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Crop BreedingDevelopmental biology

“Omics in plants”

Identify genes, promoters, mi RNAs, pathway components

Omics Platforms

Genomics• Genomics – the comprehensive study of whole sets of genes & their interactions

• Applications of Plant Genomics Gene identification and cloning Gene prediction/ discovery Genetic mapping and locating genes QTLs analysis Comparative genomics Understanding expression profiles, responses and interactions Molecular markers and MAS

Application in Maize Improvement

1) Genetic and physical maps2) QTL Mapping for Agronomic traits3) Mapping and tagging of Quality traits4) Association Mapping 5) Functional genomics6) Genome sequencing7) MAS for Maize improvement8) Genome selection

TRAIT

QTL References SMCV Resistance Smc 1 , Smc 2 Duble et al ( 2008)

Ear rot Resistance ER1 Xiang et al. (2012)

Fatty acid composition pa19 Yang et al. (2010)

Plant height qPH3.1 Teng et al. (2015)

Maize rough dwarf diseases QTL Shi et al. (2012)

Kernel oil content qk01-1, QTL Le et al. (2014) and yang et al, (2013)

Southern corn leaf blight rhm 1 Zhao et al (2010)

Northern leaf blight qNLB-1.06 & 1.02 Chung et al.(2014)

Downy mildew resistance qDMR George et al. ( 2005)

Oil content OIL3.77 Zhang et el.(2013)

Starch content qSC Dong et al. ( 2008) contd…

List of QTLs Linked to Agronomically Important Traits

TRAIT

QTL ReferencesMaize head smut Qhs2.09 Weing et al. (2012)

Grey leaf spot qgls1 Zhaing et al.(2013)

Drought tolerance mQTL Almeida et al (2014)

Early flowering time vgt 1, vgt2 Chardon et al. (2005)

Nitrogen remobilization QTLs Coque et al.(2008)

Zinc and iron concentration ZnK, ZnC , FeK, FeC Quin et al.(2010)

Leaf area QTL Liu et al(2009)

Laef angle QTL Lu et al.(2007)

Leaf orientation QTL Lu et al.(2007)

Continued………

TRAIT GENE/ QTL REFRENCES

Corn borer resistance QTLs on chromosome 7, 9, 10 . Willcox et al. (2002)

Earliness and yield QTLs on chromosome 5, 8, 10. Bouchez et al. (2002)

QPM Opaque 2 gene on chromosome 7. Dreher et al. (2003)Morris et al. ( 2003)Babu et al. (2005)Gupta et al. (2010)

Maize streak virus QTLs on chromosome 1. Abelo et al.(2009)

Maize head smut QTLs on chromosome 1. Min et al.(2012)

Successful examples of MAS in maize improvement

Genome selection

Omnia Ibrahim. Genomic Selection in Breeding Programs

Genome Selection• Genome-wide Selection (GWS), also called Genomic

Selection (GS), is one of marker-assisted selection (MAS), in which dense SNP genotypes covering the entire genome are used to predict the genetic value of a trait or individual.

• All markers are counted based on genomic estimated breeding value (gEBV) estimated as the sum of the effects of markers across the genome (Contrast to MAS in which only markers positively associated with trait are used).

Conventional MAS

GWS

QTL1

QTL2

QTL3

Genetic Gains in Grain Yield Through Genomic Selection in Eight Bi-parental Maize Populations under Drought Stress

Beyene et al. 2015

Case study

Association mapping (AM) Association mapping,it is a method of mapping QTL that take advantage of historic linkage disequlibrum to link phenotype to genotype. Tool to resolve complex trait variation down to the sequence level by exploiting historical and evolutionary recombination events at the population level.

(Nordborg & Tavare, 2002; Risch& Merikangas, 1996).

Offers greater precision in QTL location than family-based linkage analysis.

Does not require family or pedigree information , can be applied to a range of

experimental and non-experimental populations.

Need of Association Mapping in MAIZE ?

Source of cooking oil, biofuel and animal feed.

Model organism for cytogenetics, genetics, genomics, and functional genomics studies.

(Strable and Scanlon, 2009). Primary staple food in many African countries.

Map-based cloning of QTLs is time consuming and expensive process in Maize .

Association mapping can explore all recombination events and mutations in a given population and with a higher resolution .

(Yu and Buckler, 2006)

Transcriptomics • The study of the transcriptome, the complete set of RNA transcripts produced by the

genome at any one time.

