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Improve chickpea productivity for marginal environments in sub-Saharan Africa and
South Asia
Introduction
Genomic resources
Genetic resources
Trait mapping- QTLs and GWAS
Molecular breeding for drought tolerance
Enhancing Capacity of NARS
Data management and decision support tools
Contents
Introduction…
Global distribution of chickpea area
Grown on about 12 m ha across 54 countries
>6 m ha 0.5 to 1.0 m ha 150,000 to 210,000 ha 50,000 to 100,000 ha 10,000 to 40,000 ha
Production constraints Abiotic stresses 1. Drought 2. Heat 3. Salinity 4. Cold
Max. Temperature (0C) Mean Temp Min. Temperature (0C)
Harvest
0 50
100 150 200 250 300 350 400 450
1 2 3 4 5 6 7 8 9 10 11 12 Month
mm
0.0 5.0 10.0 15.0 20.0 25.0 30.0 35.0 40.0 45.0
Sowing
Terminal drought
Precipitation Evaporation
Mill
ion
(US$
)
Tota
l pro
duct
ion
Dro
ught
Low
tem
pera
ture
Wilt
Asco
chyt
a bl
ight
Pod
bore
r
Constraints in molecular breeding
Very few molecular (SSR) markers
Either no genetic map or maps with low marker density
Non-availability of appropriate germplasm, mapping populations and phenotyping data
Non-availability of trait-associated markers in breeding
Capacity and skills in molecular breeding
Genomic resources...
Resource Amount SSRs ~2,000 DArT arrays 15,360 features SNPs 9,000 GoldenGate assays 768 SNPs KASPar assays 2,068 SNPs Veracode assays 96 SNPs
Summary of marker resources
LG1 LG2
LG3 LG4 LG5 LG6 LG7
LG8
Marker Loci: 1,291 Coverage: 845.56 cM
Comprehensive genetic map
TAG 2010, 2011 PLoS One 2011 Plant Biotech J 2012
KASPars assays integrated in transcript map
Markers mapped : 1328 Map distance : 788.6cM Average number of markers/LG : 166 Average inter-marker distance : 0.59cM
TAG 2010, 2011 PLoS One 2011 Plant Biotech J 2012
Towards genome-wide physical map
Clones CAH library CAE library Old library
Total
1st 2nd 1st 2nd 1st 2nd
Clones targeted
29,664 5,376 29,568 5,376 337 773 71,094 (12X )
Clones with usable data
28,492 5,160 28,272 5,240 319 765 68, 248
Clones in FPC
18,285 3,502 22,571 3,926 319 765 49,368
Old library, 1st instance are the clones from which BES-SSR were developed
Old library, 2nd instance are the RGH hybridizing clones
Fingerprinting statistics of different BAC-libraries
Clone statistics in contigs: Total no. clones in 1,174 contigs 46,112 Range of clone in contigs 2 to 3,007 Average no. of clones in each contig 39.27 Genome coverage 8X Genome represented 615 Mb Band statistics in clones: Total no. of bands in clones 318,971 Average no. of bands in clones 271.69 Range of bands in clones 34 to 2,268 Minimum tiling path (MTP): Total no. of contigs 1,174 No of clones in MTP 4,290
Statistics of physical map Collaboration: NIPGR, India and UC-Davis, USA
Integrating sequence, physical and genetic maps
The chickpea genome
Re-sequencing in chickpea Samples: - 5 wild species - 25 landraces - 60 breeding lines/ released varieties Or - 5 wild species - 57 Desi genotypes - 28 Kabuli genotypes
Sequencing: -RAD sequencing (35 Gb) - 61 genotypes (40 desi, 16 kabuli, 5 wild) -WGRS (205 Gb) - 29 genotypes (17 desi, 12 kabuli)
Genetic resources…
Harnessing alleles from genebanks 1,700 genebanks
By 1997, the world economy had accrued annual benefits of ca. $115 billion from use of crop wild relatives
Genomic characterization of gene bank material is essential
Needs to associate allelic value with phenotype
Transfer in elite varieties
Genetic resources
300
(A) Intra-specific mapping populations: 1. ICCV 283 × ICC 8261 - 289 RILs 2. ICCV 4958 × ICC 1882 - 268 RILs
(B) Chickpea reference set -300 genotypes
(C) Pre-breeding populations ICRISAT, Patancheru - 17
ICRISAT, Nairobi - 20
Egerton Uni. Kenya - 5
EIAR, Ethiopia - 2
MAGIC populations
Genotypes Remarks ICC 4958 Drought tolerant genotype found promising in
Ethiopidrought tolerant parent of two mapping populations
