Journal of Biosciences

, Volume 37, Issue 5, pp 811–820 | Cite as

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

  • Rajeev K VarshneyEmail author
  • 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


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.


Chickpea genomic resource genotyping groundnut legume pigeonpea sequencing 

Abbreviations used


ascochyta blight


amplified fragment length polymorphism


bacterial artificial chromosome


BAC- end derived sequence


cleaved amplified polymorphic sequences


conserved intron spanning region


conserved orthologous sequence


diversity array technology


Fusarium wilt


genic molecular marker


Genomic selection




late leaf spot


late leaf spot


marker-assisted backcrossing


marker-assisted selection


next-generation sequencing


random amplified polymorphic DNA


restriction fragment length polymorphism


recombinant inbred line


semi-arid tropics


SPAD chlorophyll meter readings


specific leaf area


sterility mosaic disease


single nucleotide polymorphism


soil plant analytical development


simple sequence repeats


transcript assembly contig


transpiration efficiency


tentative unique sequences



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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Copyright information

© Indian Academy of Sciences 2012

Authors and Affiliations

  • Rajeev K Varshney
    • 1
    • 2
    Email author
  • Himabindu Kudapa
    • 1
  • Manish Roorkiwal
    • 1
  • Mahendar Thudi
    • 1
  • Manish K Pandey
    • 1
  • Rachit K Saxena
    • 1
  • Siva K Chamarthi
    • 1
  • Murali Mohan S
    • 1
  • Nalini Mallikarjuna
    • 1
  • Hari Upadhyaya
    • 1
  • Pooran M Gaur
    • 1
  • L Krishnamurthy
    • 1
  • KB Saxena
    • 1
  • Shyam N Nigam
    • 1
  • Suresh Pande
    • 1
  1. 1.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  2. 2.CGIAR Generation Challenge Programme (GCP), c/o CIMMYTMexicoMexico

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