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

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Relation http://oar.icrisat.org/112/
http://www.biomedcentral.com/1471-2229/11/56
 
Title Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)
 
Creator Bohra, A
Dubey, A
Saxena, R K
Penmetsa, R V
Poornima, K N
Kumar, N
Farmer, A D
Srivani, G
Upadhyaya, H D
Gothalwal, R
Ramesh, S
Singh, Dhiraj
Saxena, K B
Kavi Kishor, P B
Singh, N K
Town, C D
May, G D
Cook, D R
Varshney, R K
 
Subject Pigeonpea
 
Description 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.
 
Publisher BioMed Central
 
Date 2011
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/112/1/BCMPlBiol11-56_15pp_2011.pdf
Bohra, A and Dubey, A and Saxena, R K and Penmetsa, R V and Poornima, K N and Kumar, N and Farmer, A D and Srivani, G and Upadhyaya, H D and Gothalwal, R and Ramesh, S and Singh, Dhiraj and Saxena, K B and Kavi Kishor, P B and Singh, N K and Town, C D and May, G D and Cook, D R and Varshney, R K (2011) 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, 11 (1). pp. 56-70. ISSN 14712229