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

    Varshney, R K and Kudapa, H and Roorkiwal, M and Thudi, M and Pandey, M K and Saxena, R K and Chamarthi, S K and Murali Mohan, S and Mallikarjuna, N and Upadhyaya, H D and Gaur, P M and Krishnamurthy, L and Saxena, K B and Nigam, S N 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. Journal of Biosciences, 37 (5). pp. 811-820. ISSN 0973-7138

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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 speciesmentioned 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 traitassociated 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 legume

    Item Type: Article
    Divisions: UNSPECIFIED
    CRP: UNSPECIFIED
    Uncontrolled Keywords: Chickpea; genomic resource; genotyping; groundnut; legume; pigeonpea; sequencing
    Subjects: Mandate crops > Chickpea
    Mandate crops > Pigeonpea
    Mandate crops > Groundnut
    Others > Genetics and Genomics
    Others > Agriculture-Farming, Production, Technology, Economics
    Depositing User: Mr Sanat Kumar Behera
    Date Deposited: 04 Oct 2012 14:44
    Last Modified: 12 Oct 2012 06:54
    URI: http://oar.icrisat.org/id/eprint/6163
    Official URL: http://dx.doi.org/10.1007/s12038-012-9228-0
    Projects: UNSPECIFIED
    Funders: Generation Challenge Programme, Bill and Melinda Gates Foundation, Indian Council of Agricultural Research , Government of India - Department of Biotechnology , Government of India - Department of Science and Technology, Indo-German Science and Technology Centre
    Acknowledgement: 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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