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Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies

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Abstract

Molecular markers are the most powerful genomic tools to increase the efficiency and precision of breeding practices for crop improvement. Progress in the development of genomic resources in the leading legume crops of the semi-arid tropics (SAT), namely, chickpea (Cicer arietinum), pigeonpea (Cajanus cajan) and groundnut (Arachis hypogaea), as compared to other crop species like cereals, has been very slow. With the advances in next-generation sequencing (NGS) and high-throughput (HTP) genotyping methods, there is a shift in development of genomic resources including molecular markers in these crops. For instance, 2,000 to 3,000 novel simple sequence repeats (SSR) markers have been developed each for chickpea, pigeonpea and groundnut. Based on Sanger, 454/FLX and Illumina transcript reads, transcriptome assemblies have been developed for chickpea (44,845 transcript assembly contigs, or TACs) and pigeonpea (21,434 TACs). Illumina sequencing of some parental genotypes of mapping populations has resulted in the development of 120 million reads for chickpea and 128.9 million reads for pigeonpea. Alignment of these Illumina reads with respective transcriptome assemblies have provided >10,000 SNPs each in chickpea and pigeonpea. A variety of SNP genotyping platforms including GoldenGate, VeraCode and Competitive Allele Specific PCR (KASPar) assays have been developed in chickpea and pigeonpea. By using above resources, the first-generation or comprehensive genetic maps have been developed in the three legume species mentioned above. Analysis of phenotyping data together with genotyping data has provided candidate markers for drought-tolerance-related root traits in chickpea, resistance to foliar diseases in groundnut and sterility mosaic disease (SMD) and fertility restoration in pigeonpea. Together with these trait-associated markers along with those already available, molecular breeding programmes have been initiated for enhancing drought tolerance, resistance to fusarium wilt and ascochyta blight in chickpea and resistance to foliar diseases in groundnut. These trait-associated robust markers along with other genomic resources including genetic maps and genomic resources will certainly accelerate crop improvement programmes in the SAT legumes.

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Abbreviations

AB:

ascochyta blight

AFLP:

amplified fragment length polymorphism

BAC:

bacterial artificial chromosome

BES:

BAC- end derived sequence

CAPS:

cleaved amplified polymorphic sequences

CISR:

conserved intron spanning region

COS:

conserved orthologous sequence

DArT:

diversity array technology

FW:

Fusarium wilt

GMM:

genic molecular marker

GS:

Genomic selection

HTP:

high-throughput

LLS:

late leaf spot

LLS:

late leaf spot

MABC:

marker-assisted backcrossing

MAS:

marker-assisted selection

NGS:

next-generation sequencing

RAPD:

random amplified polymorphic DNA

RFLP:

restriction fragment length polymorphism

RIL:

recombinant inbred line

SAT:

semi-arid tropics

SCMR:

SPAD chlorophyll meter readings

SLA:

specific leaf area

SMD:

sterility mosaic disease

SNP:

single nucleotide polymorphism

SPAD:

soil plant analytical development

SSR:

simple sequence repeats

TAC:

transcript assembly contig

TE:

transpiration efficiency

TUS:

tentative unique sequences

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Acknowledgements

We acknowledge the collaboration and support of several colleagues and collaborators from ICRISAT, University of California, Davis (UC-Davis, USA), National Center for Genome Research (NCGR, USA), J. Craig Venter Institute (JCVI, USA), University of Frankfurt, Germany, Diversity Arrays Technology (DArT, Australia) Pty Ltd, National Research Center on Plant Biotechnology (NRCPB, India), Indian Institute of Pulse Research (IIPR, India), National Institute for Plant Genome Research (NIPGR, India), Directorate of Groundnut Research (DGR, India), University of Agricultural Sciences, Dharwad (UAS-D, India), Mahatma Phule Krishi Vidyapeeth, Rahuri (MPKV-India), Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV, India), ICAR-Agricultural Research Station, Gulbarga (ARS-Gulbarga, India), Egerton University (EU, Kenya), Ethiopian Institute of Agricultural Research (EIAR, Ethiopia) and Lake Zone Agricultural Research Development Institute (LZARDI, Tanzania) that have made it possible to develop and apply genomic resources for trait mapping and molecular breeding mentioned in the article. The authors are thankful to several funding agencies like CGIAR Generation Challenge Programme, Tropical Legume I Initiative of Bill and Melinda Gates Foundation, Indian Council of Agricultural Research (ICAR), Department of Biotechnology (DBT) and Department of Science and Technology (DST) and Indo-German Science and Technology Centre for funding genomics and breeding projects in the mentioned legume crops.

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Authors and Affiliations

  1. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India

    Rajeev K Varshney, Himabindu Kudapa, Manish Roorkiwal, Mahendar Thudi, Manish K Pandey, Rachit K Saxena, Siva K Chamarthi, Murali Mohan S, Nalini Mallikarjuna, Hari Upadhyaya, Pooran M Gaur, L Krishnamurthy, KB Saxena, Shyam N Nigam & Suresh Pande

  2. CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, 06600, Mexico, DF, Mexico

    Rajeev K Varshney

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  1. Rajeev K Varshney
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  2. Himabindu Kudapa
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  3. Manish Roorkiwal
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  4. Mahendar Thudi
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  9. Nalini Mallikarjuna
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Correspondence to Rajeev K Varshney.

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[Varshney RK, Kudapa H, Roorkiwal M, Thudi M, Pandey MK, Saxena RK, Chamarthi SK, Mohan SM, Mallikarjuna N, Upadhyaya H, Gaur PM, Krishnamurthy L, Saxena KB, Nigam SN and Pande S 2012 Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies. J. Biosci. 37 811–820] DOI 10.1007/s12038-012-9228-0

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Varshney, R.K., Kudapa, H., Roorkiwal, M. et al. Advances in genetics and molecular breeding of three legume crops of semi-arid tropics using next-generation sequencing and high-throughput genotyping technologies. J Biosci 37, 811–820 (2012). https://doi.org/10.1007/s12038-012-9228-0

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