Dataset Information

Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene.

ABSTRACT: BACKGROUND: Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc×Erhualian F2 resource population. This QTL explained more than 17% of the phenotypic variance. METHODS: Four new markers on pig chromosome 5 were genotyped across this F2 population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. RESULTS: We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the F2 population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A>G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A>G were included as a fixed effect. Furthermore, the significant association between g.2836 A>G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. CONCLUSIONS: HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL.

SUBMITTER: Li P

PROVIDER: S-EPMC3337325 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene.

Li Pinghua P Xiao Shijun S Wei Na N Zhang Zhiyan Z Huang Ruihua R Gu Yueqing Y Guo Yuanmei Y Ren Jun J Huang Lusheng L Chen Congying C

Genetics, selection, evolution : GSE 20120315

<h4>Background</h4>Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc×Erhualian F2 resource population. This QTL explained more than 17% of the phenotypic variance.<h4>Methods</h4>Four new markers on pig chromosome 5 were genotyped across this F2 population. RT-PCR was performed to obtain expression profiles of different candidate genes in e ...[more]

PMID: 22420340

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Project description:BackgroundIn a previous study, a quantitative trait locus (QTL) exhibiting large effects on both Instron shear force and taste panel tenderness was detected within the Illinois Meat Quality Pedigree (IMQP). This QTL mapped to the q arm of porcine chromosome 2 (SSC2q). Comparative analysis of SSC2q indicates that it is orthologous to a segment of human chromosome 5 (HSA5) containing a strong positional candidate gene, calpastatin (CAST). CAST polymorphisms have recently been shown to be associated with meat quality characteristics; however, the possible involvement of other genes and/or molecular variation in this region cannot be excluded, thus requiring fine-mapping of the QTL.ResultsRecent advances in porcine genome resources, including high-resolution radiation hybrid and bacterial artificial chromosome (BAC) physical maps, were utilized for development of novel informative markers. Marker density in the ~30-Mb region surrounding the most likely QTL position was increased by addition of eighteen new microsatellite markers, including nine publicly-available and nine novel markers. Two newly-developed markers were derived from a porcine BAC clone containing the CAST gene. Refinement of the QTL position was achieved through linkage and haplotype analyses. Within-family linkage analyses revealed at least two families segregating for a highly-significant QTL in strong positional agreement with CAST markers. A combined analysis of these two families yielded QTL intervals of 36 cM and 7 cM for Instron shear force and taste panel tenderness, respectively, while haplotype analyses suggested further refinement to a 1.8 cM interval containing CAST markers. The presence of additional tenderness QTL on SSC2q was also suggested.ConclusionThese results reinforce CAST as a strong positional candidate. Further analysis of CAST molecular variation within the IMQP F1 boars should enhance understanding of the molecular basis of pork tenderness, and thus allow for genetic improvement of pork products. Furthermore, additional resources have been generated for the targeted investigation of other putative QTL on SSC2q, which may lead to further advancements in pork quality.

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Dataset Information

Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene.

Publications

Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene.

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