Field (Orig. Eng.)

IJAS, April 2016, vol. 17 no. 1, p. 27–34, 1 tab., 2 ill., 38 ref.

Natural exposure of extremely low frequency electromagnetic

field (ELF-EMF) occurs in the environment and acts as one of

the abiotic factors that affect the growth and development of

organisms. This study was conducted to determine the effect

of ELF-EMF on the tissue cultured banana and slipper orchid

chlorophyll content as one of the indicators in measuring

plant photosynthetic capacity. Four days old banana (Musa sp.

cv. Berangan) corm and seven days old slipper orchid

(Paphiopedilum rothschildianum) cultures were exposed to 6

and 12 mT ELF-EMF generated by controllable ELF-EMF

built up machine for 0.5, 1, 2 and 4 hours. After exposure, the

banana and orchid cultures were incubated at 25° C for 8 and 16

weeks, respectively. The results showed that the ELF-EMF

exposure had different effects on banana and slipper orchid

cultures though both plant species belong to monocotyledon.

The highest increase in chlorophyll content on banana was

resulted by the high intensity and long duration of ELF-EMF

exposure (12 mT for 4 hours), whereas on slipper orchid the

modest and short duration of ELF-EMF exposure produced the

most excessive chlorophyll content. Different ELF-EMF

exposures (12 mT for 4 hours and 6 mT for 30 minutes) had

potential to be applied on each plant to improve in vitro plant

(banana and slipper orchid, respectively) growth. The

increased chlorophyll and carotene/xanthophyll content on

banana indicated that the banana was more tolerant to ELF-

EMF exposure compared to slipper orchid.

(Author)

Keywords: Banana, orchid, carotene, chlorophyll, electro-

magnetic field

————————————————————————UDC: 633.683

Imron Riyadi and Sumaryono (Indonesian Research Institute

for Biotechnology and Bioindustry, Bogor)

Effect of gamma irradiation on the growth and development

of sago palm (Metroxylon sagu Rottb.) calli (Orig. Eng.)

IJAS, April 2016, vol. 17 no. 1, p. 35–40, 2 tab., 3 ill., 22 ref.

The application of gamma irradiation on plant materials may

increase the genetic variation of the offspring with useful

traits. The experiment was conducted to determine the effect

of irradiation dosage of gamma ray on growth and development

of sago palm (Metroxylon sagu) calli. Friable calli of sago

palm derived from suspension culture were used as a material

source. The primary calli were initiated from apical

meristematic tissues of sago palm suckers of Alitir variety

from Merauke, Papua. The treatments used were dosage of

gamma ray irradiation at 0, 5, 10, 15, 20 and 25 Gy. The

treated calli were then subcultured on modified Murashige and

Skoog (MMS) solid medium containing 3% sucrose and 0.1%

activated charcoal and added with 1 mg l-1 2,4-D and 0.1 mg l-

1 kinetin. The results showed that at all irradiation dosages,

calli biomass increased significantly. The highest proliferation

of calli biomass of 5.33 folds from the initial culture after 4

weeks was achieved at gamma irradiation of 25 Gy, whereas

the lowest proliferation of calli biomass of 3.4 folds was

achieved at control. The best development of embryogenic

calli was obtained at 10 Gy that produced 100% somatic

embryos, whereas the lowest somatic embryo formation at 0%

was obtained at 0 and 25 Gy after one subculture. High

response of somatic embryo induction to gamma irradiation at

10 Gy may increase production of somatic embryos. These

results can be used in in vitro breeding of sago palm via

mutagenesis to create new elite varieties.

(Author)

Keywords: Metroxylon sagu, gamma irradiation, embryogenic

calli, somatic embryo

————————————————————————UDC: 634.441.2-167

Nani Heryani, Budi Kartiwa, Yayan Apriyana and Haris

Syahbuddin (Indonesian Agroclimate and Hydrology Research

Institute, Bogor)

Production and Quality Enhancement of Mango Using Fan Jet

Sprayer Irrigation Technique (Orig. Eng.)

IJAS, October 2016, vol. 17 no. 2, p. 41–48, 6 tab., 4 ill., 36

ref.

Lack of water in reproductive phases (flowering, fruit

formation and maturation) of mango can reduce fruit

production and quality. In these phases the plant must be

protected from water stress. The aim of the research was to

assess the effect of irrigation on the productivity and quality

of mango fruits. The study was conducted at the Cukurgondang

Experimental Station, Pasuruan, East Java, from April to

December 2013, using 40 mango trees of 21 year-old Arum

Manis variety. Mangoes were planted on five rows with eight

plants for each row and 6 m x 6 m spacing within the row. Fan

jet sprayer irrigation was installed using hose according to

plant diameter. The irrigation technique of fan jet sprayer with

four nozzles per plant was applied at 125, 100, 75, 50 and 0%

of crop water requirements or equal to 828, 663, 497, 331 and

0 liters of water per tree, every seven days. The parameters

observed were the number and weight of fallen fruits and the

number, weight and quality of mangoes harvested. The results

showed that irrigation of 50% and 75% of crop water

requirement had the highest and lowest number of fallen fruits

(26% and 14% of total production), respectively. The highest

and lowest total number of mangoes were 3.108 and 1904

fruits, respectively, which were achieved at irrigation of 50%

and 75% of crop water requirement. Further, the highest and

lowest total weight of mango fruits were 1036.2 and 677.9 kg

respectively which were achieved at irrigation of 50% and

125% of crop water requirement. Mango fruits produced were

dominated by grades 2 and 3 with A quality.

(Author)

Keywords: Mango, production, quality, fan jet sprayer

————————————————————————

UDC: 633.15-152

Edy Listanto, Eny Ida Riyanti and Sustiprijatno (Indonesian

Center for Agricultural Biotechnology and Genetic Resources

Research and Development, Bogor)

Agrobacterium tumefaciens-Mediated In-Planta Transforma-

tion of Indonesian Maize Using plG121Hm-Cs Plasmid

Containing nptll and hpt Genes (Orig. Eng.)

IJAS October 2016, vol. 17 no. 2, p. 49–56, 1 tab., 5 ill., 33 ref.

Maize (Zea mays L.) productivity in Indonesia is challenged to

be increased using genetic engineering. Recent advances in

Agrobacterium tumefaciens-mediated in-planta transforma-

tion makes it possible to transform maize with low cost, and

simple method. This study aimed to confirm pIG121Hm-Cs

plasmid in A. tumefaciens, and to estimate the efficiency level

of A. tumefaciens-mediated in-planta transformation of

Indonesian maize by using pIG121Hm-Cs plasmid containing

nptII and hpt genes. A series of studies were conducted

including confirmation of gene construct of pIG121Hm-Cs

plasmid in A. tumefaciens, transformation of four maize lines

through A. tumefaciens-mediated in-planta technique,

acclimatization of transformant plants and molecular analysis

of selected plants using polymerase chain reaction (PCR). The

pIG121Hm-Cs plasmid was confirmed via PCR analysis using

specific primers of nptII and hpt genes and resulted 700 bp and

500 bp for fragments of nptII and hpt, respectively. After

selection, acclimatization and molecular analysis steps, the

efficiency levels of transformation of four maize lines were

low, ranging from 3.8% to 12.8%. The level of transformation

efficiency of ST-27 line was the highest accounting for 12.8%

of 45 planted embryos on selection medium based on PCR

analysis using specific primer for nptII gene. Overall, A.

tumefaciens-mediated in planta transformation on maize floral

pistil in this study proved to be successful and rapid. Therefore,

this enhanced transformation method will be beneficial for

Indonesian maize genetic engineering.

(Author)

Keywords: Maize, Agrobacterium tumefaciens, in-planta

transformation

————————————————————————UDC: 633.74-152

I Made Tasmaa, Dani Satyawana, Habib Rijzaania, Ida

Rosdiantia, Puji Lestaria and Rubiyob (aIndonesian Center for

Agricultural Biotechnology and Genetic Resources Research

and Development, Bogor, bIndonesian Industrial and Beverage

Crop Research Institute, Pakuwon)

Genomic Variation of Five Indonesian Cacao (Theobroma

cacao L.) Varieties Based on Analysis Using Next Generation

Sequencing (Orig. Eng.)

IJAS October 2016, vol. 17 no. 2, p. 57–64, 3 tab., 2 ill., 42

ref.

Indonesian cacao productivity is still low mainly due to the

lack availability of superior cacao planting materials. A new

breeding method is necessary to expedite cacao yield

improvement programs. To date, no study has yet been done

to characterize Indonesian cacao varieties at the whole

genome level. The objective of this study was to characterize

genomic variation of five superior Indonesian cacao varieties

using next-generation sequencing. Genetic materials used were

five Indonesian cacao varieties, i.e. ICCRI2, ICCRI3, ICCRI4,

SUL2 and ICS13. Genome sequences were mapped to the cacao

reference genome sequence of Criollo variety. Sequence

alignment and genomic variation discovery were done using

Bowtie2 and mpileup software of Samtools, respectively. A

total of 2,326,088 single nucleotide polymorphisms (SNPs)

and 362,081 insertions and deletions (Indels) were obtained

from this study. In average, a DNA variant was identified in

every 121 nucleotides of the genome sequence. Most of the

DNA variants were located outside the genes. Only 347,907

SNPs and Indels (13.18%) were located within protein coding

region (exon). Among the DNA variations within exon,

188,949 SNPs caused missense mutation and 1,535 SNPs

induced nonsense mutation. Unique gene-based SNPs were also

discovered from this study that can be used as fingerprints for

the particular cacao variety. The DNA variants obtained were

excellent DNA marker resources to support cacao breeding

programs. The SNPs discovered are useful as materials for

genome-wide SNP chip development to be used for gene and

QTL tagging of important traits for expediting national cacao

breeding program.

(Author)

Keywords: Theobroma cacao, genome sequencing, genome

variation, SNP, next generation sequencing

————————————————————————UDC: 633.3-152

Reflinura, Puji Lestaria and Suk-Ha-Leeb (aIndonesian Center

for Agricultural Biotechnology and Genetic Resources

Research and Development, Bogor, bDepartment of Plant

Science and Research Institute for Agriculture and Life

Sciences, Seoul National University)

The Potential Use of SSR Markers to Support the

Morphological Identification of Indonesian Mungbean

Varieties (Orig. Eng.)

