猪小体型相关受选择基因位点的研究

Identifying Signatures of Selection Related to Small Body Size in Pigs

旨在通过对比大、小体型两组中国地方猪种在基因组上的遗传分化,检测出全基因组选择信号,以期能鉴别出影响猪体型大小的相关基因及可能的突变位点,解析小体型猪种形成的分子机制。本研究选用小体型的五指山猪和巴马香猪,以大体型的金华猪、二花脸、河套大耳猪为对照,基于全基因组重测序数据,使用两组猪群间的遗传分化系数(Fst)和小体型猪组内的杂合度(Heterozygosity)检测体型选择信号。Fst值较大而杂合度小的染色体区段作为体型相关的受选择候选区域。对这些候选区域所包含的基因进行基因功能及通路的注释分析、以及突变位点的搜寻,试图揭示与猪体型大小相关的可能受选择的基因和突变。结果,通过筛选全基因组重测序数据,我们得到32 475 218个高质量的SNPs,利用40kb的滑动窗口进行Fst和杂合度的计算。Fst值经Z转换(Z(Fst))后大于5的区段有242个。取杂合度最小值的前200个区间与242个Z(Fst)>5的区间的交集,确定了13个受选择候选区域,其中共包含28个基因。通过PANTHER进行基因注释,发现了17个与体型性状相关的候选基因,包括IGF1R、GUCY1A3等功能候选基因。本研究基于高通量测序数据,结合群体遗传学分析手段,确定了与体型大小相关的受选择区域,综合分析推测五指山和巴马香小体型猪的形成可能是由于处于非基因编码区域的一个或者多个突变造成。

In this study,we analyzed genetic differentiation between small-and large-sized Chinese indigenous pigs,aiming to detect signatures of selection and to identify candidate genes and mutations related to small body size.Fixation index（Fst）and heterozygosity were calculated based on whole-genome resequencing data from miniature pigs（Wuzhishan and Bamaxiang）and large-sized pigs（Jinhua,Erhualian and Hetao）.The regions with larger Fst values and lower heterozygosity were regarded as candidate regions of selection.Through further annotation on gene function,pathway and mutations of the genes located in the candidate regions,we sought to screen genes and mutations related to body size.In total,32 475 218 SNPs were obtained after stringent filtering from whole-genome resequencing data.Fst and heterozygosity were calculated using 40 kb sliding window strategy.And 242 putative selection regions were kept byapplying a Z-transformed Fst（Z（Fst））〉5.There are 13 regions overlapped between these 242 regions and the 200 regions with lowest Z-transformed heterozygosity（Z（H））,encompassing 28 genes.Seventeen out of the 28 genes are found to be associated with growth or body size through PANTHER annotation.Among these genes,IGF1 Rand GUCY1A3were the most promising candidate genes.Together,by applying population genetic methods,we can detect regions of signature of selection related to body size in pigs.And after comprehensive analysis in gene function and mutations,we proposed that mutation（s）associated with small-sized phenotype in Wuzhishan and Bamaxiang pigs might be located in the non-coding regions detected.