Whole-Genome Sequencing of Pigeonpea: Requirement, Background History, Current Status and Future Prospects for Crop Improvement

Abstract

Despite of being a very important crop, pigeonpea did not have genomic resources until 2005. Pigeonpea Genomics Initiative (PGI) supported by Indian Council of Agricultural Research (ICAR) under Indo-US Agriculture Knowledge Initiative was the first major initiative that delivered first set of molecular markers in large numbers, first set of mapping populations, first set of transcriptome assemblies, etc. Subsequently, two consortia—1) International Initiative for Pigeonpea Genomics (IIPG), led by International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and 2) Led by National Research Centre on Plant Biotechnology (NRCPB)—delivered two draft genome assemblies for Asha (ICPL 87119) variety. In summary, all these genomic resources transformed pigeonpea from an ‘orphan crop’ to ‘genomics resources-rich crop’. After publication of draft genome sequences, a detailed plan was developed to utilize draft genome information for pigeonpea improvement. This plan in the form of a proposal was approved by Ministry of Agriculture, Government of India and United States Agency for International Development (USAID)—India. In addition to this major project, two additional projects were funded by Department of Biotechnology, Government of India. All these efforts have established high-density genotyping platforms such as genotyping by sequencing (GBS) and ​‘Axiom® CajanusSNP Array’, produced the first generation HapMap, generated whole-genome re-sequencing data of >400 pigeonpea lines, evaluated several mapping populations for desired traits, established marker–trait association for several traits of interest to breeders and also identified best-performing lines. Additionally, multi-parent advance generation inter-cross (MAGIC) and nested association mapping (NAM) populations are being developed. With the availability of above-mentioned information, next few years will be witnessing application of genomics-assisted breeding for pigeonpea improvement. It is anticipated that improved pigeonpea lines developed through genomics interventions will reach to farmers’ fields and elevate the game towards pulse sufficiency for poor farmers in arid and semi-arid regions of the world in near future.