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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 PBK, 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 BIOLOGY 2011; 11:56. [PMID: 21447154 PMCID: PMC3079640 DOI: 10.1186/1471-2229-11-56] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 03/29/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Pigeonpea [Cajanus cajan (L.) Millsp.] is an important legume crop of rainfed agriculture. Despite of concerted research efforts directed to pigeonpea improvement, stagnated productivity of pigeonpea during last several decades may be accounted to prevalence of various biotic and abiotic constraints and the situation is exacerbated by availability of inadequate genomic resources to undertake any molecular breeding programme for accelerated crop improvement. With the objective of enhancing genomic resources for pigeonpea, this study reports for the first time, large scale development of SSR markers from BAC-end sequences and their subsequent use for genetic mapping and hybridity testing in pigeonpea. RESULTS A set of 88,860 BAC (bacterial artificial chromosome)-end sequences (BESs) were generated after constructing two BAC libraries by using HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes. Clustering based on sequence identity of BESs yielded a set of >52K non-redundant sequences, comprising 35 Mbp or >4% of the pigeonpea genome. These sequences were analyzed to develop annotation lists and subdivide the BESs into genome fractions (e.g., genes, retroelements, transpons and non-annotated sequences). Parallel analysis of BESs for microsatellites or simple sequence repeats (SSRs) identified 18,149 SSRs, from which a set of 6,212 SSRs were selected for further analysis. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, we identified 842 polymorphic SSR markers that will have utility in pigeonpea improvement. Based on these markers, the first SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. Utility of developed SSR markers was also demonstrated by identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment in commercial hybrid breeding programme. CONCLUSION In summary, while BAC libraries and BESs should be useful for genomics studies, BES-SSR markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in pigeonpea.
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Affiliation(s)
- Abhishek Bohra
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
- Department of Genetics, Osmania University, Hyderabad 500007, India
| | - Anuja Dubey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
- Department of Biotechnology and Bioinformatics Centre, Barkatullah University, Bhopal 462026, India
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
- Department of Genetics, Osmania University, Hyderabad 500007, India
| | - R Varma Penmetsa
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - KN Poornima
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
- Department of Biotechnology, University of Agricultural Sciences (UAS), Bangalore 560065, India
| | - Naresh Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
- Department of Plant Breeding and Genetics, CCS Haryana Agricultural University (CCSHAU), Hisar 125004, India
| | - Andrew D Farmer
- National Center for Genome Resources (NCGR), Santa Fe, N M 87505, USA
| | - Gudipati Srivani
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
| | - Ragini Gothalwal
- Department of Biotechnology and Bioinformatics Centre, Barkatullah University, Bhopal 462026, India
| | - S Ramesh
- Department of Biotechnology, University of Agricultural Sciences (UAS), Bangalore 560065, India
| | - Dhiraj Singh
- Department of Plant Breeding and Genetics, CCS Haryana Agricultural University (CCSHAU), Hisar 125004, India
| | - Kulbhushan Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
| | - PB Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad 500007, India
| | - Nagendra K Singh
- National Research Center on Plant Biotechnology (NRCPB), New Delhi 110012, India
| | | | - Gregory D May
- National Center for Genome Resources (NCGR), Santa Fe, N M 87505, USA
| | - Douglas R Cook
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India
- Generation Challenge Programme (GCP), c/o CIMMYT, 06600 Mexico DF, Mexico
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Narasimhamoorthy B, Bouton JH, Olsen KM, Sledge MK. Quantitative trait loci and candidate gene mapping of aluminum tolerance in diploid alfalfa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:901-13. [PMID: 17219204 PMCID: PMC1805042 DOI: 10.1007/s00122-006-0488-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2006] [Accepted: 12/16/2006] [Indexed: 05/13/2023]
Abstract
Aluminum (Al) toxicity in acid soils is a major limitation to the production of alfalfa (Medicago sativa subsp. sativa L.) in the USA. Developing Al-tolerant alfalfa cultivars is one approach to overcome this constraint. Accessions of wild diploid alfalfa (M. sativa subsp. coerulea) have been found to be a source of useful genes for Al tolerance. Previously, two genomic regions associated with Al tolerance were identified in this diploid species using restriction fragment length polymorphism (RFLP) markers and single marker analysis. This study was conducted to identify additional Al-tolerance quantitative trait loci (QTLs); to identify simple sequence repeat (SSR) markers that flank the previously identified QTLs; to map candidate genes associated with Al tolerance from other plant species; and to test for co-localization with mapped QTLs. A genetic linkage map was constructed using EST-SSR markers in a population of 130 BC(1)F(1) plants derived from the cross between Al-sensitive and Al-tolerant genotypes. Three putative QTLs on linkage groups LG I, LG II and LG III, explaining 38, 16 and 27% of the phenotypic variation, respectively, were identified. Six candidate gene markers designed from Medicago truncatula ESTs that showed homology to known Al-tolerance genes identified in other plant species were placed on the QTL map. A marker designed from a candidate gene involved in malic acid release mapped near a marginally significant QTL (LOD 2.83) on LG I. The SSR markers flanking these QTLs will be useful for transferring them to cultivated alfalfa via marker-assisted selection and for pyramiding Al tolerance QTLs.
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Affiliation(s)
- B Narasimhamoorthy
- The Samuel Roberts Noble Foundation, 2510, Sam Noble Pkway, Ardmore, OK, 73402, USA.
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