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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; 26:393-408. [PMID: 20976284 PMCID: PMC2948155 DOI: 10.1007/s11032-009-9327-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 08/05/2009] [Indexed: 05/18/2023]
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 molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an 'orphan legume crop' to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.
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Affiliation(s)
- R. K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
- Genomics Towards Gene Discovery Subprogramme, Generation Challenge Program (GCP), c/o CIMMYT, Int APDO Postal 6-641, 06600 Mexico DF, Mexico
| | - R. V. Penmetsa
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
| | - S. Dutta
- National Research Centre on Plant Biotechnology, IARI Campus, New Delhi, 110 012 India
| | - P. L. Kulwal
- Dr. Panjabrao Deshmukh Agricultural University (PDAU), Krishinagar, Akola, Maharasthra 444 104 India
| | - R. K. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - S. Datta
- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh 208024 India
| | - T. R. Sharma
- National Research Centre on Plant Biotechnology, IARI Campus, New Delhi, 110 012 India
| | - B. Rosen
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
| | - N. Carrasquilla-Garcia
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
| | - A. D. Farmer
- National Center for Genome Resources (NCGR), 2935 Rodeo Park Drive East, Santa Fe, NM 87505 USA
| | - A. Dubey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - K. B. Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - J. Gao
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
| | - B. Fakrudin
- University of Agricultural Sciences, Dharwad, Karnataka 580005 India
| | - M. N. Singh
- Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - B. P. Singh
- National Research Centre on Plant Biotechnology, IARI Campus, New Delhi, 110 012 India
| | - K. B. Wanjari
- Dr. Panjabrao Deshmukh Agricultural University (PDAU), Krishinagar, Akola, Maharasthra 444 104 India
| | - M. Yuan
- Tuskegee University, Tuskegee, AL 36088 USA
| | - R. K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - A. Kilian
- Diversity Arrays Technology Pty Ltd, 1 Wilf Crane Crescent, Yarralumla, ACT 2600 Australia
| | - H. D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - N. Mallikarjuna
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502324 India
| | - C. D. Town
- J. Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, MD 20850 USA
| | - G. E. Bruening
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
| | - G. He
- Tuskegee University, Tuskegee, AL 36088 USA
| | - G. D. May
- National Center for Genome Resources (NCGR), 2935 Rodeo Park Drive East, Santa Fe, NM 87505 USA
| | - R. McCombie
- Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - S. A. Jackson
- Department of Agronomy, Purdue University, West Lafayette, IN 47907-2054 USA
| | - N. K. Singh
- National Research Centre on Plant Biotechnology, IARI Campus, New Delhi, 110 012 India
| | - D. R. Cook
- Department of Plant Pathology, University of California, 354 Hutchison Hall, One Shields Avenue, Davis, CA 95616-8680 USA
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