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Cajanus cajan (pigeon pea)


Pigeonpea, domesticated 3,500 years ago in India, is a member of the millettioid (warm-season legume) clade within the sub-family Papilionoideae. Many important legume food crop belong to this group including soybean, cowpea, mungbean and common bean. Pigeonpea, being a very important legume food crop, is the main protein source for more than a billion people in the developing world. It is grown mainly in the semi-arid tropic regions (Asia, Africa and Central/South America). A more detailed discussion of its agronomic significance to the developing world can be found here.

Of Special Interest

A high-quality transcriptome assembly is available on these pages, at the Reference Data tab. Also see the LIS genome browser for the pigeon pea 1.0 release.

NCBI taxon3821
GRIN taxon8319

Wikipedia entry

Genome Summary

C. cajan has a moderate-sized diploid genome. The genotype “ICPL 87119” (also known as “Asha”) is being sequenced and assembled by the WGS approach (whole-genome shotgun) using short paired-end reads (Illumina).

Chromosomes2n = 22
Genome size 833 (Mbp)


BAC library and clonesSee linked document to order clonesLinkout »
genome assembly and annotationspseudomolecules, gene modelsLinkout »
genome browserLIS GBrowse for Cajanus cajan (pigeon pea) 1.0Linkout »
primer sequencesIntron-spanning primers based on lista_cajca-201012 (CcTA v2)Linkout »

Reference Data

Transcript AssemblyTranscript assembly lista_cajca-201012 (CcTA v2)LIS reference setsDownload »

Selected References

Current publications on Cajanus cajan at PubMed.

Kudapa H, Bharti AK, Cannon SB, Farmer AD, Mulaosmanovic B, Kramer R, Bohra A, Weeks NT, Crow JA, Tuteja R, Shah T, Dutta S, Gupta DK, Singh A, Gaikwad K, Sharma TR, May GD, Singh NK & Varshney RK. A comprehensive transcriptome assembly of pigeonpea (Cajanus cajan L.) using Sanger and Second-generation sequencing platforms. Molecular Plant 2011; In Press.

Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MTA, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuetja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang S-P, Shah T, Saxena KB, Todd Michael, McCombie WR, Yang B, Zhang G, Yang H, Jun W, Spillane C, Cook DR, May GD, Xu X, Jackson SA. Decoding the genome of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor smallholder farmers in Asia and Africa. Nature Biotech 2011; Nov 6. doi: 10.1038/nbt.2022. [Epub ahead of print]

Dubey A, Farmer A, Schlueter J, Cannon SB, Abernathy B, Tuteja R, Woodward J, Shah T, Mulasmanovic B, Kudapa H, Raju NL, Gothalwal R, Pande S, Xiao Y, Town CD, Singh NK, May GD, Jackson S, Varshney RK. Defining the Transcriptome Assembly and Its Use for Genome Dynamics and Transcriptome Profiling Studies in Pigeonpea (Cajanus cajan L.). DNA Res 2011; 18: 153-64.

Saxena RK, Cui X, Thakur V, Walter B, Close TJ, Varshney RK. Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.). Funct Integr Genomics 2011; May 6.

Bohra A, Dubey A, Saxena RK, Penmetsa RV, Poornima KN, Kumar N, Farmer AD, Srivani G, Upadhyaya HD, Gothalwal R, Ramesh S, Singh D, Saxena K, Kishor PB, Singh NK, Town CD, May GD, Cook DR, Varshney RK. Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.). BMC Plant Biol 2011; 11: 56.

Raju NL, Gnanesh BN, Lekha P, Jayashree B, Pande S, Hiremath PJ, Byregowda M, Singh NK, Varshney RK. The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.). BMC Plant Biol 2010; 10: 45.

Varshney RK, Penmetsa RV, Dutta S, Kulwal PL, Saxena RK, Datta S, Sharma TR, Rosen B, Carrasquilla-Garcia N, Farmer AD, Dubey A, Saxena KB, Gao J, Fakrudin B, Singh MN, Singh BP, Wanjari KB, Yuan M, Srivastava RK, Kilian A, Upadhyaya HD, Mallikarjuna N, Town CD, Bruening GE, He G, May GD, McCombie R, Jackson SA, Singh NK, Cook DR. Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.). Mol Breed. 2010 Oct;26(3):393-408.

Dutta S, Kumawat G, Singh BP, Gupta DK, Singh S, Dogra V, Gaikwad K, Sharma TR, Raje RS, Bandhopadhya TK, Datta S, Singh MN, Bashasab F, Kulwal P, Wanjari KB, K Varshney R, Cook DR, Singh NK. Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biol 2011; 11: 17.