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

• Main Authors: Li Pinghua, Xiao Shijun, Wei Na, Zhang Zhiyan, Huang Ruihua, Gu Yueqing, Guo Yuanmei, Ren Jun, Huang Lusheng, Chen Congying
• Format: Article
• Language: deu
• Published: BMC 2012-03-01
• Series: Genetics Selection Evolution
• Online Access: http://www.gsejournal.org/content/44/1/6
• ISSN: 0999-193X; 1297-9686

<p>Abstract</p> <p>Background</p> <p>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 F₂resource population. This QTL explained more than 17% of the phenotypic variance.</p> <p>Methods</p> <p>Four new markers on pig chromosome 5 were genotyped across this F₂population. 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.</p> <p>Results</p> <p>We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. <it>HMGA2</it>, <it>SOX5 </it>and <it>PTHLH </it>that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the F₂population. Of the seven SNP, <it>HMGA2 </it>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 <it>HMGA2 </it>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 <it>HMGA2 </it>was similar to that explained by the QTL and at a much higher level than by <it>SOX5</it>. More interestingly, <it>HMGA2 </it>is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size.</p> <p>Conclusions</p> <p><it>HMGA2 </it>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.</p>