Mapping of quantitative trait Loci underlying cold tolerance in rice seedlings via high-throughput sequencing of pooled extremes

Download
  1. (PDF, 606 KB)
  2. Get@NRC: Mapping of quantitative trait Loci underlying cold tolerance in rice seedlings via high-throughput sequencing of pooled extremes (Opens in a new window)
DOIResolve DOI: http://doi.org/10.1371/journal.pone.0068433
AuthorSearch for: ; Search for: ; Search for: ; Search for: ; Search for: ; Search for: ; Search for:
TypeArticle
Journal titlePLoS ONE
ISSN1932-6203
Volume8
Issue7
Pagese68433:1e68433:7; # of pages: 7
Subjectarticle; booting stage; bulked segregant analysis; chromosome 1; chromosome 10; chromosome 2; chromosome 5; chromosome 8; cold tolerance; developmental stage; DNA sequence; high throughput sequencing; next generation sequencing; nonhuman; plant breeding; quantitative trait locus mapping; rice; seedling; single nucleotide polymorphism
AbstractLow temperature is a major limiting factor in rice growth and development. Mapping of quantitative trait loci (QTLs) controlling cold tolerance is important for rice breeding. Recent studies have suggested that bulked segregant analysis (BSA) combined with next-generation sequencing (NGS) can be an efficient and cost-effective way for QTL mapping. In this study, we employed NGS-assisted BSA to map QTLs conferring cold tolerance at the seedling stage in rice. By deep sequencing of a pair of large DNA pools acquired from a very large F3 population (10,800 individuals), we obtained ~450,000 single nucleotide polymorphisms (SNPs) after strict screening. We employed two statistical methods for QTL analysis based on these SNPs, which yielded consistent results. Six QTLs were mapped on chromosomes 1, 2, 5, 8 and 10. The three most significant QTLs on chromosomes 1, 2 and 8 were validated by comparison with previous studies. Two QTLs on chromosomes 2 and 5 were also identified previously, but at the booting stage rather than the seedling stage, suggesting that some QTLs may function at different developmental stages, which would be useful for cold tolerance breeding in rice. Compared with previously reported QTL mapping studies for cold tolerance in rice based on the traditional approaches, the results of this study demonstrated the advantages of NGS-assisted BSA in both efficiency and statistical power.
Publication date
LanguageEnglish
AffiliationNational Research Council Canada; Aquatic and Crop Resource Development
Peer reviewedYes
NRC number55564
NPARC number21268636
Export citationExport as RIS
Report a correctionReport a correction
Record identifier3850677b-ee20-4765-bb7b-e4c6ca24d6c9
Record created2013-11-05
Record modified2016-05-09
Bookmark and share
  • Share this page with Facebook (Opens in a new window)
  • Share this page with Twitter (Opens in a new window)
  • Share this page with Google+ (Opens in a new window)
  • Share this page with Delicious (Opens in a new window)