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

Publication Overview
TitleAnalysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)
AuthorsBohra 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
TypeJournal Article
Journal NameBMC Plant Biology
Volume11
Year2011
CitationBohra 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.

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.
Features
This publication contains information about 3,072 features:
Feature NameUniquenameType
CcM00251CcM00251genetic_marker
CcM00252CcM00252genetic_marker
CcM00253CcM00253genetic_marker
CcM00254CcM00254genetic_marker
CcM00255CcM00255genetic_marker
CcM00256CcM00256genetic_marker
CcM00257CcM00257genetic_marker
CcM00258CcM00258genetic_marker
CcM00259CcM00259genetic_marker
CcM00260CcM00260genetic_marker
CcM00261CcM00261genetic_marker
CcM00262CcM00262genetic_marker
CcM00263CcM00263genetic_marker
CcM00264CcM00264genetic_marker
CcM00265CcM00265genetic_marker
CcM00266CcM00266genetic_marker
CcM00267CcM00267genetic_marker
CcM00268CcM00268genetic_marker
CcM00269CcM00269genetic_marker
CcM00270CcM00270genetic_marker
CcM00271CcM00271genetic_marker
CcM00272CcM00272genetic_marker
CcM00273CcM00273genetic_marker
CcM00274CcM00274genetic_marker
CcM00275CcM00275genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
Pigeon_pea-ICP_28/ICPW_94-F2
Stocks
This publication contains information about 4 stocks:
Stock NameUniquenameType
ICP_28ICP_28accession
ICPL_87119ICPL_87119accession
ICPW_94ICPW_94accession
ICP_28/ICPW_94-F2ICP_28/ICPW_94-F2population
Properties
Additional details for this publication include:
Property NameValue
URLhttps://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-11-56