ARS | Publication request: Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.)

Submitted to: DNA Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 3, 2011
Publication Date: May 12, 2011
Citation: Dubey, A., Farmer, A., Schlueter, J., Cannon, S.B., Abernathy, B., Tuteja, R., Woodward, J., Varshney, R.K. 2011. Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.). DNA Research. 18(3):153-164.

Interpretive Summary: Pigeonpea is an important crop in the semi-arid tropics, with high levels of consumption in countries such as India, Indonesia, Eastern Africa, and Central America. It is a hardy, drought-tolerant crop, with protein-rich seeds used for grain or flour. The crop has, however, received little attention using modern breeding methods. Strong breeding programs could help produce healthier plants, free of diseases such as fusarium wilt and sterility mosaic disease. This study reports the sequencing of most of the genes of this crop, and comparison of gene responses from both healthy and disease-challenged plants. The study also provides thousands of new genetic markers, between ten different pigeonpea varieties, which breeders can use in new breeding efforts. These results will be important to breeders working to produce higher-yielding, more disease-resistant pigeonpea varieties. The study will also help researchers understand disease-response mechanisms found in pigeonpea and in related crops such as common bean and soybean.

Technical Abstract: This study reports generation of large-scale genomic resources for pigeonpea, a so-called ‘orphan crop species’ of the semi-arid tropic regions. Roche FLX/454 sequencing was carried out on a normalized cDNA pool prepared from 31 tissues produced 494,353 short transcript reads (STRs). Cluster analysis of these STRs, together with 10,817 Sanger ESTs, resulted in 127,754 transcript assemblies (TAs). Functional analysis of these TAs highlights several active pathways and processes in the sampled tissues. Comparison of the TAs with the soybean genome showed similarity to between 10,857 and 16,367 soybean gene models (depending on alignment methods). Additionally, Illumina 1G sequencing was performed on Fusarium wilt (FW)- and sterility mosaic disease (SMD)-challenged root tissues of 10 resistant and susceptible genotypes. More than 160 million sequence tags were used to identify FW- and SMD-responsive genes. Sequence analysis of TAs and the Illumina tags identified a large new set of markers for use in genetics and breeding, including 8,137 simple sequence repeats (SSRs), 12,141 single nucleotide polymorphisms (SNPs) and 5,845 intron spanning regions (ISRs). Genomic resources developed in this study should be useful for basic and applied research, not only for pigeonpea improvement but also for other related, agronomically important legumes.