IJAS, October 2016, vol. 17 no. 2, p. 65–74, 4 tab., 2 ill., 31 ref.

Mungbean varieties were mainly characterized based on

morphological traits. Molecular genetic approach is expected

to help the breeder in identification of mungbean varieties in

more detail and to protect intellectual property right. This

study aimed to identify Indonesian mungbean varieties based

on DNA fingerprint profile using a marker set to support

morphological characters. A total of 22 Indonesian mungbean

accessions were characterized based on 21 morphological traits

and 55 simple sequence repeats (SSRs) primers. Of the total 22

mungbean varieties used in the present study, 16 varieties were

improved varieties and remaining six varieties were local

varieties originated from Java, Nusa Tenggara and Sulawesi

collected in GeneBank of ICABIOGRAD. The results showed

that the 21 morphological characters were not sufficient to

differentiate 22 mungbean varieties, while SSR analysis

revealed that eight multi-alleles markers and high polymorphic

information content (PIC) values have been successfully

selected for varietal identification. The selected markers

enabled to differentiate each mungbean variety according to

their genetic marker with the lowest distance of 0.125,

demonstrating the robustness of the selected marker set as a

tool to identify a specific DNA fingerprint profile as a varietal

identity (ID). The genetic identity of a variety was shown by

digital barcoding which represented a series of alleles produced

by corresponding markers. The DNA fingerprint profile of

each variety would be beneficial as reference identities of a

mungbean variety.

(Author)

Keywords: Mungbean, morphological characters, SSR markers,

DNA fingerprint, varietal identity

————————————————————————UDC: 631.445.1

Muhammad Imam Nugrahaa, Wahida Annisab, Lailan Syaufinac

and Syaiful Anward (aGraduate Student at Bogor Agricultural

University, Bogor, bIndonesian Swampland Agricultural

Research Istitute, Banjarbaru, cFaculty of Forestry, Bogor

Agricultural University, dFaculty of Agriculture, Bogor

Agricultural University)

Capillary Water Rise in Peat Soil as Affected by Various

Groundwater Levels (Orig. Eng.)

IJAS, October 2016, vol. 17 no. 2, p. 75–83, 3 tab., 6 ill., 31 ref.

Capillary water in peatlands has a very important role in

supplying water to the root zone of plants. The current water

content in the root zone depends mainly on groundwater levels

in some areas with shallow water levels. The study aimed to

measure the capillary water dynamics in peat soils at various

soil densities and groundwater levels which were observed from

the changes in peat color, moisture distribution, water content

and hydrophobicity of peat soil. The study was conducted in

the greenhouse of Indonesian Swampland Agricultural Research

Institute, Banjarbaru, South Kalimantan. The experiment was

arranged in a randomized block design with two factors and

three replications. The first factor was the bulk density (BD)

of peat, namely BD-1 (on actual condition, 0.1 g cm-3) and

BD-2 (compressed into 0.2 g cm -3). The second factor was

simulated groundwater levels (GWL) consisting of GWL-1 (-

100 cm), GWL-2 (-70 cm) and GWL-3 (-40 cm) from soil

surfaces. The results showed that the rise of capillary water in

peat soil reached a maximum height of 50 cm which was

characterized by the increase in water content at the top layer

in the range of 105–127% for BD-1 and 141–181% for BD-2.

The highest value of water content (308%) was achieved in

the treatment of GWL-3 with BD-2 and the lowest (37%) was

in the treatment of GWL-1 with BD-1. The rate of capillary

water rose progressively corresponded to the increase in BD

value because the number of micropores of BD-2 was greater.

(Author)

Keywords: Peat soil, capillary water, groundwater level, bulk

density, water content

INDONESIAN JOURNAL OF AGRICULTURAL SCIENCE

ISSN 1411-982X (versi tercetak) Volume 17, 2016

E-ISSN 2354-8509 (versi elektronik)

Kata kunci yang dicantumkan adalah istilah bebas. Lembar abstrak ini boleh dikopi tanpa izin dan biaya.

UDC: 631.87

Wahida Annisa dan Dedi Nursyamsi (Balai Penelitian Pertanian

Lahan Rawa, Banjarbaru)

Dinamika Besi dan Hubungannya dengan Potensi Redoks

Tanah dan Pertumbuhan Tanaman di Tanah Sulfat Masam

Kalimantan Selatan, Indonesia (Orig. Eng.)

IJAS, April 2016, vol. 17 no. 1, p. 1–8, 1 tab., 8 ill., 27 ref.

Bahan organik memiliki fungsi mempertahankan kondisi

reduktif tanah dan mengkelat unsur beracun di tanah sulfat

masam. Penelitian bertujuan untuk mempelajari dinamika besi

ferro di tanah sulfat masam serta korelasinya dengan potensi

redoks (Eh) tanah dan pertumbuhan tanaman. Penelitian

menggunakan rancangan faktorial dua faktor dan diulang tiga

kali. Faktor pertama adalah jenis bahan organik, yaitu (1)

kontrol (tanpa bahan organik), (2) jerami padi, dan (3) gulma

purun (Eleocharis dulcis). Faktor kedua adalah waktu

dekomposisi bahan organik, yaitu I1 = 2 minggu, I

2 = 4 minggu,

I3 = 8 minggu, dan I

4 = 12 minggu (pola petani Banjar). Hasil

penelitian menunjukkan bahwa secara umum konsentrasi besi

ferro (Fe2+) di tanah sulfat masam berkisar 782–1308 mg kg-1

selama pertumbuhan tanaman padi. Konstanta tertinggi

kecepatan reduksi besi (k Fe2+) terdapat pada perlakuan jerami

padi dan gulma purun dengan waktu inkubasi 8 minggu, masing-

masing 0,016 dan 0,011 per hari. Sementara konstanta

terendah ditunjukkan pada perlakuan tanpa bahan organik,

yakni 0,077 per hari. Reduksi besi ferri (Fe3+) merupakan

fungsi dari nilai Eh tanah yang ditunjukkan dengan adanya

korelasi negatif antara besi ferro dan nilai Eh dengan r = -

0,856*. Bahan organik dapat menurunkan konsentrasi besi

tukar dalam tanah melalui pengkelatan. Terdapat korelasi

negatif antara konsentrasi besi dalam akar dengan yang larut

dalam tanah dengan nilai r = -0.62*. Pemberian kompos jerami

padi dengan waktu inkubasi 8 minggu meningkatkan tinggi

tanaman padi yang mencapai 105,67 cm. Nilai skor keracunan

besi pada tanaman pada umur 8 minggu setelah tanam berkisar

2–3 dan disimpulkan tanaman padi cukup toleran di lahan

sulfat masam karena tidak menunjukkan gejala keracunan besi.

(Penulis)

Kata kunci: Besi ferro, potensial redoks, pertumbuhan tanaman,

tanah sulfat masam

————————————————————————UDC: 634.471.1-18

Yosi Zendra Jonia, Riry Prihatinia, Darda Efendib dan Ika

Roostikac (aBalai Penelitian Tanaman Buah Tropika, Solok,bDepartemen Agronomi dan Hortikultura, Institut Pertanian

Bogor, Bogor, cBalai Besar Penelitian dan Pengembangan

Bioteknologi dan Sumberdaya Genetik Pertanian, Bogor)

Pengaruh Sumber Zat Pengatur Tumbuh Tanaman yang

Berbeda pada Induksi dan Pengembangan Embrio Somatik

Manggis (Orig. Eng.)

IJAS, April 2016, vol. 17 no. 1, p. 9–16, 1 tab., 9 ill., 26 ref.

Embriogenesis somatik merupakan proses pembentukan

embrio dari sel somatik pada berbagai spesies tanaman. Teknik

ini bermanfaat untuk perbanyakan benih tanaman secara

massal dan perbaikan bahan tanaman dengan teknik rekayasa

genetik. Penelitian bertujuan untuk mengetahui pengaruh

beberapa zat pengatur tumbuh tanaman, yakni 6-bensiladenin

(BA) dan thidiazuron (TDZ) terhadap induksi kalus

embriogenik serta kasein hidrolisat dan ekstrak malt terhadap

pembentukan embrio somatik manggis. Eksplan yang

digunakan adalah batang muda in vitro manggis klon

Leuwiliang. Penelitian terdiri atas dua percobaan, yaitu induksi

kalus embriogenik dan pembentukan embrio somatik.

Percobaan induksi kalus embriogenik disusun secara faktorial

dalam rancangan acak lengkap. Faktor pertama adalah BA (0

dan 0,7 mg l-1) dan faktor kedua adalah TDZ (0; 0,1; 0,5 dan

1,0 mg l-1). Percobaan pembentukan embrio somatik terdiri

atas perlakuan kasein hidrolisat (500 dan 1.000 mg l-1) dan

ekstrak malt (500 dan 1.000 mg l-1). Hasil penelitian

menunjukkan bahwa media terbaik untuk induksi kalus

embriogenik adalah MS yang diperkaya TDZ 0,1 mg l-1 yang

menghasilkan kalus embriogenik dengan struktur agak remah.

Kasein hidrolisat dan ekstrak malt tidak berpengaruh nyata

dalam menginduksi pembentukan embrio somatik manggis.

Setelah dua kali subkultur pada media yang sama, yaitu MS

yang diperkaya TDZ 0,5 mg l-1 dan BA 0,7 mg l-1, dihasilkan

33,8 embrio per eksplan. Keberhasilan embrio-genesis somatik

ini akan mendukung program pemuliaan tanaman dan

perbanyakan benih massal manggis secara in vitro.

(Penulis)

Kata kunci: Garcinia mangostana, zat pengatur tumbuh,

induksi kalus, embrio somatik

————————————————————————UDC: 635.356-152

Nur Kholilatul Izzaha, Reflinurb dan Tae-Jin Yangc (aBalai

Penelitian Tanaman Industri dan Penyegar, Pakuwon,

Sukabumi, bBalai Besar Penelitian dan Pengembangan

Bioteknologi dan Sumberdaya Genetik Pertanian, BogorcDepartemen Ilmu Tanaman dan Balai Penelitian Pertanian

dan Biologi, Universitas Nasional Seoul, Seoul)

Pengembangan Marka EST-SSR untuk Analisis Keragaman

Genetik Tanaman Brokoli dan Kerabatnya (Orig. Eng.)

