中国农业科学Issue(6)：1190-1199,10.
苏尼特羊全基因组选择信号检测
Genome-wide Detection of Selection Signature on Sunite Sheep
摘要
Abstract
Objective]Selection signatures are the selective footprints across the genome because of the effects of selection in the process of species under natural and artificial selection. It could not only reflect the effect of selection in new breed cultivation but also used as a method for QTL mapping which is correlated with economically important traits. Sunite sheep is one of the excellent indigenous sheep breeds distributed in Inner Mongolia through long time artificial selection-, which could adapt to the harsh Gobi natural environment condition. Selection signature detection could be used to search candidate genes due to positive selection and reveal genetic mechanism of economically important traits. Moreover, it could provide genetic evidences for traits undergoing positive selection for a long time in the breed formation process of Sunite sheep. [Method] The integrated haplotype score (iHS) method was used to detect genomic selection signatures in the Sunite sheep population based on the Illumina Ovine SNP50K BeadChip data. After quality control, 42616 SNP markers were retained for linkage disequilibrium (LD) analysis and haplotype construction. According to ancestral allelic information, 30537 SNP makers were left to calculate the iHS values. All the iHS values within one window with 500kb length, which was split the whole genome into non-overlapping segments, were averaged. After significant test, the genomic regions with selection signals were annotated. To investigate the biological function of candidate genes, gene ontology enrichment analysis was carried out.[Result] The LD decay map of Sunite sheep was constructed. Linkage disequilibrium analysis suggested that LD decreased with marker distances increase, but few pair markers with long distance had high LD levels. There were 204 genomic regions with selection signatures harboring 845 candidate genes were detected. For example, RXFP2 confers the absence of horns in sheep and ASIP could regulate a series of alleles for black and white coat color. HTR4 and SOX10 involved on nervous system development, SOX10 was closely related to neural crest development in embryonic period. E2F2 had an important effect in skeletal development which could activate transcription factor-2 in skeletal growth control. PLA2G6 could affect growth of skeleton and muscle. RPL7 promoted synthesis of ribosomal protein and POL was linked with Ovine Pulmonary Carcinoma. MATR3 could regulate innate and adaptive immune response. Furthermore, candidate genes also included ZWINT, PPP1R1B, GPR98, LUC7L3, CAPZA1 and MYT1L connected with the development of nervous system and disease traits. Bioinformatics analysis found 24 GO items in biological process, 4 GO items in molecular function and 2 GO items in cellular component, respectively. These GO items were mainly related to protein synthesis, macromolecular substances metabolic degradation, targeted transportation of protein, molecular activity, ribosomal components and ribosomal subunits. [Conclusion] The first LD map and genome-wide selection signatures map on Chinese sheep breeds were constructed. Many candidate genes related with economically important traits were found through genome-wide selection signatures detection. Some of them have very important significance in the process of sheep domestication. This study provided important reference for further understanding the process of artificial selection on sheep and also provided a theoretical basis for the breeding of Chinese sheep.关键词
全基因组/连锁不平衡/选择信号/苏尼特羊Key words
whole genome/linkage disequilibrium/selection signature/Sunite sheep引用本文复制引用
王光凯,曾滔,王慧华,张淑珍,张莉,魏彩虹,赵福平,杜立新..苏尼特羊全基因组选择信号检测[J].中国农业科学,2014,(6):1190-1199,10.基金项目
国家项目现代农业产业技术体系建设专项（CARS-39-04B）、国家自然科学基金项目（31200927）、中国农业科学院北京畜牧兽医研究所中央级公益性科研院所基本科研业务费专项资金项目 （）