ICCV 10 Widely adapted drought tolerant cultivar found promising in India and Kenya
JAKI 9218 Farmer-preferred cultivar in central and southern India
JG 11 Farmer-preferred cultivar in southern India and also performing well in Kenya
JG 130 Farmer-preferred cultivars from central India
JG 16 Farmer-preferred cultivar in northern and central India
ICCV 97105 Farmer-preferred elite line identified in Kenya and Tanzania
ICCV 00108 Farmer-preferred elite line identified in Tanzania
Eight well performing elite chickpea lines (TLI & TLII)
Trait mapping…
Experiment of chickpea root growth in rain out shelter
(ROS)
Crane for lifting root cylinders for moisture under water stress
determinations
Semi-automated precise high-throughput phenotyping
Phenotyping in rainfed and irrigated conditions
Phenotyping in Sub-Saharan Africa (Kenya, Ethiopia)
Phenotyping in India (Pantcheru, Kanpur, Bangalore)
“QTL- hotspot” on CaLG04
ICC 4958 × ICC1882 Consensus map ICC283 × ICC8261
PVE 58.2%
Saturating “QTL- hotspot” region 701.049 million reads 59030.7 Mbp 828 SNPs
Genotyping data on Reference set
Homozygote
KASPar assays
Homozygote
Heterozygote
SSR analysis (CE)
SNPs in candidate genes
Marker data on reference set
SSR - 35 DArT - 1157 SNPs - 651 Gene based SNPs - 113 Total 1,956
Candidate genes Abscisic acid stress and ripening gene (ASR) DREB2A ERECTA Sucrose synthase (SuSy) Sucrose phosphate synthase (SPS) AKIN (SNF1 related protein kinase) Aminoaldehyde dehydrogenase (AMADH) Dehydrin (DHN), Myb transcription factor
Root related traits Root traits Traits Seasons Root length (cm) 3 Root length density (cm cm-3) Root volume (cm3) 3 Root dry weight (g) 3 Rooting depth (cm) 3 Root surface area 3 R-T ratio(%) 3 Shoot dry weight (g) 3 Stem dry weight (g) 3 Leaf dry weight (g) 3 Projected area 2 Average diameter 2
Water stress determination
Exp. of chickpea root growth in ROS
Agronomic traits Morphological traits
Yield related traits
Traits Seasons Traits Seasons Plant height (cm) 14 Pods/plant 2 Plant width (cm) 7 100 SDW (g) 10 Plant stand 7 Yield (g/m2) 3 Apical primary branch
7 Yield (Kg/ha) 10
Apical secondary branch
7 Yield per plant 7
Basal primay branch 7 Production 7 Basal secondary branch
7 Biomass 6
Teritiary branches 7 Biomass/plant 2 Phenological traits Harvest index 6 Days to flowering 13 TDM weight
(g/m2) 2
Days to maturity 9 Transpiration efficiency Seeds per pod 7 13C 2 Seeds/plant 2 SPAD 2
Field phenotyping under rainfed and irrigated environments
Heat tolerance phenotyping
Δ Carbon on LG4
Yield under rainfed on LG4
.
….
GWAS for ΔC and Yield
Root length density
Harvest index
GWAS for RLD and HI
GWAS for 100 seed weight
Molecular breeding for drought tolerance…
MABC, MARS and GS approaches seem to most
promising for crop improvement
Need to have genomic resources and cost-effective
genotyping platforms
Precise phenotyping platforms required
Breeders-friendly pipelines and decision support tools required for prediction of phenotype
Modern breeding approaches for enhancing genetic gains
Marker-assisted backcross (MABC) method for introgressing genomic region controlling root and
other drought tolerance related traits Donors
Cultivars
JG 11 Chefe KAK 2
Phenotyping of MABC products in ROS
BC3F3 lines phenotyped in ROS for assessing root traits
0
500
1000
1500
2000
2500
3000
3500
4000
4500
5000
Yield
(kg
/ha)
Irrigated
Rainfed
QTL introgression into JG 11
Enhanced root length density
Enhanced yield The Plant Genome, 2013
Institution Cross/parents Current status ICRISAT, India JG 11 × ICC 4958 20 BC3F5 lines
Chefe × ICC 8261 8 BC3F5 lines KAK2 × ICC 8261 2 BC3F5 lines ICCV 10 × ICC 4958 22 BC3F5
IIPR, India DCP92-3 × ICC 4958 60BC1F1 KWR 108 × ICC 4958 7 BC1F1
IARI, India Pusa 362 × ICC 4958 170 BC2F1 EIAR, Ethiopia Ejere × ICC 4958 384 BC2F1
Arerti × ICC 4958 27 BC3F4 lines EU, Kenya ICCV 97105 × ICC 4958 33 BC3F1
ICCV 95423 × ICC 4958 10 BC3F5 lines
