Arid
DOI10.1007/s11032-009-9327-2
Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)
Varshney, R. K.1,2; Penmetsa, R. V.3; Dutta, S.4; Kulwal, P. L.5; Saxena, R. K.2; Datta, S.6; Sharma, T. R.4; Rosen, B.3; Carrasquilla-Garcia, N.3; Farmer, A. D.7; Dubey, A.2; Saxena, K. B.2; Gao, J.3; Fakrudin, B.8; Singh, M. N.9; Singh, B. P.4; Wanjari, K. B.5; Yuan, M.10; Srivastava, R. K.2; Kilian, A.11; Upadhyaya, H. D.2; Mallikarjuna, N.2; Town, C. D.12; Bruening, G. E.3; He, G.10; May, G. D.7; McCombie, R.13; Jackson, S. A.14; Singh, N. K.4; Cook, D. R.3
通讯作者Varshney, R. K.
来源期刊MOLECULAR BREEDING
ISSN1380-3743
EISSN1572-9788
出版年2010
卷号26期号:3页码:393-408
英文摘要

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.


英文关键词Molecular markers Genetic mapping Trait mapping Genomics Next generation sequencing Gene discovery Crop improvement
类型Article
语种英语
国家Mexico ; India ; USA ; Australia
收录类别SCI-E
WOS记录号WOS:000282426600002
WOS关键词MICROSATELLITE MARKERS ; GENETIC DIVERSITY ; MALE-STERILITY ; GLYCINE ; DIVERSIFICATION ; DUPLICATION ; INFORMATION ; ARRAYS ; LEVEL
WOS类目Agronomy ; Plant Sciences ; Genetics & Heredity ; Horticulture
WOS研究方向Agriculture ; Plant Sciences ; Genetics & Heredity
来源机构University of California, Davis ; International Crops Research Institute for the Semi-Arid Tropics
资源类型期刊论文
条目标识符http://119.78.100.177/qdio/handle/2XILL650/165687
作者单位1.CIMMYT, GCP, Genom Gene Discovery Subprogramme, Mexico City 06600, DF, Mexico;
2.Int Crops Res Inst Semi Arid Trop, Patancheru 502324, Andhra Pradesh, India;
3.Univ Calif Davis, Dept Plant Pathol, Davis, CA 95616 USA;
4.Natl Res Ctr Plant Biotechnol, New Delhi 110012, India;
5.PDAU, Akola 444104, Maharashtra, India;
6.IIPR, Kanpur 208024, Uttar Pradesh, India;
7.NCGR, Santa Fe, NM 87505 USA;
8.Univ Agr Sci, Dharwad 580005, Karnataka, India;
9.Banaras Hindu Univ, Varanasi 221005, Uttar Pradesh, India;
10.Tuskegee Univ, Tuskegee, AL 36088 USA;
11.Div Arrays Technol Pty Ltd, Yarralumla, ACT 2600, Australia;
12.JCVI, Rockville, MD 20850 USA;
13.Watson Sch Biol Sci, Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA;
14.Purdue Univ, Dept Agron, W Lafayette, IN 47907 USA
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GB/T 7714
Varshney, R. K.,Penmetsa, R. V.,Dutta, S.,et al. Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)[J]. University of California, Davis, International Crops Research Institute for the Semi-Arid Tropics,2010,26(3):393-408.
APA Varshney, R. K..,Penmetsa, R. V..,Dutta, S..,Kulwal, P. L..,Saxena, R. K..,...&Cook, D. R..(2010).Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.).MOLECULAR BREEDING,26(3),393-408.
MLA Varshney, R. K.,et al."Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)".MOLECULAR BREEDING 26.3(2010):393-408.
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