IJAS, April 2016, vol. 17 no. 1, p. 17–26, 5 tab., 4 ill., 31 ref.

Pengembangan marka Expressed Sequence Tag-Simple Sequence

Repeat (EST-SSR) yang berasal dari database publik dikenal

lebih efisien, cepat, dan berbiaya rendah. Tujuan penelitian ini

adalah untuk mendapatkan satu set marka EST-SSR baru untuk

brokoli dan kerabatnya, serta kegunaannya untuk analisis

keragaman genetik. Sebanyak 202 sekuen EST dari Brassica

oleracea yang diperoleh dari NCBI digunakan dalam penelitian

ini, yang selanjutnya dikelompokkan menjadi 172 unigenes

dengan menggunakan program CAP3. Identifikasi motif SSR

dilakukan menggunakan program RepeatMasker, sedangkan

marka EST-SSR didesain menggunakan program Primer3.

Sebanyak 12 SSR berhasil dideteksi dan di antara SSR yang

teridentifikasi, trinukleotida merupakan jenis pengulangan

yang paling banyak ditemukan, yaitu sekitar 50%. Selain itu,

delapan pasang primer berhasil didesain dan menghasilkan

produk amplifikasi. Hasil amplifikasi menunjukkan lima

primer bersifat polimorfis dan menghasilkan 30 alel dengan

rata-rata enam alel per lokus. Marka polimorfis tersebut

kemudian digunakan untuk menganalisis keragaman genetik 36

kultivar B. oleracea, yang meliputi 22 brokoli, 5 kol bunga,

dan 9 kohlrabi berdasarkan matriks kemiripan genetik seperti

yang diterapkan dalam program NTSYS. Pada koefisien

kesamaan 61%, UPGMA dendrogram berhasil mengelompok-

kan 36 genotipe menjadi tiga kelompok utama. Sebanyak 30

dari 36 genotipe tersebut berhasil dibedakan satu dengan yang

lainnya. Hasil yang diperoleh dalam penelitian ini dapat

membantu para pemulia dalam memilih tetua yang digunakan

untuk persilangan. Selain itu, marka EST-SSR yang didesain

pada penelitian ini merupakan suatu alat yang berharga untuk

membedakan kultivar-kultivar brokoli dan kerabatnya.

(Penulis)

Kata kunci: Brokoli, kol bunga, kohlrabi, Marka EST-SSR,

keragaman genetik

————————————————————————UDC: 634.773+635.965.274

Riry Prihatinia dan Norihan Mohamad Salehb (aBalai Penelitian

Buah Tropika, Solok, bDepartment Sel dan Biologi Molekuler,

Fakultas Bioteknologi dan Ilmu Biomolekuler, Universiti Putra

Malaysia 43400 UPM Serdang Selangor DEE)

Sensitivitas Kandungan Pigmen pada Kultur Jaringan Tanaman

Pisang dan Anggrek yang Terpapar Medan Elektromagnetik

Frekuensi Sangat Rendah (Orig. Eng.)

IJAS, April 2016, vol. 17 no. 1, p. 27–34, 1 tab, 2 ill., 38 ref.

Paparan alami medan elektromagnetik frekuensi sangat rendah

(ME-FSR) terdapat di lingkungan dan merupakan salah satu

faktor abiotik yang memengaruhi pertumbuhan dan perkem-

bangan makhluk hidup. Penelitian bertujuan untuk mengetahui

pengaruh paparan ME-FSR pada kandungan pigmen kultur

jaringan pisang dan anggrek sliper sebagai indikasi kapasitas

fotosintesis. Kultur pisang (Musa sp. cv. Berangan) dan

anggrek sliper (Paphiopedilum rothschildianum) dipapar

dengan ME-FSR 6 dan 12 mT selama 0,5; 1, 2, dan 4 jam.

Hasil penelitian menunjukkan bahwa paparan ME-FSR ber-

pengaruh berbeda terhadap kultur jaringan pisang dan anggrek

sliper, meskipun keduanya termasuk ke dalam monokotiledon.

Kandungan klorofil dan karoten/xantofil pada pisang yang

terpapar ME-FSR meningkat seiring dengan peningkatan

intensitas dan durasi paparan ME-FSR. Sebaliknya, kandungan

klorofil dan karoten/xantofil pada anggrek sliper berkurang

seiring dengan peningkatan intensitas dan durasi paparan ME-

FSR. Perbedaan paparan ME-FSR (12 mT selama 4 jam dan

16 mT selama 30 menit) berpeluang untuk diaplikasikan pada

kedua tanaman tersebut untuk meningkatkan pertumbuhan

tanaman. Penemuan ini mengindikasikan bahwa eksplan

pisang lebih toleran terhadap paparan MF-FSR dibandingkan

dengan anggrek sliper.

(Penulis)

Kata kunci: Pisang, anggrek, klorofil, karoten, medan

elektromagnetik

————————————————————————UDC: 633.683

Imron Riyadi dan Sumaryono (Balai Penelitian Bioteknologi

dan Bioindustri, Bogor)

Pengaruh Iradiasi Sinar Gamma terhadap Pertumbuhan dan

Perkembangan Kalus Tanaman Sagu (Metroxylon sagu Rottb.)

(Orig. Eng.)

IJAS, April 2016, vol. 17 no. 1, p. 35–40, 2 tab., 3 ill., 22 ref.

Aplikasi iradiasi sinar gamma pada bahan tanaman dapat

meningkatkan keragaman genetik pada keturunan baru dengan

sifat-sifat unggul yang bermanfaat. Percobaan ini bertujuan

untuk menentukan pengaruh dosis iradiasi sinar gamma pada

pertumbuhan dan perkembangan kalus sagu (Metroxyon sagu).

Kalus remah sagu yang berasal dari kultur suspensi digunakan

sebagai sumber bahan penelitian. Kalus primer tersebut berasal

dan hasil induksi jaringan meristem pucuk dari anakan sagu

varietas Alitir yang berasal dari Merauke, Papua. Perlakuan

yang diuji adalah dosis iradiasi sinar gamma yang terdiri atas 0,

5, 10, 15, 20, dan 25 Gy. Kalus yang telah diberi perlakuan

iradiasi sinar gamma kemudian disubkultur pada media padat

Murashige dan Skoog yang dimodifikasi (MMS) mengandung

3% sukrosa dan 0,1% arang aktif, serta zat pengatur tumbuh

2,4-D 1 mg l -1 dan kinetin 0,1 mg l -1. Hasil penelitian

menunjukkan bahwa semua perlakuan dosis iradiasi sinar

gamma dapat meningkatkan biomassa kalus secara nyata.

Penggandaan biomassa kalus tertinggi sebesar 5,33 kali lipat

dari awal kultur setelah empat minggu dicapai pada perlakuan

dosis sinar gamma 25 Gy, sedangkan penggandaan biomassa

kalus terendah sebesar 3,4 kali lipat diperoleh pada kontrol.

Perkembangan kalus embriogenik terbaik dicapai pada

perlakuan 10 Gy yang mampu menghasilkan embrio somatik

100%, sedangkan pembentukan embrio somatik terendah

diperoleh pada kontrol dan 25 Gy setelah disubkultur satu kali.

Respons yang tinggi dari induksi embrio somatik terhadap

sinar gamma pada dosis 10 Gy meningkatkan produksi embrio

somatik. Hasil yang diperoleh dapat digunakan dalam

pemuliaan in vitro tanaman sagu melalui mutagenesis untuk

menghasilkan varietas unggul baru.

(Penulis)

Kata kunci: Metroxylon sagu, iradiasi sinar gamma, kalus

embriogenik, embrio somatik

————————————————————————UDC: 634.441.2-167

Nani Heryani, Budi Kartiwa, Yayan Apriyana dan Haris

Syahbuddin (Balai Penelitian Agroklimat dan Hidrologi, Bogor)

Peningkatan Produksi dan Kualitas Mangga Melalui Teknik

Irigasi Curah (Orig. Eng.)

IJAS, October 2016, vol. 17 no. 2, p. 41–48, 6 tab., 4 ill., 36 ref.

Kekurangan air pada fase reproduksi (pembungaan, pembentuk-

an buah, dan pematangan) dapat menurunkan produksi dan

kualitas mangga. Dengan demikian pada fase-fase tersebut

tanaman harus terhindar dari cekaman air. Tujuan penelitian

adalah mengukur pengaruh pemberian irigasi terhadap hasil dan

kualitas buah mangga. Penelitian dilaksanakan di Kebun

Percobaan Cukurgondang, Pasuruan, Jawa Timur, pada April–

Desember 2013 menggunakan 40 pohon mangga varietas

Arum Manis umur 21 tahun, dengan jarak tanam 6 m x 6 m.

Teknik irigasi curah (fan jet sprayer) menggunakan selang

dipasang sesuai diameter pohon dengan empat buah nozzle per

pohon. Lima perlakuan irigasi yang diaplikasikan yaitu 125,

100, 75, 50, dan 0% dari kebutuhan air tanaman atau berturut-

turut setara dengan 828, 663, 497, 331, dan 0 liter air per

tujuh hari per pohon. Parameter yang diamati yaitu jumlah dan

berat buah rontok, jumlah dan berat buah yang dipanen, serta

kualitas buah. Hasil penelitian menunjukkan bahwa perlakuan

irigasi 50% dan 75% dari kebutuhan tanaman masing-masing

menghasilkan jumlah buah rontok terbanyak dan terendah,

yaitu berturut-turut 26% dan 14% dari total produksi. Jumlah

buah total tertinggi dan terendah masing-masing terdapat pada

perlakuan irigasi 50% dan 75% dari kebutuhan air tanaman,

berturut-turut 3.108 dan 1.904 buah. Total berat buah tertinggi

dan terendah terdapat pada perlakuan irigasi 50% dan 125%

dari kebutuhan air tanaman, yaitu berturut-turut 1036,2 dan

677,9 kg. Berat buah mangga yang dihasilkan umumnya

termasuk kelas 2 dan 3 dengan kualitas A.