MABC for enhancing drought tolerance in Asia and sub-Saharan Africa
MABC status @ IARI (Indian project) 4 BC2F1 plants (with >96% genome recovery) were
used in making backcrosses with recurrent parent Pusa 362 to generate BC3F1 (105 seeds)
BC2F2 seeds also harvested from plants with more than 96% genome recovery
Popu
latio
n de
velo
pmen
t R
ecom
bina
tion
Popu
latio
n de
velo
pmen
t
1st Recombination cycle
2nd Recombination cycle
3rd Recombination cycle
Multilocation phenotyping
Genotyping
Parent 1 × Parent 2
F1
F2
F3
F3:4
F3:5
Single seed descent
282 F3 progenies
282 progenies
Multilocation phenotyping
A B C D E F G H
F1 F1 F1 F1
F1 F1
F1
F2
F3
F3:4
10 plants/family (A-H), 6 sets of 8 families/cross
QTL detection
JG 11 × ICC 04112 JG 130 × ICC 05107
Kenya, Ethiopia and India Rainfed and irrigated environments
(2010-11)
70 marker 92 markers
QTL analysis completed
Marker-assisted recurrent selection (MARS)
MARS lines for RC selected
OptiMAS
Indian project
TLI Phase II
First RC completed
Second RC in progress
×
JG 130 X ICCV 05107
×
JG 11 X ICCV 04112
Exploring genomic selection in chickpea
320 elite-breeding lines;>3000 markers
GS
ISMU V2
Raw Reads
Reference
Assemble & Align Raw Reads Mine SNPs Generate Marker Matrix Visualize in TABLET and FLAPJACK Export in FLAT Files
GDMS Genotypic
Matrix & QTLs
Lines selected for further crossing in
GS
External Genotyping Platforms
Called SNPs
ISMU V2.0
44
Enhancing capacity of NARS in modern breeding…
NARS partners practicing modern breeding
Serah Alice
Paul examining the crosses Robert
Musa Jarso marker analysis for MABC crosses
Mosses oyier marker analysis for MABC crosses
4th International Workshop on
Next generation genomics and integrated breeding for
crop improvement, Feb 19-21,2014,
NARS partners practicing modern breeding
Products Reference set, pre-breeding populations,
MAGIC lines >3000 SSRs, 2068 KASPar, DArT arrays High density genetic maps and physical
map Draft genome sequence and re-sequencing
of 90 lines MABC lines with enhanced drought
tolerance in the genetic background of JG11, KAK2 and Chefe
Summary Well characterized reference set and 39 pre-breeding
populations developed
1200 F8 MAGIC lines developed ready for genotyping and phenotyping
Large scale markers (SSRs, SNPs, DArTs) and several maps developed
A genome-wide physical map developed (574 Mb) that contributed to genome sequencing of chickpea
A most promising “QTL-hotspot” with about 50 markers for MABC for drought tolerance
Promising introgression (BC3F5) lines with higher yield in rainfed conditions
Next generation of molecular breeders (4 PhD and 8 MSc students from NARS, >50 researchers) trained
TLI Phase I and Phase II datasets curated into IBWS
ICRISAT, Patancheru, India: Pooran Gaur, Hari Upadhyaya, L Krishnamurthy, Junichi Kashiwagi, Abhishek Rathore, Trushar Shah, Mahendar Thudi, Manish Roorkiwal, Rachit Saxena, Ashish Kumar, Murali Mohan, HimaBindu, Shailesh, Pavana, Neha, Serah, Gafoor UC-Davis, USA: Doug Cook, R Varma Penmetsa NCGR, Santa Fe, USA: Greg May, Andrew Farmer Uni Georgia, USA: Scott Jackson; JCVI, USA: Chris Town, Yongli Xiao DArT Pty Ltd, Australia: Andrzej Killian Uni Frankfurt, Germany: Peter Winter, Guenter Kahl Osmania University: PB Kavikishor NRCPB, New Delhi, India: NK Singh, TR Shrma, R Srinivasan, PK Jain NIPGR, New Delhi, India: AK Tyagi, Sabhyata Bhatia IIPR-Kanpur, India: SK Chaturvedi, Aditya Garg, S Datta IARI, New Delhi, India: Jitendra Kumar, C Bharadwaj, S MPKV, Rahuri, India: L Mhase, P N Harer, PL Kulwal JNKVV, Jabalpur, India: A Babbar, N Saini, O Gupta ARS-Gulburga, India: D Mannur, Jayalaksmi UAS-Bangalore, India: Sheshashayee, M Udayakumar, KP Vishwanath Egerton University, Kenya: Paul Kimurto, Richard Mulwa EIAR, Addis Abba, Ethiopia: Asnake Fikre, Million Eshete LZARDI, Debre Zeit, Tanzania: Robert Kileo
Many thanks to all contributors
Collaborators and partners