Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)

被引：102

作者：

Bohra, Abhishek ^{[2
,3
]}

Dubey, Anuja ^{[2
,4
,5
]}

Saxena, Rachit K. ^{[2
,3
]}

Varma Penmetsa, R. ^{[1
]}

Poornima, K. N. ^{[2
,6
]}

Kumar, Naresh ^{[2
,7
]}

Farmer, Andrew D. ^{[8
]}

Srivani, Gudipati ^{[2
]}

Upadhyaya, Hari D. ^{[2
]}

Gothalwal, Ragini ^{[4
,5
]}

Ramesh, S. ^{[6
]}

Singh, Dhiraj ^{[7
]}

Saxena, Kulbhushan ^{[2
]}

Kishor, P. B. Kavi ^{[3
]}

Singh, Nagendra K. ^{[9
]}

Town, Christopher D. ^{[10
]}

May, Gregory D. ^{[8
]}

Cook, Douglas R. ^{[1
]}

Varshney, Rajeev K. ^{[2
,11
]}

机构：

[1] Univ Calif Davis, Dept Plant Pathol, Davis, CA 95616 USA

[2] Int Crops Res Inst Semi Arid Trop, Hyderabad 502324, Andhra Pradesh, India

[3] Osmania Univ, Dept Genet, Hyderabad 500007, Andhra Pradesh, India

[4] Barkatullah Univ, Dept Biotechnol, Bhopal 462026, India

[5] Barkatullah Univ, Bioinformat Ctr, Bhopal 462026, India

[6] UAS, Dept Biotechnol, Bangalore 560065, Karnataka, India

[7] CCSHAU, Dept Genet & Plant Breeding, Hisar 125004, Haryana, India

[8] NCGR, Santa Fe, NM 87505 USA

[9] NRCPB, New Delhi 110012, India

[10] JCVI, Rockville, MD 20850 USA

[11] CIMMYT, GCP, Mexico City 06600, DF, Mexico

来源：

BMC PLANT BIOLOGY | 2011年 / 11卷

基金：

美国国家科学基金会;

关键词：

MICROSATELLITE MARKERS; MEDICAGO-TRUNCATULA; FUSARIUM-WILT; GENOME; MAP; DIVERSITY; L; POPULATIONS; INTEGRATION; FREQUENCY;

D O I：

10.1186/1471-2229-11-56

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

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.

引用

页数：15

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