Application of Transcriptomics

• Differential expression of genes

• Co expression of genes

• Gene interaction

• Alternative splicing of genes

ProteomicsThe study of proteome, the structure and function of complete set of protein in a cell at a given time. Applications of proteomics

• Protein Mining – catalog all the proteins present in a tissue, cell, organelle, etc.

• Differential Expression Profiling – Identification of proteins in a sample as a function of a particular state: differentiation, stage of development, disease state, response to stimulus or environments.

• Network Mapping – Identification of proteins in functional networks: biosynthetic pathways, signal transduction pathways, multiprotein complexes.

• Mapping Protein Modifications – Characterization of posttranslational modifications: phosphorylation,

glycosylation, oxidation, etc.

Metabolomics • Study of metabolome, collection of all metabolites in a cell, tissue, organ or organism.

Applications of metabolomics Characterization of metabolism

Identification of regulated key sites in network.

Biofortification and genetic modification

Investigation of gene function under stress conditions

Application Proteomics transcriptomics and metabolomics in maize improvement

Aboitic stress toleranceBoitic tolerance

Drought • Drought tolerance is important for the success of maize hybrids grown in

drought prone regions.• The maize response to drought stress is a crucial and complex process.• Drought affects many processes involved in plant growth and

development, including osmotic adjustment, antioxidant capabilities, photosynthetic rate reduction, and abscisic acid (ABA) accumulation (Cramer et al., 2011). These processes are controlled by many proteins,

• which are expressed differentially in various stress tolerant species, in various functions and biochemical pathways, and at various developmental stages

• The drought response of maize has been extensively studied in seeds, leaves, and roots, mainly using two-dimensional gel electrophoresis MS based proteomics

• As determined by omics studies, the proteins involved in the maize drought response primarily include

• Protective proteins (such as HSPs) (Benesova et al., 2012; Hu et al., 2010a; Li et al., 2009; Luo et al., 2010),

• Late embryogenesis abundant proteins (LEAs) (Benesova et al., 2012; Huang et al., 2012),

• Stress response-related proteins (such as NBSLRR resistance-like protein) (Hu et al., 2012), 14-3-3-like proteins (Huang et al., 2012; Li et al., 2009),

• Phytohormone related proteins, and signaling proteins (such as auxin repressed protein and serine/threonine protein kinase) (Bonhomme et al., 2012; Hu et al., 2011; Luo et al., 2010).

Summary of Recent Years Publications on Drought Response of MaizeMaize genotype Stage/tissue Treatment Protein/gene

classification Identified major proteins/genes Reference

Zhengdan 958(cultivar, China) 14-d-old leaves

-0.7 MPa PEG

protective proteins,metabolism

HSP17.4, HSP17.2, HSP26,guanine nucleotide-binding protein, b-subunit-like protein, granule-bound starch synthase

(Hu et al., 2010)

vp5 (ABA-deficientmutant); Vp5(wild-type)

14-d-old roots) -1.0 MPa Regulatory proteins,energy and metabolism, redox homeostasis

Nuclear transport factor 2, glycine-rich RNA binding protein 2, pathogenesis-related protein 10, transcription factor BTF3, serine/threonine-protein kinase receptor

(Hu et al., 2011)

Zhengdan958 -for 8 h

14-d-old roots 0.7 MPa PEG Transporters, signaltransduction, metabolism,disease/defense,cell growth/division

Alcohol dehydrogenase 1, O-methyltransferase, APx1-cytosolic ascorbate peroxidase, aquaporin PIP2-5, glutathione S-transferase 4 glycine-rich RNA-binding protein 2

(Liu et al., 2013)

B73Fertilized ovary andleaf meristem tissue

Irrigation was withheld at theonset of silkemergence

Carbon metabolism, cellcycle and division,programmed cell death,

Chlorophyll a/b-binding family protein, ABA response element-binding factor, sucrosetransporter 1, phosphorylase, 1,4-a-glucan-branching enzyme 2

(Kakumanu et al.,2012)

LX9801, Qi319, etc.(drought-tolerant inbred lines); B73,Ye478, Ji853

14-d-old Water stres Plant hormone regulation, carbohydrate and sugar metabolism,

524 nsSNPs (Xu et al., 2014)

Six maize hybrids Leaf blades, ears, husks, sheath, and silk

Stopping irrigation for 12 d before flowering

Amino acids, sugars, sugaralcoholsandintermediates of the TCAcycle, etc

524 nsSNPs – (Witt et al., 2014)

Maize genotype Treatment Tissue Target DifferentiallyExpressedproteins/genes

Primary results Reference

R12 (salt-resistanthybrid)

25 mM; 1, 2, 4 h Chloroplasts Total proteins 20 Na+ accumulates quickly and excessively in maize chloroplasts under moderate short-term saltstress. A defined set of specific chloroplast proteins in maize change instantaneously inresponse to salt stress.