(Penulis)

Kata kunci: Mangga, produksi, kualitas, irigasi curah

————————————————————————UDC: 633.15-152

Edy Listanto, Eny Ida Riyanti dan Sustiprijatno (Balai Besar

Penelitian dan Pengembangan Bioteknologi dan Sumberdaya

Genetik Pertanian, Bogor)

Transformasi Tanaman Jagung Indonesia dengan Plasmid

pIG121Hm-Cs yang Mengandung Gen nptII dan hpt melalui

Agrobacterium tumefaciens secara In-Planta (Orig. Eng.)

IJAS October 2016, vol. 17 no. 2, p. 49–56, 1 tab., 5 ill., 33 ref.

Upaya peningkatan produktivitas jagung dapat dilakukan

melalui rekayasa genetik tanaman. Proses transformasi

merupakan kunci keberhasilan dalam rekayasa genetik

tanaman. Metode transformasi in-planta menggunakan

Agrobacterium tumefaciens merupakan metode transformasi

yang sederhana dan murah. Penelitian ini bertujuan melakukan

konfirmasi konstruksi gen pada plasmid pIG121Hm-Cs di

dalam A. tumefaciens, dan menduga tingkat efisiensi

transformasi melalui Agrobacterium secara in planta pada

tanaman jagung Indonesia dengan plasmid pIG121Hm-Cs yang

mengandung gen nptII dan hpt. Penelitian dilaksanakan

melalui beberapa tahapan secara berurutan, yaitu konfirmasi

konstruksi gen pada plasmid pIG121Hm-Cs dalam A.

tumefaciens, transformasi empat galur jagung melalui A.

tumefaciens dengan teknik in-planta, aklimatisasi tanaman

transforman, dan analisis molekuler tanaman transforman

terseleksi menggunakan polymerase chain reaction (PCR).

Keberadaan plasmid pIG121Hm-Cs dikonfirmasi dengan

analisis PCR menggunakan primer spesifik untuk gen nptII dan

hpt dan dihasilkan fragmen DNA berukuran 700 pb untuk gen

nptII dan 500 pb untuk gen hpt. Setelah tahap seleksi,

aklimatisasi, dan analisis molekuler, efisiensi transformasi

keempat galur jagung masih rendah, berkisar antara 3,8–

12,8%. Tingkat efisiensi transformasi tertinggi ditunjukkan

oleh galur jagung ST-27, yaitu 12,8% dari 45 embrio yang

ditanam pada media seleksi berdasarkan analisis PCR

menggunakan primer spesifik untuk gen nptII. Berdasarkan

hasil tersebut, transformasi tanaman jagung melalui A.

tumefaciens secara in-planta pada putik bunga terbukti berhasil

dan cepat. Metode transformasi ini akan bermanfaat untuk

rekayasa genetik pada tanaman jagung.

(Penulis)

Kata kunci: Jagung, Agrobacterium tumefaciens, transformasi

in-planta

————————————————————————UDC: 633.74-152

I Made Tasmaa, Dani Satyawana, Habib Rijzaania, Ida

Rosdiantia, Puji Lestaria dan Rubiyob (aBalai Besar Penelitian

dan Pengembangan Bioteknologi dan Sumberdaya Genetik

Pertanian, Bogor, bBalai Penelitian Tanaman Industri dan

Penyegar, Pakuwon)

Variasi Genom Lima Varietas Kakao (Theobroma cacao L.)

Indonesia Berdasarkan Analisis Menggunakan Next Generation

Sequencing (Orig. Eng.)

IJAS October 2016, vol. 17 no. 2, p. 57–64, 3 tab., 2 ill., 42 ref.

Produktivitas kakao Indonesia masih rendah antara lain

karena kurang tersedianya bahan tanaman unggul. Metode

pemuliaan baru perlu diterapkan untuk mempercepat program

pemuliaan kakao nasional. Sampai saat ini belum ada

penelitian untuk mengkarakterisasi varietas kakao Indonesia

pada level genom total. Penelitian ini bertujuan untuk

mengidentifikasi variasi genom varietas unggul kakao

Indonesia menggunakan next generation sequencing. Materi

genetik yang digunakan adalah lima varietas unggul kakao

Indonesia, yaitu ICCRI2, ICCRI3, ICCRI4, SUL2, dan ICS13.

Data sekuen genom kelima varietas tersebut dijajarkan dengan

sekuen genom rujukan kakao varietas Criollo. Penjajaran

sekuen dilakukan menggunakan software Bowtie2 dan

identifikasi variasi genom (SNP dan Indel) dilakukan dengan

software mpileup dari Samtools. Penelitian ini meng-hasilkan

variasi genom sebanyak 2.688.169 yang terdiri atas 2.326.088

SNP dan 362.081 insersi dan delesi (Indel). Secara rata-rata

satu variasi genom (SNP atau Indel) ditemukan pada setiap 121

basa dari sekuen genom kakao. Dari seluruh SNP yang

diidentifikasi, 347.907 SNP (13,18%) berlokasi pada protein

coding region. Dari jumlah ini, 188.949 SNP menyebabkan

mutasi yang mengubah susunan asam amino pada protein

(missense mutation) dan 1.535 SNP menyebabkan mutasi yang

menghasilkan stop codon (nonsense mutation). Ditemukan

juga SNP berbasis gen yang unik pada setiap genotipe kakao

yang dapat digunakan sebagai sidik jari dari setiap genotipe

kakao yang diuji. Variasi genom yang dihasilkan merupakan

sumber daya marka DNA bernilai tinggi untuk studi genetika

dan pemuliaan kakao. SNP hasil penelitian ini dapat digunakan

sebagai materi untuk pembuatan SNP chip kapasitas tinggi yang

bermanfaat untuk pelabelan gen unggul dan QTL yang terkait

karakter penting untuk mendukung percepatan program

pemuliaan kakao nasional.

(Penulis)

Kata kunci: Theobroma cacao, sekuensing genom total, variasi

genom, SNP, next generation sequencing

————————————————————————UDC: 633.3-152

Reflinura, Puji Lestaria dan Suk-Ha-Leeb (aBalai Besar

Penelitian dan Pengembangan Bioteknologi dan Sumberdaya

Genetik Pertanian, Bogor, bDepartemen Ilmu Tanaman dan

Balai Penelitian Pertanian dan Biologi, Universitas Nasional

Seoul)

Potensi Penggunaan Marka SSR dalam Mendukung Identifikasi

Morfologi Varietas Kacang Hijau Indonesia (Orig. Eng.)

IJAS, October 2016, vol. 17 no. 2, p. 65–74, 4 tab., 2 ill., 31 ref.

Karakterisasi kacang hijau pada umumnya dilakukan

berdasarkan sifat-sifat morfologi. Pendekatan genetika

molekuler diharapkan dapat membantu pemulia dalam

mengidentifikasi kacang hijau dan melindungi hak kekayaan

intelektual pemulia. Penelitian ini bertujuan untuk

mengidentifikasi varietas kacang hijau Indonesia berdasarkan

penampilan sidik jari DNA dengan menggunakan satu set

marka untuk mendukung karakterisasi secara morfologi.

Sebanyak 22 aksesi kacang hijau Indonesia telah dianalisis

berdasarkan 21 karakter morfologi dan secara molekuler

menggunakan 55 primer simple sequence repeats (SSR). Di

antara 22 varietas kacang yang digunakan pada penelitian ini,

16 varietas merupakan varietas unggul dan enam varietas

merupakan varietas lokal asal Jawa, Nusa Tenggara, dan

Sulawesi yang dikoleksi di BankGen BB Biogen. Hasil

penelitian menunjukkan bahwa 21 karakter morfologi yang

digunakan belum cukup informatif untuk membedakan 22

varietas kacang hijau. Berdasarkan analisis SSR, delapan marka

dan nilai informasi polimorfis yang tinggi telah terseleksi

sebagai marka untuk identifikasi varietas kacang hijau. Set

marka terseleksi tersebut mampu membedakan masing-masing

varietas dengan jarak genetik terendah sebesar 0,125 dan

secara spesifik dapat digunakan sebagai alat bantu yang andal

untuk identitas varietas (ID). Identitas genetik dari varietas

tersebut ditunjukkan oleh angka barcoding yang merupakan

rentetan dari alel-alel yang dihasilkan oleh masing-masing

marka. Profil sidik jari DNA dari masing-masing varietas

kacang hijau akan sangat bermanfaat terutama sebagai referensi

identitas varietas kacang hijau.

(Penulis)

Kata kunci: Kacang hijau, karakter morfologi, SSR, sidik jari

DNA, identitas varietas

UDC: 631.445.1

Muhammad Imam Nugrahaa, Wahida Annisab, Lailan Syaufinac

dan Syaiful Anward, aMahasiswa Pascasarjana di Institut

Pertanian Bogor, bBalai Penelitian Pertanian Lahan Rawa,

Banjarbaru, cFakultas Kehutanan, Institut Pertanian Bogor,dFakultas Pertanian, Institut Pertanian Bogor)

Kenaikan Air Kapiler di Tanah Gambut Akibat Pengaruh

Berbagai Ketinggian Muka Air Tanah (Orig. Eng.)

IJAS, October 2016, vol. 17 no. 2, p. 75–83, 3 tab., 6 ill., 31 ref.

Air kapiler di lahan gambut memiliki peranan yang sangat

penting dalam menyediakan air untuk zona perakaran

tanaman. Kadar air tanah aktual pada zona perakaran sangat

bergantung pada tinggi muka air tanah pada suatu kawasan

yang mempunyai tinggi muka air yang dangkal. Tujuan

penelitian adalah untuk mengukur dinamika kapilaritas tanah

gambut pada berbagai faktor kepadatan tanah dan tinggi muka

air tanah yang diamati dari perubahan warna, distribusi

kelembapan, kadar air, dan hidrofobisitas tanah gambut.

Penelitian dilaksanakan di rumah kawat Balai Penelitian

Pertanian Lahan Rawa, Banjarbaru, Kalimantan Selatan.

Penelitian menggunakan rancangan acak kelompok faktorial

dengan dua faktor yang diulang tiga kali. Faktor pertama

adalah tingkat kepadatan gambut (BD), yaitu BD-1 (kondisi

aktual, 0,1 g cm-3) dan BD-2 (dipadatkan menjadi 0,2 g cm-3).

