Liu X-X, Pan J-F, Zhao Q-J, He X-H, Pu Y-B, Han J-L, Ma Y-H, Jiang L
Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
J Anim Breed Genet. 2018 Feb;135(1):84-92. doi: 10.1111/jbg.12314.
The X chromosome shows a special interaction between demographic factors and genetic variation, and the analysis of X-linked genomic variation can therefore provide insights into the unique effects of demography and selection on the horse genome that cannot be readily detected by autosomal markers. Debao (DB) ponies have experienced intense selective pressure for the development of their small stature (<106 cm at adult height). To identify selective sweeps on the X chromosome of the DB pony, we performed a genome-wide scan of three Chinese horse breeds using an Equine SNP70 BeadChip. Using Yili and Mongolian horses (>134 cm at adult height) as reference groups, both F and XP-EHH revealed that five regions on the X chromosome were under strong selection, resulting in 95 overlapping genes. Seven of these genes, SMS, PHEX, ACSL4, CHRDL1, CACNA1F, DKC1 and CDKL5, are involved in bone development, growth hormone secretion and fat deposition. The region showing the strongest selection pressure was located at the position of 86.6-87.5 Mb. The subsequent genome-wide association analysis of the adult height of three Chinese horse breeds detected the two most significant SNPs in the same region, and these two SNPs overlapped with the gene CHRDL1. As a member of the bone morphogenetic protein (BMP) superfamily, CHRDL1 antagonizes the function of BMP4 and plays an important role in embryonic bone formation and cartilage generation. Our results provide new insights into the X-linked selection in Chinese Debao pony.
X染色体显示出人口统计学因素与基因变异之间的特殊相互作用，因此，对X连锁基因组变异的分析可以深入了解人口统计学和选择对马基因组的独特影响，而这些影响是常染色体标记难以轻易检测到的。德保（DB）矮马在其矮小体型（成年身高<106厘米）的发育过程中经历了强烈的选择压力。为了确定德保矮马X染色体上的选择性清除区域，我们使用马SNP70基因芯片对三个中国马种进行了全基因组扫描。以伊犁马和蒙古马（成年身高>134厘米）作为参考群体，F统计量和XP-EHH分析均表明，X染色体上有五个区域受到强烈选择，共有95个重叠基因。其中七个基因，SMS、PHEX、ACSL4、CHRDL1、CACNA1F、DKC1和CDKL5，参与骨骼发育、生长激素分泌和脂肪沉积。显示出最强选择压力的区域位于86.6-87.5兆碱基的位置。随后对三个中国马种成年身高进行的全基因组关联分析在同一区域检测到两个最显著的单核苷酸多态性（SNP），这两个SNP与CHRDL1基因重叠。作为骨形态发生蛋白（BMP）超家族的成员，CHRDL1拮抗BMP4的功能，并在胚胎骨形成和软骨生成中发挥重要作用。我们的研究结果为中国德保矮马的X连锁选择提供了新的见解。
