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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 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
Article

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.

Keywords

Chickpea genomic resource genotyping groundnut legume pigeonpea sequencing 

Abbreviations used

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

Notes

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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Copyright information

© Indian Academy of Sciences 2012

Authors and Affiliations

  • Rajeev K Varshney
    • 1
    • 2
  • 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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