Faktor kedua adalah simulasi tinggi muka air tanah (GWL)

berdasarkan tinggi pipa mika, yaitu GWL-1 (-100 cm), GWL-

2 (-70 cm), dan GWL-3 (-40 cm). Hasil penelitian menunjuk-

kan tinggi kenaikan air kapiler di tanah gambut maksimum

mencapai 50 cm yang dicirikan dengan meningkatnya nilai

kelembapan tanah antara 105–127% pada BD-1 dan 141–

181% pada BD-2. Nilai kadar air tanah tertinggi terlihat pada

perlakuan GWL-3 dengan BD-2 sebesar 308% dan yang

terendah pada perlakuan GWL-1 dengan BD-1 sebesar 37%.

Kecepatan kenaikan air kapiler semakin tinggi dengan

meningkatnya nilai BD tanah karena terkait dengan jumlah

pori mikro yang lebih banyak pada BD-2.

(Penulis)

Kata kunci: Tanah gambut, air kapiler, tinggi muka air tanah,

kepadatan gambut, kelembapan tanah

INTRODUCTION

Mungbean (Vigna radiata L. (Wilczek)), a second

economically important legume crop in Indonesia

after soybean, is an important source of protein,

vitamin and mineral (Tomooka et al. 2002; Lambrides

and Godwin 2007; Somta and Srinives 2007; Mondalet al. 2012). In spite of the best efforts for improving

mungbean varieties, the yield of this crop remains

low. According to the Central Bureau Statistics of

Indonesia, the national mungbean productivity was

1.12 ton ha"1 with the total area of 182,058 ha (BPS

2013). Therefore, the genetic improvement of mung-

satu set marka untuk mendukung karakterisasi secara morfologi.Sebanyak 22 aksesi kacang hijau Indonesia telah dianalisisberdasarkan 21 karakter morfologi dan secara molekulermenggunakan 55 primer simple sequence repeats (SSR). Di antara22 varietas kacang yang digunakan pada penelitian ini, 16 varietasmerupakan varietas unggul dan enam varietas merupakan varietaslokal asal Jawa, Nusa Tenggara, dan Sulawesi yang dikoleksi diBankGen BB Biogen. Hasil penelitian menunjukkan bahwa 21karakter morfologi yang digunakan belum cukup informatif untukmembedakan 22 varietas kacang hijau. Berdasarkan analisis SSR,delapan marka dan nilai informasi polimorfis yang tinggi telahterseleksi sebagai marka untuk identifikasi varietas kacang hijau.Set marka terseleksi tersebut mampu membedakan masing-masingvarietas dengan jarak genetik terendah sebesar 0,125 dan secaraspesifik dapat digunakan sebagai alat bantu yang andal untukidentitas varietas (ID). Identitas genetik dari varietas tersebutditunjukkan oleh angka barcoding yang merupakan rentetan darialel-alel yang dihasilkan oleh masing-masing marka. Projil sidikjari DNA dari masing-masing varietas kacang hijau akan sangatbermanfaat terutama sebagai referensi identitas varietas kacanghijau.

[Kata kunci: Kacang hijau, karakter morfologi, SSR, sidik jari DNA,identitas varietas]

ABSTRAK

Karakterisasi kacang hijau pada umumnya dilakukan berdasarkansifat-sifat morfologi. Pendekatan genetika molekuler diharapkandapat membantu pemulia dalam mengidentifikasi kacang hijaudan melindungi hak kekayaan intelektual pemulia. Penelitian inibertujuan untuk mengidentifikasi varietas kacang hijau Indonesiaberdasarkan penampilan sidik jari DNA dengan menggunakan

ABSTRACT

Mungbean varieties were mainly characterized based onmorphological traits. Molecular genetic approach is expectedto help the breeder in identification of mungbean varieties inmore detail and to protect intellectual property right. Thisstudy aimed to identify Indonesian mungbean varieties based onDNA fingerprint profile using a marker set to supportmorphological characters. A total of 22 Indonesian mungbeanaccessions were characterized based on 21 morphological traitsand 55 simple sequence repeats (SSRs) primers. Of the total 22mungbean varieties used in the present study, 16 varieties wereimproved varieties and remaining six varieties were localvarieties originated from Java, Nusa Tenggara and Sulawesicollected in GeneBank of ICABIOGRAD. The results showedthat the 21 morphological characters were not sufficient todifferentiate 22 mungbean varieties, while SSR analysisrevealed that eight multi-alleles markers and high polymorphicinformation content (PIC) values have been successfully selectedfor varietal identification. The selected markers enabled todifferentiate each mungbean variety according to their geneticmarker with the lowest distance of 0.125, demonstrating therobustness of the selected marker set as a tool to identify aspecific DNA fingerprint profile as a varietal identity (ID). Thegenetic identity of a variety was shown by digital barcodingwhich represented a series of alleles produced by correspondingmarkers. The DNA fingerprint profile of each variety would bebeneficial as reference identities of a mungbean variety.

[Keywords: Mungbean, morphological characters, SSR markers,DNA fingerprint, varietal identity]

THE POTENTIAL USE OF SSR MARKERS TO SUPPORT THE MORPHOLOGICALIDENTIFICATION OF INDONESIAN MUNGBEAN VARIETIES

Potensi Penggunaan Marka SSR dalam Mendukung Identifikasi MorfologiVarietas Kacang Hijau Indonesia

Reflinur3, Puji Lestari" and Suk-Ha Leeb

"Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and DevelopmentJalan Tentara Pelajar No. 3A, Bogor 16111, West Java, Indonesia

Phone +62 251 8337975, Fax. +62 251 8338820bDepartment of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University

Corresponding author: reflinur@yahoo.com

Submitted 16 March 2016; Revised 13 September 2016; Accepted 20 September 2016

DOI: http//dx.doi.org/10.21082/ijas.vl7n2.2016.p65-74Indonesian Journal of Agricultural ScienceVol. 17 No. 2 October 2016: 65-74

MATERIALS AND METHODS

Plant Materials

A total of 22 Indonesian mungbean varieties consisted

of 16 improved varieties and six local varieties as a

comparison were subjected to both morphological

and molecular analyses (Table 1). All of the accessions

belonged to the genebank of the Indonesian Center

for Biotechnology and Genetic Resources Research

and Development (ICABIOGRAD), Bogor, West Java.

previously. In this study, a total of 30 newly SSR

simple sequence repeat (SSR) markers which were

developed from the genome of Korean mungbean

varieties (Sunhwanokdu and Gyeonggijaerae 5)

proved their application to detect genetic variability

of 83 accessions of Indonesian mungbean to support

breeding program and conservation strategy.

Moreover, these markers were able to identify

improved mungbean varieties that were genetically

similar to some landraces from one of the main

mungbean-producing regions in Indonesia (Lestari et

al. 2014). Considering the prospecting SSR markers

(Lestari et al. 2014), our current study applied those

markers in addition to other markers for varietal

identification rather than genetic diversity study. The

use of molecular markers which discriminate varieties

in nucleotide sequences are unaffected by

environments and becomes more desirable in varietal

identification and differentiation.

SSR markers have been the most widely-used

genotyping markers in many plant species over the

past decade due to their stability, ease of application,

representing highly polymorphic, abundant presence

in the genome, reproducible, co-dominant, and

multiallelic types of variation (Minamiyama et al.

2006; Yi et al. 2006; Lorenzo et al. 2007; Portis et al.

2007; Agarwal et al. 2008; Senthilvel et al. 2008;Sundaram et al. 2008; Kumar et al. 2009). The working

group on biochemical and molecular techniques of

UPOV has identified SSR markers as the predominant

markers for plant varietal characterization (UPOV

2011). A specific set of SSRs can be used indifferentsets of genotypes, making them particularly useful for

DNA fingerprinting.

The objective of this study was to identifyIndonesian mungbean varieties based on DNA

fingerprint profile using a set of developed markers to

support the morphological characters.

bean should be based on the genetic information of

the plant.

Conservation of the genetic resources of mungbean

is vital for future breeding programs and food

security, therefore, characterization and proper

assignation of individual genotypes to species is

required (Karp 1996; Vincent et al. 2013). TheInternational Union for the Protection of New

Varieties of Plants (UPOV) has provided guidelines onestablishing the uniqueness of a variety through

testing for distinctiveness, uniformity and stability

(DUS) (UPOV 2011). Through the adoption of theUPOV system, a breeder is obliged to protect a

variety for commercial exploitation. Protection can be

granted if a variety of the crop is distinct from the

existing ones supported with sufficiently uniform and

stable genetic characteristics. Hence, the varietal

identification of mungbean becomes a critical

importance.Traditionally, the accessions of mungbean in

Indonesia are characterized based on their

morphological and physiological traits (Van den

Bosch 1987; Hakim 2008). Van den Bosch (1987)reported an intercropping of mungbean landraces

originated from East Java with maize. After three

cycles of selection, a yield of intercropped mungbean

increased 24% as compared to the original mungbean

landraces, and the yield of maize in the mixture was

not affected by the increase in mungbean landrace

yield. In another study, Hakim (2008) evaluated 350

mungbean accessions for their agronomic characters

in the field. A number of these characters (days to

maturity, plant height, pods per plant and seed size)

were known to be significantly varied. Number of

pods per plant and plant height were important

characters that can be used as the selection criteria in

mungbean breeding in the early generation stage

(Hakim 2008). However, this traditional method is

costly and time-consuming since numbers of existing

varieties are quite large that require wide land and

skilled personnel, and often subjective decisions

(Cooke 1995; Kumar et al. 2009). Therefore, reliable

and cost-effective methods for identifying varieties

are desirable to differentiate the increasing numbers

of new varieties and eliminate duplicates from

germplasm collections. An effective method for

variety identification such as DNA fingerprinting is

essential for DUS testing of new varieties and for

protection of intellectual property right of new

varieties (Lu et al. 2009).

