上海白猪(上系)遗传多样性和群体结构分析  

Genetic Diversity and Population Structure Analysis of Shanghai White Pig(Sus scrofa)

作　　者：盛中华[1,2] 张哲[3] 肖倩[3] 王起山[3] 陈国宏[1] 潘玉春[3] 

机构地区：[1]扬州大学动物科学与技术学院,扬州225009 [2]上海市闵行区动物疫病预防控制中心,上海201109 [3]上海交通大学农业与生物学院,上海200240

出　　处：《农业生物技术学报》2016年第9期1293-1301,共9页Journal of Agricultural Biotechnology

基　　金：上海市农业基层推广体系项目(沪农科推字(2015)第6-2号);上海市生猪产业技术体系项目(沪农科产字(2015)第6号);上海市闵行区自然科学研究课题(2015MHZ018)

摘　　要：上海白猪(上系)(Sus scrofa)是上海市闵行区的地方培育品种,近年来,由于引进品种的冲击,其各项生产指标严重衰退,且对其种质特性、遗传基础和杂交性能等缺乏应有的了解。本研究应用全基因组范围内的遗传标记,对上海白猪(上系)群体进行了遗传多样性和群体结构的分析。首先对反映群体内遗传多样性的3个重要指标-等位基因的丰度(allelic richness,AR)、标记多态性的比例(proportion of polymorphic markers,PN)和期望杂合度(expected heterozygosity,He)进行了分析和计算。结果表明,上海白猪(上系)与太湖和西方猪种对比,其遗传多样性最高(PN=0.731,AR=1.709,He=0.221)。上海白猪(上系)与太湖品种之间的遗传分化程度(0.237±0.007)大于其与西方品种之间的遗传分化程度(0.219±0.008)。另外,用主成分分析(principal components analysis,PCA)、STRUCTURE和系统进化树等对群体结构进行了分析。结果显示,上海白猪(上系)群体内的遗传多样性比太湖猪种和西方猪种高;群体间遗传距离显示上海白猪(上系)相对于太湖猪种更接近西方猪种;主成分分析、聚类分析与群体结构分析皆显示上海白猪(上系)能够形成独立的分组。以上结果表明,从分子水平上看,将上海白猪(上系)作为一个独立的培育品种是合理的,特别是其具有独特的遗传结构,应进一步加强其保护、开发和利用。Shanghai white pig （Sus scrofa） has many outstanding economic traits, such as high prolific, high disease resistance, high resistance to crude feed and heterosis. Revealing the molecular genetic architechture of these complex traits is an important issue for genetic study. With the development of genetic study and biotechnologies as well as upgrading of study methods, the requirement to reveal the genetic mechanism of these complex traits in the genome level rather than in the single or several genes level is becoming more intense. However, up to date, no studies performed genetic variation analysis for Shanghai white pig on the genome-wide. What＇s more, the genetic mechanism for their outstanding traits is still unclear. Therefore, this study will be performed as follows： 1）Next generation sequencing technology was used to detect the genome- wide of genetic variations using . The genetic variants of 99 Shanghai white pigs, 252 pigs from Taihu pig breeds （Meishan, Erhualian, Mi, Fengjing, Shawutou and Jiaxing Black） and 156 foreign pigs were genotyped according to the genotyping by genome reducing and sequencing （GGRS） protocol （http：//klab.sjtu.edu.cn/ GGRS/）. Briefly, high molecular weight genomic DNA samples were extracted from ear tissue, digested with Ava 1I, and then ligated with a unique adapter-barcode. Next, the samples were pooled and enriched to construct a sequencing library. Finally, the sequence libraries （fragments ranging from 300-400 bp, including the adapter-barcode sequence） were sequenced on an Illumina Hiseq2000 （the sequencing process is given in detail by the manufacturer, Illumina） instrument with a paired-end （2× 100 bp） pattern. The SNPs of more than 75 （30%） samples were genotyped and an average sequencing depth greater than 5 × was achieved. In total, 100 120 SNP were identified in the genomes of the current pig population. These results were helpful to know the genome information of the Shanghai white pig and enrich the database of genetic mar

关 键 词：上海白猪(上系) 猪基因组 遗传距离 群体结构 

分 类 号：Q38[生物学—遗传学]