Zo¨rb et al., 2009

SR12 25 mM; 1 h Roots Total proteins;phosphoproteins;dephosphoproteins

14; 10; 6 This study provides new insights for the initial reaction of the proteome and phosphoproteome of maize roots after adjustment to saline conditions and reveals early members of sugar signalling and cell signalling pathways, e.g. calmodulin, 14-3-3 proteins.

(Zo¨rb et al., 2010)

BeiDan1 (cultivar,China)

0.1 M, 7 d; 0.2 M,7d

Embryos Total proteins 51; 79 Identified proteins are mainlyinvolved in seed storage, energymetabolism, stress response, andprotein metabolism. Notably, theexpression of proteins thatrespond to ABA signals increasedin response to salt stress.

(Meng et al., 2014)

contd……

Summary of Recent Years’ Publications on Salt Response of Maize

Maize genotype Treatment Tissue Target DifferentiallyExpressedproteins/genes

Primary results Reference

YQ7-96 (inbred line) 100 mM; 72 h Leaves androots

Total RNA 296 The salt-induced genes are related to catalytic activity, nucleic acid binding, protein binding and structural molecule activity.

(Qing et al., 2009)

A cultivar fromZenecaAgrochemicals

50 or 150 mM; 2, 4and 6 d

Roots andshoots

Metabolites - The levels of alanine, glutamate, asparagine, glycine-betaine and sucrose are increased and malic acid, trans-aconitic acid and glucose are decreased saline treated shoots.

(Gavaghan et al.,2012)

Continued……

Maize genotype

Treatment Tissue Target DifferentiallyExpressedproteins/genes

Primary results Reference

Nongda108 (cultivar,China)

150 mM; 24 h Leaves Phosphoproteins;dephosphoproteins

47 Cell signaling pathway members(e.g. calmodulin and 14-3-3proteins) are regulated in response to 24-h salt stress, multiple putative salt-responsivephosphoproteins seem to beinvolved in the regulation ofphotosynthesis-related processes

(Hu et al., 2013)

NC286 (salt-tolerantinbred line)Huangzao4 (saltsensitiveinbredlines)

200 mM; 0.5, 5,24 h

Roots mRNA 98 Salt-responsive mRNAss areinvolved in the regulation ofmetabolic, morphological andphysiological adaptations ofmaize seedlings at the posttranscriptional level.

(Ding et al., 2009)

contd……

Continued….

Summary of others aboitic stress

Phenomics • Phenomics, the study of the phenome, where phenotypes are

characterized in a rigorous and formal way, and link these traits to the associated genes and gene variants (alleles).

Understanding how particular genotypes result in specific phenotypic properties is a core goal of modern biology

However, prediction of phenotype from genotype is generally a difficult problem due to the large number of genes and gene products that contribute to most phenotypes in concert with complex and changeable environmental influences.

Now that digital DNA data are available in abundance, we face an acute need to quantify individual phenotypes in a way that can be explicitly matched to individual genotypes. If this challenge can be mastered, we face the promise of gaining a deeper insight into the components of complex traits such as yield or stress resistance in economically important plants

A report of the Phenomics workshop sponsored by the USDA and NSF

Why Phenomics ?

Essential for assessing pleiotropic effects of genetic variation .

Study the fitness to understand evolution – Pleiotropic effects on phenotype and their interaction with environment .

Ideally identify relationships between genotype and phenotype as well as reveal correlations between seemingly unrelated phenotypes.

Conclusion

• Improves understanding about DNA variation, transcription patterns , and protein expression profiling.

• Make maize as a model crop among cereals , provide new insight about orthologous and paralogous maize genes

• To study the structure of genomes and genetic mechanism behind economically important traits.

• Integration of omics reveals the identification of key genes in biological processes and aided in design of new plants in maize for betterment of humankind

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