The use of molecular markers for differentiating

mungbean varieties of Indonesia has been reported

Indonesian Journal of Agricultural Science Vol. 17 No. 2 October 2016: 65-7466

PCR Amplification

PCR reactions were conducted in a total volume of 20

pi and contained 20 ng genomic DNA, 0.25 pM each

primer (forward and reverse), 0.125 mM each dNTP,

0.16 units AmpliTaq Gold® DNA Polymerase (AppliedBiosystem, Warrington, UK), and lx AmpliTaq buffer

with MgCl2. The PCR amplification was performed

using a 96-well plate in a tetrad thermal cycler (DNA

Engine Tetrad, MJ Research). The amplification

conditions were as recommended by the manu

facturer's protocol (Applied Biosystem, Warrington,

UK) that consisted of an initial denaturation step of 5

minutes at 94 C, followed by 35 cycles of 45 seconds

at 94 C, 30 seconds at 55 C, 30 seconds at 72 C

with a final extension at 72 C for 10 minutes. PCR

products were first separated on 2% (w/v) agarose

(Gelvin and Schilperoort 1995). For an initialscreening, a total of 55 SSR markers developed in the

Crop Genomic Laboratory, Seoul National University

were used on the basis of de novo sequencing data

of Korean mungbean cultivars (Sunhwanokdu and

Gyeonggijaere). Then the DNA polymorphisms of 22Indonesian mungbean varieties were checked by a

fluorescence-based capillary electrophoresis.

DNA Isolation

Young and healthy leaves of three to four day-old

mungbean seedlings were harvested for DNA

extraction. The leaf tissues were ground into a fine

powder in a liquid nitrogen by a pestle and mortar.

The genomic DNA was extracted using a standard

cetyltrimethylammonium bromide (CTAB) method

Morphological Characterization

All genetic materials were grown at the Experimental

Farm of Seoul National University in Suwon, Korea

(altitude: 74 m, longitude: 127362 E, latitude: 37512 N)following the standard cultural practices. Two

individual plants were grown in each pot with two

replications. Twenty one qualitative morphological

characters related to growth habit, leaf, stem and pod

were observed and scored according to the guidelines

for conducting tests for distinctness, homogeneity and

stability criteria provided by the UPOV (UPOV 2011).All recorded characters were converted to numerical

numbers which could be designed as digital morpho

logical markers of each mungbean variety. Based on

the qualitative morphological data, a phylogenetic tree

was generated using PowerMarker software.

Si WalikSelected from a population in JenepontoArta IjoSelected from local varieties originating from Sumenep, MaduraManyarIntroduced varieties from AVRDC (Taiwan)BhaktiSelected from introduced varieties from Sri LankaNo. 129Selected from introduced varieties from PhilippinesNuriSelected from introduced varieties from AVRDC (Taiwan)KenariIntroduced from AVRDC, Taiwan 1987, single cross from VC 1178B as

male and VC 1624 as femaleBetetSelected from cross of MB 129 x SiwalikGelatikSelected from introduced varieties from AVRDC (Taiwan)ParkitPHLV-18/VC.1177 1979MerpatiSelcted from F4 generation of introduced lines from TaiwanWaletSelected from introduced varieties from AVRDC (Taiwan)CamarDeveloped using Gamma irradiation of 0.1 kGy dose on Manyar varietyMerakSelected from introduced varieties from PhilippinesPerkututIntroduced from AVRDC, TaiwanVima-1Synthetic crossing of VC 1973 A and 2750ANilonSulawesiLok BeluNusa TenggaraLok GarutJavaTecer HijauJavaLok NTBNusa TenggaraLok Muntaha K2 Sulawesi

Genetic background/originVariety

Table 1. Twenty two Indonesian mungbean varieties used in this study together withtheir origin or genetic background.

67The potential use of SSR markers to support the morphological ... (Reflinur, Puji Lestari and Suk-Ha Lee)

RESULTS AND DISCUSSION

Variability of Mungbean Varieties Based onMorphological Characters

Twenty one qualitative morphological characters of

22 Indonesian mungbean varieties were presented on

Table 2. The present data indicated that a low

variation (0.28) was evidenced in all mungbean

varieties evaluated. Seven morphological characters

were uniform, whereas the remaining ones were

considerably varied ranging from low (0.04) for

mature pod color to the highest (0.81) for leaf

pubescence character. A moderate degree of variation

was observed in the leaf color, stem color and seed

size. All varieties showed no lobe of leaf, ovate

lanceolate shape of primary leaf, deltate of terminal

leaf, drum of seed, yellow flower, pod pubescence

and green color of premature pod. Majority (> 80%)

of varieties had seed pubescence, straight of pod

curvature and green seed. According to mature pod

characteristics, only a local variety of Tecer Hijau

from Java had a brown color in contrast the green

one of the rest varieties.

The morphological character data showed common

on both improved and local varieties, and some traits

might be specific to genotypes as demonstrated in

our study. The morphological characters of released

varieties could be selected as important descriptor for

breeding program (Stoilova et al. 2013). While, local

varieties with better adaptation to local growing

regions possessed valuable character for cultivation

in different agroecological conditions (Stoilova and

Sabeva2006).To simply identify, the total of 21 characters were

scored and converted to numerical number (Table 1).

When morphological characters were used as

markers, it was noted that each genotype either

improved variety or local variety had its own identity.

However, these total morphological characters were

enabled to differentiate each mungbean variety yet.

As a representative, a variety named Parkit with

morphological identity of "221231211111213211211"and a variety named No. 129 with its code of

"121231211111213211211" seemed to be close anddiffered based on only one character, plant habit as

SSR motif observed on each primer. This digital code

transformation would be done for total SSR in the

formulated marker set and the digital codes

represented the ID of each mungbean variety

(Risliawati etal. 2015).

Data Analysis

Genotypic data were subjected to PowerMarker

software to analyze the polymorphic information

content (PIC) values of the tested primers, for the

calculation of allele number, allele frequency,

heterozygosity, gene diversity, and probability of

identity per locus. The PIC values of each SSR marker

were calculated for the total population (Liu 2001). SSRmarkers that exhibit high value of PIC (> 0.5) were

chosen to be recommended as valuable SSR markers

on DNA fingerprinting of Indonesian mungbean

varieties. Such information is important to be used as

basic criteria to select molecular markers candidate for

varietal identification. In parallel with selection of SSRs

for marker set, estimated calculation of genetic distance

through generating phylogenetic tree was performed

to maximize the varietal differentiation efficiency.

The polymorphic bands of 22 mungbean varieties

were scored as binary characters for their presence

(1) or absence (0) and the resulting data were

analyzed using NTSYS-PC (Numerical Taxonomy and

Multivariate Analysis System) version 2.1 (Rohlf

1998). Genetic similarity between cultivars was

calculated based on the simple matching coefficient

using the SIMQUAL subprogram. Cluster analysis

was performed using the Unweighted Pair Group with

Arithmetic Mean (UPGMA) method in the SAHNsubprogram of NTSYS-PC. This phylogenetic

analysis assisted to formulate SSR marker set to

identify mungbean variety.

The genetic identity (ID) of mungbean variety wasthen determined by a digital value which represented

a series of alleles produced by corresponding marker.

In this step, the allele size was transformed to two

digits of numerical number produced by each marker.

The two digital codes were started from "01" for each

gel containing GelRed (Biotium) in 0.5x TBE buffer.

The amplicons were visualized under UV light, and

the sizes were estimated relative to the 100 bp DNA

ladder.For further determination of polymorphism, the

amplicons were run in a fluorescence-based capillary

electrophoresis using Fragment Analyzer CE System

(Advanced Analytical Technologies, Inc., USA). To

ensure reproducibility of amplification products, the

analyses were repeated at least twice. Allele sizes

were determined for each SSR locus using fragment

analysis software which was automatically offered by

the capillary electrophoresis Fragment Analyzer CE

System.

Indonesian Journal of Agricultural Science Vol. 17 No. 2 October 2016: 65-7468

effective to discriminate among improved mungbean

varieties along with the local ones. This results is in

agreement and relevant with the previous report

showing that the genetic differentiation based on

morphological characters in the species level of Vigna

is less sufficient (Tantasawat et al. 2010).

denoted by "2" on variety Parkit and "1" on variety

No 129. While between Walet and Perkutut were not

distinct each other as reflected by the same identity

of "211241311111113211211". These results suggestedthat the numerical morphological characters which

reflect the differences in the mungbean organs are not

Abbreviations: PH = plant habit, GH = growth habit, StC = stem color, SP = stem pubescence, LP = leaf pubescence, LL = leaf lobe, LC= leaf color, LVC = leaf vein color, PLS = primary leaf shape, TLS = terminal leaf shape, SSh = seed shape, PCv = pod curvature, BP =branching pattern, FC = flower color, SS = seed size, PP = pod pubescence, PPC = premature pod color, MPC = mature pod color, SL = seedlusture, SC = seed color, H = hypocotyle

1.Plant habit: 1 = ID (indeterminate), 2 = D (determinate)2.Growth habit: 1 = SE (semierect), 2 = SHE (semierect-horizontal)3.Stem color: 1 = LG (light green), 2 = DG (dark green), 3 = GP (mixed green-purple)4.Stem pubescence: 1 = G (globrous/absent of hair), 2 = P (pubescence/present of hair)5.Leaf pubescence: 1 = VSP (very sparsely pubescence), 2 = SP (sparsely pubescence), 3 = MP (moderately pubescence), 4 = VMP (very

moderately pubescence)6.Leaf lobe: 1 = no lobe, 2 = having lobe7.Leaf color: 1 = LG (light green), 2 = G (green), 3 = DG (dark green)8.Leaf vein color: 1 = G (green), 2 = GP (greenish purple)9.Primary leaf shape: 1 = OL (ovate lanceolate)10.Terminal leaf shape: 1 = deltate11.Seed shape: 1 = D (drum)12.Pod curvature: 1 = S (straight), 2 = C (curvature)13.Branching pattern: 1 = all, 2 = central14.Flower color: 1 = yellow.15.Seed size: 1 = small, 2 = medium, 3 = big16.Pod pubescence: 1 = globrous, 2 = pubescence17.Premature pod color: 1 = green18.Mature pod color: 1 = black, 2 = brown19.Seed lusture: 1 = dull, 2 = shiny20.Seed color: 1 = green, 2 = black, 3 = green yellowish, 4 = yellow21.Hypocotyl color: 1 = green, 2 = purple

2122221111111211212222

1111111131111131111111

1222121222222112122211

2 12 I2 12 12 12 12222222222222222 -

2313133332323333233222

1111111111111111111111

211 2 2

112221211122

1 1I 2I 21 21 11 11 21 1

lllilililillii ;i ;11111

2 1 11 1 12 1 12 1 12 1 12 1 11 1 11 1 11 1 11 1 11 1 11 1 11 1 11 1 11 1 11 1 12 1 11 1 12 1 12 1 12 1 12 1 1

3223122321322223223233

2321 131 14443443334333343

1 2 31 2 2

212 3 11 2 1

12

1 21 2I 2I 2I 2i 2I 2I 2I 2I 2I 21 21 2I 2'. 2

1112 :2222111221112

1212122222212211212111

VR1069VR1057VR1079VR1077VR1005VR997

VR1074VR1058VR423VR224VR222VR220VR219VR218VR217VR196VR137VR129VR116VR110VR26VR9-1

Tecer HijauLok GarutLok NTBLok BeluLok Muntaha K.2NilonLima-1PerkututMerakCamarWaletMerpatiParkitGelatikBetetKenariNuriNo.129BhaktiManyarArta IjoSi Walik

PH GH StC SP LP LL LC LVC PLS TLS SSh PCv BP FC SS PP PPC MPC SL SC HReg.number

Variety

name

Table 2. Morphological characteristics of 22 mungbean varieties used in present study.

