RAD测序法用于鸡双向选择家系群体遗传差异分析

SNPs遗传标记已成为群体遗传学和数量遗传学研究重要工具。RAD测序法是基于新一代高通量测序技术进行SNPs开发最为有效、经济的方法之一。研究以针对脂肪性状进行双向选择的髙脂-低脂鸡家系和针对体重性状进行双向选择的高体重鸡-低体重鸡家系为对象,利用RAD测序法进行简化基因组测序及群体遗传差异分析。测序和分析结果显示,实验共获得57.88 M reads,平均每个个体检测到98 671个SNPs。群体pairwise Fst结果发现,在高脂-低脂鸡双向选择家系中,许多位点存在差异性,其中部分位点与前人研究结果相一致。在高脂-低脂双向选择家系中,例如5号染色体上的NOVA1区域呈现显著差异,表明该区域可能与鸡脂类代谢和腹脂沉积有重要关联;在高体重-低体重鸡双向选择家系中,存在一些群体差异缺失标签,例如高体重鸡的13号染色体上SH3RF2除第一个外显子以外区域基因信息的缺失,导致鸡体重显著增加,推测这种结构缺失变异可能与高强度人工选择有关。研究表明,RAD测序法不仅能够快速、准确地获得高通量SNPs遗传标记,而且具有较高分辨率,能够适用于诸如双向选择家系这种存在微小遗传差异群体间的遗传检测和分析。

Analyses of Population Genetic Difference in Chicken Divergently Selected Lines Using RAD-seq

Single nucleotide polymorphisms（SNPs） genetic marker has been one of key tools for population genetics and quantitative genetics.Restriction-site-associated DNA sequencing （RAD-seq） is one of the most effective methods based on next-generation sequencing （NGS） technology for SNP discovery.We chose the 2 lines as samples based on abdominal fat and weight to make representation genome sequencing and population genetic difference analyses using RAD-seq.A total of 57.88 million utilized reads were sequenced by illumina Hiseq2000 for the lines and there was an average of 98 671 SNPs for per individual.The line population pairwise Fst showed that in high-fat and low-fat lines,there were some differences regions,which were perfectly consisting with previous results.Such as NOVA1 region in chromosome 5 showed difference,indicating that the region is related with lipid metabolism and abdominal fat deposition.And in high weight and low-weight lines,there were many population discrepant deleted regions,such as the missing all but the first exon region of the gene SH3RF2 in chromosome 13 could obviously increase weight.Those missing regions may be influenced by high-strength artificial selection.In this study,we confirmed that RAD-seq is availability and predictability on finding high-through SNPs and it is effective and potential applications on SNPs discovery and population genetic difference analyses in chicken lines with divergent selection.