Dataset Information

Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice.

ABSTRACT: To identify genetic loci influencing lipid levels, we performed quantitative trait loci (QTL) analysis between inbred mouse strains MRL/MpJ and SM/J, measuring triglyceride levels at 8 weeks of age in F2 mice fed a chow diet. We identified one significant QTL on chromosome (Chr) 15 and three suggestive QTL on Chrs 2, 7, and 17. We also carried out microarray analysis on the livers of parental strains of 282 F2 mice and used these data to find cis-regulated expression QTL. We then narrowed the list of candidate genes under significant QTL using a "toolbox" of bioinformatic resources, including haplotype analysis; parental strain comparison for gene expression differences and nonsynonymous coding single nucleotide polymorphisms (SNP); cis-regulated eQTL in livers of F2 mice; correlation between gene expression and phenotype; and conditioning of expression on the phenotype. We suggest Slc25a7 as a candidate gene for the Chr 7 QTL and, based on expression differences, five genes (Polr3 h, Cyp2d22, Cyp2d26, Tspo, and Ttll12) as candidate genes for Chr 15 QTL. This study shows how bioinformatics can be used effectively to reduce candidate gene lists for QTL related to complex traits.

SUBMITTER: Leduc MS

PROVIDER: S-EPMC3151687 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature

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Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice.

Leduc Magalie S MS Hageman Rachael S RS Verdugo Ricardo A RA Tsaih Shirng-Wern SW Walsh Kenneth K Churchill Gary A GA Paigen Beverly B

Journal of lipid research 20110526 9

To identify genetic loci influencing lipid levels, we performed quantitative trait loci (QTL) analysis between inbred mouse strains MRL/MpJ and SM/J, measuring triglyceride levels at 8 weeks of age in F2 mice fed a chow diet. We identified one significant QTL on chromosome (Chr) 15 and three suggestive QTL on Chrs 2, 7, and 17. We also carried out microarray analysis on the livers of parental strains of 282 F2 mice and used these data to find cis-regulated expression QTL. We then narrowed the li ...[more]

PMID: 21622629

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Project description:BACKGROUND:In recent years, the planting area of sweet corn in China has expanded rapidly. Some new varieties with high yields and good adaptabilities have emerged. However, the improvement of edible quality traits, especially through the development of varieties with thin pericarp thickness, has not been achieved to date. Pericarp thickness is a complex trait that is the key factor determining the edible quality of sweet corn. Genetic mapping combined with transcriptome analysis was used to identify candidate genes controlling pericarp thickness. RESULTS:To identify novel quantitative trait loci (QTLs) for pericarp thickness, a sweet corn BC4F3 population of 148 lines was developed using the two sweet corn lines M03 (recurrent parent) and M08 (donor parent). Additionally, a high-density genetic linkage map containing 3876 specific length amplified fragment (SLAF) tags was constructed and used for mapping QTLs for pericarp thickness. Interestingly, 14 QTLs for pericarp thickness were detected, and one stable QTL (qPT10-5) was detected across multiple years, which explained 7.78-35.38% of the phenotypic variation located on chromosome 10 (144,631,242-145,532,401). Forty-two candidate genes were found within the target region of qPT10-5. Moreover, of these 42 genes, five genes (GRMZM2G143402, GRMZM2G143389, GRMZM2G143352, GRMZM6G287947, and AC234202.1_FG004) were differentially expressed between the two parents, as revealed by transcriptome analysis. According to the gene annotation information, three genes might be considered candidates for pericarp thickness. GRMZM2G143352 and GRMZM2G143402 have been annotated as AUX/IAA transcription factor and ZIM transcription factor, respectively, while GRMZM2G143389 has been annotated as FATTY ACID EXPORT 2, chloroplastic. CONCLUSIONS:This study identified a major QTL and candidate genes that could accelerate breeding for the thin pericarp thickness variety of sweet corn, and these results established the basis for map-based cloning and further functional research.

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Dataset Information

Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice.

Publications

Integration of QTL and bioinformatic tools to identify candidate genes for triglycerides in mice.

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