69The potential use of SSR markers to support the morphological ... (Reflinur, Fuji Lestari and Suk-Ha Lee)

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Both morphological and molecular data demon

strated the diversity level of the Indonesian mung

bean varieties. Aphylogenetic analysis was generated

to initial estimation of varieties differentiation, leading

to the identification of each variety as a distinctive

individual (Fig. 2). Therefore, a dendrogram of the 22

Indonesian mungbean varieties was performed using

the genetic similarity matrix generated by the Nei

1973 similarity coefficient based on alleles producedby eight SSR markers. Two main clades appeared to

group 10 varieties (clade I) and the remainingvarieties (clade II). Both clades contained improved

varieties together with three local varieties, in which

Lok Belu (Nusa Tenggara), Lok Garut (Java), Tecer

Hijau (Java) belonged to clade I, and Nilon (Sulawesi),Lok NTB (Nusa Tenggara) and Lok Muntaha K2(Sulawesi) into clade II. Importantly, each variety was

clearly distinct with each other without the same

genetic distance.Based on the allele size of DNA fingerprint profile

using a marker set containing eight SSR loci, finally a

barcoding in the form of digital ID of each mungbean

variety was successfully developed (Table 4). For

example an improved variety of Si Walik had ID"0401030804010503", while Nuri which was found tohave heterozygote alleles automatically had two IDs

depending on the harbored alleles, 0501040504020102and 0101020705030207. Notably, local varieties fromJava (LokGarut and Tecer Hijau) seemed to be

discrepancy according to their barcoding. Two

improved varieties (Walet and Perkutut) that were not

able to be differentiated based on morphological

characters, by using eight markers finally were

SSR Marker Set Development and SpecificIdentity of Mungbean Varieties

To design marker set to identify DNA fingerprintprofile of variety as genetic identity needs several

steps including selection of marker candidate, design

method for marker set and creation of varietal ID in

the digital barcode. In this study, based on PIC, gene

diversity and allele number of each marker, finally 14

SSR loci candidate were selected from a total of 55

primers surveyed. Out of the chosen 14 SSR primers,

further selection was done to obtain eight primers as

a basis in the marker set formulation. These markers

included those with high PIC values ranging from0.63 to 0.79, namely P33, P95, P57, P87, P27, P29, P36

and P17. This simple SSR analysis containing

minimized markers (eight) could be a suitable method

for routine identification of mungbean varieties,awhich is in good agreement with the previousjeport

(Prammanee et al. 2000).

Gene diversity of this mungbean collection was

relatively high, 0.68. Loci P87 which had the highestPIC value, showed the highest gene diversity (0.82),

suggesting a positive correlation between PIC and

gene diversity. Discrepancy of genetic diversity based

PIC demonstrated that the choice of markers and

varieties affected the variation of molecular markers

used. Markers with high PIC value and are informative

turned out to be a marker set for DNA fingerprinting

analysis for identification and differentiation of

particular varieties (Bredemeijer et al. 2002).

0.63

0.720.530.540.750.650.630.790.530.640.570.670.510.750.59

PIC

0.003

0.000.000.000.050.000.000.000.000.000.000.000.000.000.00

Heterozygosity

0.68

0.740.610.610.780.700.660.820.580.700.640.710.580.780.67

diversityGene

5.14

84565784434383

numberAllele

0.43

0.450.500.500.300.410.550.270.590.410.450.410.550.320.36

frequencyMajor allele

Means

P17P16P69P36P29P27P87P74P57P45P95P7P33P59

Marker

Table 3. Summary of statistics of 14 simple sequence repeat (SSR) markersobserved in 22 Indonesian mungbean varieties.

71The potential use of SSR markers to support the morphological ... (Reflinur, Puji Lestari and Suk-Ha Lee)

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Agarwal, M., N. Shrivastava and H. Padh. 2008. Advances inmolecular marker techniques and their applications in plantsciences. Plant Cell Rep. 27: 617-631.

BPS. 2013. Production and harvested areas of mungbean byprovince. Badan Pusat Statistik. http://www.bps.go.id. [19 Juni2016].

Bredemeijer, M., J. Cooke, W. Ganal, R. Peeters, P. Isaac, Y.Noordijk, S. Rendell, J. Jackson, S. Roder, K. Wendehake, M.Dijcks, M. Amelaine, V. Wickaert, L. Bertrand and B. Vosman.2002. Construction and testing of a microsatellite containingmore than 500 tomato varieties. Theor. Appl. Genet. 105:1019-1026.

Chen, H., L. Qiao, L. Wang, S. Wang, M.W Blair and X. Cheng.2015. Assessment of genetic diversity and population structureof mungbean (Vigna radiatd) germplasm using EST-based andgenomic SSR markers. Gene 566: 175-183.

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Lestari, P., S.K. Kim, Reflinur, Y.J. Kang, N. Dewi and S.H. Lee.2014. Genetic diversity of mungbean (Vigna radiata L.)germplasm in Indonesia. Plant Genetic Res. 12(S1): S91-S94.

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Mondal, M.M.A., A.B. Puteh, M.A. Malek, M.R. Ismail, M.Y.Rafii and M.A. Latif. 2012. Seed yield of mungbean {Vignaradiata (L.) Wilczek) in relation to growth and developmentalaspects. Sci. World J. Vol. 2012, Article ID 425168, 7 pages,2012. doi:10.1100/2012/425168

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REFERENCES

financially supported by a grant from the Next-

Generation BioGreen 21 Program of the Rural

Development Administration, Republic of Korea.

ACKNOWLEDGEMENT

Authors highly thank to Dr. Yang Jae Kang and Dr.

Sue K. Kim, Crops Genomics Laboratory, Seoul

National University, Korea for their assistance during

conducting this research work. This research was

CONCLUSION

A total of 22 improved and local varieties of

Indonesian mungbean showed a common morpho

logical characteristic with a low variation (0.28).

Seven morphological characters, i.e. leaf lobe,

primary leaf shape, terminal leaf shape, seed shape,

flower color, pod pubescence and premature pod

color were uniform and found a considerable level of

variability ranging from low (0.04) for mature pod

color to the highest (0.81) for leaf pubescence

character. The use of the eight SSR markers proved

usefulness for differentiating the Indonesian

mungbean varieties. Eight of the SSR markers have

facilitated a specific DNA fingerprint profile andcould be used as the reference genetic identity for

identification of Indonesian mungbean varieties.

distinguished the two with genetic distance of 0.125.

Thus, this analysis proved that the eight SSR markers

enabled to create specific DNA fingerprint profile on

each of the Indonesian mungbean varieties. These

barcodes which possibly provided reference genetic

identity (ID) along with marker set in our study could

assist effective protection and management of

mungbean germplasm/collection in genebank and

market in Indonesia. Importantly, molecular ID could

protect a variety for commercial exploitation and a

plant breeder can be granted and also would be useful

to protect local variety from claim of other countries

and tracking their local origin.

The marker set developed in this study could be

utilized as a recommended molecular test for

identification of new mungbean varieties to support

the phenotypic assay of DUS requirement in the

plant variety protection in Indonesia. This study is in

agreement with the previous study by Lestari et al.

(2014) and has also confirmed the usefulness of the

SSR molecular marker set to identify mungbean

varieties which had a narrow genetic background

(Sestili et al. 2011), suggesting to open new

perspectives towards protection of released varieties

and conservation of Indonesian mungbean genetic

resources.

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Sestili, S., A. Giardini and N. Ficcadenti. 2011. Genetic diversityamong Italian melon inodorus (Cucumis melo L.) germplasmrevealed by ISSR analysis and agronomical traits. Plant GeneticR^^sour. 9(2): 214-217.

