ARS | Publication request: A comprehensive transcriptome assembly of pigeonpea (Cajanauscajan L.) using sanger and second-generation sequencing platforms

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 11, 2011
Publication Date: January 11, 2012
Citation: Kudapa, H., Bharti, A.K., Cannon, S.B., Farmer, A.D., Deonovic, B., Kramer, R., Bohra, A., Weeks, N.T., Crow, J.A., Tuteja, R., Shah, T., Dutta, S., Gupta, D.K., Singh, A., Gaikwad, K., Sharma, T.R., May, G.D., Singh, N.K., Varshney, R.K. 2012. A comprehensive transcriptome assembly of pigeonpea (Cajanauscajan L.) using sanger and second-generation sequencing platforms. Molecular Plant. 5(5):1020-1028.

Interpretive Summary: Pigeonpea is an important legume crop in many tropical areas. It produces a protein-rich bean, with characteristics similar to soybean but with better palatability and better growing characteristics in areas that are prone to heat and drought. To-date, the plant has not been subject to modern breeding methods. Two key tools that would be helpful in speeding the breeding process in this crop are gene sequences, and genetic markers. Gene sequences provide the basis for understanding how a plant responds to stresses such as drought or heat. Genetic markers can help plant breeders hone in more efficiently on improved varieties. This study reports a much-improved set of gene sequences (in comparison with those from an earlier report), and a large set of candidate genetic markers. The study also reports the locations of these candidate markers in the soybean genome -- which also suggests the approximate locations in pigeonpea. These gene sequences, genetic markers, and provisional marker locations, will help produce better, more resilient crop plants, especially for poorer areas in the world.

Technical Abstract: A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18,353 Sanger expressed sequenced tags (ESTs) from more than 16 genotypes. The resultant transcriptome assembly, referred as CcTA v2, comprised of 21,434 transcript assembly contigs (TACs) with an N50 of 1,510 bp, the largest one being ~8 kb. 16,622 (77.5%) of the 21,434 TACs could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10,009 primer pairs were designed from 5,033 TACs for amplifying intron spanning regions (ISRs). By using in silico mapping of BAC-end derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping positions at the chromosome level were predicted for 6,284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of 8 genotypes. While 116 markers were validated, 70 markers showed 1-3 alleles with an average of 0.16 polymorphism information content (PIC) value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as useful resource to accelerate genetic research and breeding applications in pigeonpea.