Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)

Abstract

Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an ‘orphan crop legume’. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation’s Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecu...

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

“…This is an inbred line and a widely cultivated medium duration Indian variety resistant to several important diseases (Fusarium wilt (FW) and sterility mosaic disease (SMD)), for which a number of genetic and genomic resources have been recently developed 8 . This is the first draft genome sequence for a grain legume as well as the first for an orphan legume crop and probably the first for a nonindustrial crop.…”

“…Moreover, no major duplications (similar to the duplication of chromosomes [5][6][7][8] found in M. truncatula (Nevin Young, personal communication) were retained from the 58 Myr ago whole-genome duplication that occurred in all members of Papilionoideae. These observations indicate that there was most likely a period of extensive rearrangements after the whole-genome duplication 58 Myr ago, which stabilized before the split between the millettioid and galegoid clades 54 Myr ago, and that some of these rearrangements are lineage specific.…”

The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers

“…One of the reasons for slow progress in the molecular breeding of the important legume crop like pigeon pea has been attributed to the limited availability of molecular markers and non-availability of any linkage map so far. Although, tremendous progress has been made in terms of availability of genomic resources in this orphan legume crop in recent times (Varshney et al 2009(Varshney et al , 2010, availability of a framework linkage map was lacking. In the present study, we report the first framework linkage map of pigeon pea based on an interspecific F 2 mapping population using DArT markers.…”

“…In addition, availability of the first linkage map will allow map-based cloning of genes from wild relatives in future, such as genes for biotic and abiotic stress tolerance/resistance in pigeon pea. This will be facilitated particularly with the utilization of a large number of SSR and SNP markers that will be available soon in public domain in this crop (Varshney et al 2010).…”

“…Although genomics research in pigeon pea has gained momentum recently (Varshney et al 2010), the limited availability of genomics tools in the past has impeded progress in this important crop. For example, to date, there is no linkage map available.…”