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Indonesian Journal of Agricultural Science Vol. 17 No. 2 October 2016: 65—7474

85

INDONESIAN JOURNAL OF AGRICULTURAL SCIENCE

Vol. 17, 2016: 1–83

Author Index

A

Annisa, Wahida, "Iron Dynamics and Its Relation to Soil Redox

Potential and Plant Growth in Acid Sulphate Soil of South

Kalimantan, Indonesia", 17(1): 1–8

Annisa,Wahida, "Capillary Water Rise in Peat Soil As Affected By

Various Groundwater Levels", 17(2): 75–83

Anwar, Syaiful, "Capillary Water Rise in Peat Soil As Affected By

Various Groundwater Levels", 17(2): 75–83

Apriyana,Yayan, "Production and Quality Enhancement of Mango

Using Fan Jet Sprayer Irrigation Technique", 17(2): 41–48

E

Efendi, Darda, "Effect of Different Sources of Plant Growth

Regulator on The Induction and Development of Mangosteen

Somatic Embryos", 17(1): 9–16

H

Heryani, Nani, "Production and Quality Enhancement of Mango

Using Fan Jet Sprayer Irrigation Technique", 17(2): 41–48

I

Izzah, Nur Kholilatul, "Development of EST-SSR Markers to Assess

Genetic Diversity of Broccoli and Its Related Species", 17(1): 17–26

K

Kartiwa, Budi, "Production and Quality Enhancement of Mango

Using Fan Jet Sprayer Irrigation Technique", 17(2): 41–48

L

Lestari, Puji, "Genomic Variation of Five Indonesian Cacao

(Theobroma cacao L.) Varieties Based on Analysis Using Next

Generation Sequencing", 17(2): 57–64

Lestari, Puji, "The Potential Use of SSR Markers to Support the

Morphological Identification of Indonesian Mungbean Varieties",

17(2): 65–74

Listanto, Edy, "Agrobacterium tumefaciens-Mediated In-Planta

Transformation of Indonesian Maize Using plG121Hm-Cs

Plasmid Containing nptII and hpt Genes", 17(2): 49–56

N

Nugraha, Muhammad Imam, "Capillary Water Rise in Peat Soil As

Affected By Various Groundwater Levels", 17(2): 75–83

Nursyamsi, Dedi, "Iron Dynamics and Its Relation to Soil Redox

Potential and Plant Growth in Acid Sulphate Soil of South

Kalimantan, Indonesia", 17(1): 1–8

J

Joni, Yosi Zendra, "Effect of Different Sources of Plant Growth

Regulator on The Induction and Development of Mangosteen

Somatic Embryos", 17(1): 9–16

Indonesian Journal of Agricultural Science/Author Index 85-1

P

Prihatini, Riry, "Effect of Different Sources of Plant Growth

Regulator on The Induction and Development of Mangosteen

Somatic Embryos", 17(1): 9–16

Prihatini, Riry, "Sensitivity of Pigment Content of Banana and Orchid

Tissue Culture Exposed to Extremely Low Frequency

Electromagnetic Field", 17(1): 27–34

R

Reflinur, "Development of EST-SSR Markers to Assess Genetic

Diversity of Broccoli and Its Related Species", 17(1): 17–26

Reflinur, "The Potential Use of SSR Markers to Support the

Morphological Identification of Indonesian Mungbean Varieties",

17(2): 65–74

Rijzaani, Habib, "Genomic Variation of Five Indonesian Cacao

(Theobroma cacao L.) Varieties Based on Analysis Using Next

Generation Sequencing", 17(2): 57–64

Riyadi, Imron, "Effect of Gamma Irradiation on The Growth and

Development of Sago Palm (Metroxylon sagu Rottb.) Calli",

17(1): 35–40

Riyanti, Eny Ida, "Agrobacterium tumefaciens-Mediated In-Planta

Transformation of Indonesian Maize Using plG121Hm-Cs

Plasmid Containing nptII and hpt Genes", 17(2): 49–56

Roostika, Ika, "Effect of Different Sources of Plant Growth

Regulator on The Induction and Development of Mangosteen

Somatic Embryos", 17(1): 9–16

Rosdianti, Ida, "Genomic Variation of Five Indonesian Cacao

(Theobroma cacao L.) Varieties Based on Analysis Using Next

Generation Sequencing", 17(2): 57–64

Rubiyo, "Genomic Variation of Five Indonesian Cacao (Theobroma

cacao L.) Varieties Based on Analysis Using Next Generation

Sequencing", 17(2): 57–64

S

Saleh, Norihan Mohamad, "Sensitivity of Pigment Content of Banana

and Orchid Tissue Culture Exposed to Extremely Low Frequency

Electromagnetic Field", 17(1): 27–34

Satyawan, Dani, "Genomic Variation of Five Indonesian Cacao

(Theobroma cacao L.) Varieties Based on Analysis Using Next

Generation Sequencing", 17(2): 57–64

Suk-Ha-Lee, "The Potential Use of SSR Markers to Support the

Morphological Identification of Indonesian Mungbean Varieties",

17(2): 65–74

Sumaryono, "Effect of Gamma Irradiation on The Growth and

Development of Sago Palm (Metroxylon sagu Rottb.) Calli",

17(1): 35–40

Sustiprijatno, "Agrobacterium tumefaciens-Mediated In-Planta

Transformation of Indonesian Maize Using plG121Hm-Cs

Plasmid Containing nptII and hpt Genes", 17(2): 49–56

Syahbuddin, Haris, "Production and Quality Enhancement of Mango

Using Fan Jet Sprayer Irrigation Technique", 17(2): 41–48

Syaufina, Lailan, "Capillary Water Rise in Peat Soil As Affected By

Various Groundwater Levels", 17(2): 75–83

8686-2 Indonesian Journal of Agricultural Science/Author Index

T

Tasma, I Made, "Genomic Variation of Five Indonesian Cacao

(Theobroma cacao L.) Varieties Based on Analysis Using Next

Generation Sequencing", 17(2): 57–64

Y

Yang, Tae-Jin, "Development of EST-SSR Markers to Assess Genetic

Diversity of Broccoli and Its Related Species", 17(1): 17–26

87

INDONESIAN JOURNAL OF AGRICULTURAL SCIENCE

Vol. 17, 2016

Subject Index

Indonesian Journal of Agricultural Science/Subject Index 87-1

Banana

Carotene 27

Chlorophyll 27

Electro-magnetic field 27

Orchid 27

Broccoli

Cauliflower 17

EST-SSR markers 17

Genetic diversity 17

Kohlrabi 17

Ferrous iron

Acid sulphate soil 1

Plant growth 1

Redox potential 1

Garcinia mangostana

Callus induction 9

Plant growth regulator 9

Somatic embryo 9

Maize

Agrobacterium tumefaciens 49

In-planta transformation 49

Mango

Fan jet sprayer 41

Production 41

Quality 41

Metroxylon sagu

Embryogenic calli 35

Gamma irradiation 35

Somatic embryo 35

Mungbean

DNA fingerprint 65

Morphological characters 65

SSR markers 65

Varietal identity 65

Peat soil

Bulk density 75

Capillary water 75

Groundwater level 75

Water content 75

Somatic embryo

Garcinia mangostana 9

Metroxylon sagu 35

Theobroma cacao

Genome sequencing 57

Genome variation 57

Next generation sequencing 57

SNP 57

88

ACKNOWLEDGEMENT OF REVIEWERS

The editorial staff of IJAS would like to acknowledge the scientists who reviewed articles published in 2016.

Their contributions ensure scientific quality of the publication.

Name Address Discipline

Prof. Ika Mariska Indonesian Center for Agricultural Plant Physiologi and

Biotechnology and Genetic Resources Biotechnology

Research and Development

Jalan Tentara Pelajar No. 3A

Bogor 16111, Indonesia

Dr. Backki Kim Texas A&M University, College Station, Biochemistry, Genetics and

TX 77843, United States Molecular Biology

Kularb Laosatit Faculty of Agriculture at Kamphaeng Saen, Genetic and Molecular

Kasetsart University, Kamphaeng Saen, Biology

Nakhon Pathom, 73140, Thailand

Dr. Sutoro Indonesian Center for Agricultural Agronomy

Biotechnology and Genetic Resources

Research and Development

Jalan Tentara Pelajar No. 3A

Bogor 16111, Indonesia

Dr. Made Jana Mejaya Indonesian Center for Food Crops Plant Breeding

Research and Development

Jalan Merdeka No. 147

Bogor 16111, Indonesia

Dr. Ahmad Kurnain Lambung Mangkurat University Soil Science

Banjarmasin, Indonesia

Prof. Purwiyatno Hariyadi Bogor Agricultural University Postharvest

IPB Dramaga Campus,

Bogor 16680, Indonesia

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Soil Till Res. 150: 10–20

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Sudaryono, A. Taufik, dan A. Wijanarko. 2007. Peluang

peningkatan produksi kedelai di Indonesia. hlm. 130–167.

Dalam Kedelai: Teknik produksi dan pengembangannya.

Sumarno, Suyamto, A. Widjono, Hermanto, dan H. Kasim

(Ed.). Pusat Penelitian dan Pengembangan Tanaman

Pangan, Bogor, Indonesia.

Dissertation/theses

Simpson, B.K. 1984. Isolation, Characterization, and Some

Application of Tripsin from Greenland Cod (Gadus

morhua). PhD Thesis. Memorial University of New-

foundland, St. John’s, Newfoundland, Canada. 179 pp.

Conference proceedings

Tangendjaja, B. and E. Wina. 2000. Tannins and ruminant

production in Indonesia. p. 40–43. In J.D. Brooker (Ed.)

Tannins in Livestock and Human Nutrition. Proceedings

of an International Workshop, Adelaide, Australia, 31

May–2 June 1999. ACIAR Proceedings No. 92.

Budi, D.S. 2000. Toleransi kedelai (Glycine max (L.) Merr.)

terhadap genangan air statis pada berbagai fase pertum-

buhan. hlm. 207–212. Dalam V.W. Gunawan, N. Sunarlin,

T. Handayani, B. Soegiarto, W. Adil, B. Priyanto, dan

Suwarno (Ed.). Prosiding Lokakarya Penelitian dan

Pengembangan Produksi Kedelai di Indonesia. Direktorat

Teknologi Lingkungan, Jakarta, Indonesia.

Conference paper

Chin, L.J., L.M. Tan, and K. Wegleitner. 2007. The occurrence

of mycotoxins in feed samples from Asia. A continuation

of the Bromin mycotoxin survey program. Paper presented

in 15th Annual ASA-IM Southeast Asian Feed Technology

and Nutrition Workshop, 27–30 May 2007, Bali-Indonesia.

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Heidhues, P. and B. Kassogi. 2005. The Impact of Consumer

Loss Aversion on Pricing. Centre for Economic Policy

Research Discussion Paper 4849.

Article online

Hawk, A. 2004. Mycotoxins. Proc. Grain Elevator and

Processing Society (GEAPS). http://www.geaps.com/

proceedings/2004/Hawk.ctm. (1 July 2008).

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Husen, E., A.T. Wahyudi, A. Suwanto, and R. Saraswati.

2008. Prospective use of ACC deaminase-producing

bacteria for plant growth promotion and defense against

biotic and abiotic stresses in peat-soil-agriculture.

Microbiol. Indones. (in press).

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