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Advances in Pigeonpea Genomics

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Legumes in the Omic Era

Abstract

Pigeonpea, a member of family Fabaceae, is one of the important food legumes cultivated in tropical and subtropical regions. Due to its inherent properties to withstand harsh environments, it plays a critical role in ensuring sustainability in the subsistence agriculture. Furthermore, plasticity in the maturity duration imparts it a greater adaptability in a variety of cropping systems. In the post genomics era, the importance of pigeonpea is further evident from the fact that pigeonpea has emerged as first non-industrial legume crop for which the whole genome sequence has been completed. It revealed 605.78 Mb of assembled and anchored sequence as against the predicted 833 Mb genome consequently representing 72.8 % of the whole genome. In order to perform genetic and genomic analysis various molecular markers like random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), diversity array technology (DArT), single feature polymorphism (SFP), and single nucleotide polymorphism (SNP) were employed. So far four transcriptome assemblies have been constructed and different sets of EST-SSRs were developed and validated in a panel of diverse pigeonpea genotypes. Extensive survey of BAC-end sequences (BESs) provided 3,072 BES-SSRs and all these BES-SSRs were further used for linkage analysis and trait mapping. To make the available linkage information more useful, six intra-specific genetic maps were joined together into a single consensus genetic map providing map positions to a total of 339 SSR markers at map coverage of 1,059 cM. However, earlier very few linkage maps were available in the crop because of non-availability of genomic resources. Several quantitative trait loci (QTLs) associated with traits of agronomic interest including QTLs for sterility mosaic disease, fertility restoration, plant type and earliness have been identified and validated. To strengthen the traditional breeding, plenty of genomics tools and technologies are now available for integration in regular pigeonpea breeding schemes. This article presents the progress made in the area of pigeonpea genomics and outlines its applications in crop breeding for pigeonpea improvement.

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Acknowledgements

Authors from ICRISAT are thankful to United States Agency for International Development (USAID) for financial support to utilize genome sequence information for pigeonpea improvement. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes.

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Authors and Affiliations

  1. Crop Improvement Division, Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

    Abhishek Bohra Ph.D.

  2. Center of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Andhra Pradesh, 502324, India

    Rachit K. Saxena Ph.D. & Rajeev K. Varshney Ph.D.

  3. Pigeonpea Breeding, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India

    K. B. Saxena Ph.D. & C. V. Sameerkumar Ph.D.

Authors
  1. Abhishek Bohra Ph.D.
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  2. Rachit K. Saxena Ph.D.
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  3. K. B. Saxena Ph.D.
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  4. C. V. Sameerkumar Ph.D.
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  5. Rajeev K. Varshney Ph.D.
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Corresponding author

Correspondence to Rajeev K. Varshney Ph.D. .

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Editors and Affiliations

  1. Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

    Sanjeev Gupta

  2. Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India

    Nagasamy Nadarajan

  3. Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA

    Debjyoti Sen Gupta

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Bohra, A., Saxena, R.K., Saxena, K.B., Sameerkumar, C.V., Varshney, R.K. (2014). Advances in Pigeonpea Genomics. In: Gupta, S., Nadarajan, N., Gupta, D. (eds) Legumes in the Omic Era. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8370-0_5

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