Self-confirmation and ascertainment of the candidate genomic regions of complex trait loci - A none-experimental solution

Lishi Wang, Yan Jiao, Yongjun Wang, Mengchen Zhang, Weikuan Gu

Research output: Contribution to journalArticle

Abstract

Over the past half century, thousands of quantitative trait loci (QTL) have been identified by using animal models and plant populations. However, the none-reliability and imprecision of the genomic regions of these loci have remained the major hurdle for the identification of the causal genes for the correspondent traits. We used a none-experimental strategy of strain number reduction for testing accuracy and ascertainment of the candidate region for QTL. We tested the strategy in over 400 analyses with data from 47 studies. These studies include: 1) studies with recombinant inbred (RI) strains of mice. We first tested two previously mapped QTL with well-defined genomic regions; We then tested additional four studies with known QTL regions; and finally we examined the reliability of QTL in 38 sets of data which are produced from relatively large numbers of RI strains, derived from C57BL/6J (B6) X DBA/2J (D2), known as BXD RI mouse strains; 2) studies with RI strains of rats and plants; and 3) studies using F2 populations in mice, rats and plants. In these cases, our method identified the reliability of mapped QTL and localized the candidate genes into the defined genomic regions. Our data also suggests that LRS score produced by permutation tests does not necessarily confirm the reliability of the QTL. Number of strains are not the reliable indicators for the accuracy of QTL either. Our strategy determines the reliability and accuracy of the genomic region of a QTL without any additional experimental study such as congenic breeding.

Original languageEnglish (US)
Article numbere0153676
JournalPloS one
Volume11
Issue number5
DOIs
StatePublished - May 1 2016

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Quantitative Trait Loci
quantitative trait loci
genomics
loci
Rats
Inbred Strains Mice
Genes
mice
Inbred Strains Rats
Animals
rats
Population
Breeding
Testing
genes
Animal Models
animal models
testing
breeding

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

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Self-confirmation and ascertainment of the candidate genomic regions of complex trait loci - A none-experimental solution. / Wang, Lishi; Jiao, Yan; Wang, Yongjun; Zhang, Mengchen; Gu, Weikuan.

In: PloS one, Vol. 11, No. 5, e0153676, 01.05.2016.

Research output: Contribution to journalArticle

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