综合组学策略鉴定猪骨骼肌肌纤维类型构成相关基因及其适应性进化机制

Pig has been under artificial selection for long time, and it is a domestic animal with clear evolution and domestication history compared to others. Pig is one of important livestock for meat production. Muscle fibers (I type and II type) compose skeletal muscle and their number and diameter determine the meat production capability. I and II type fiber composition has been changed greatly due to captivity and high density selection of long time, and it is shown between wild, domestic and commercial developed pig breeds. Based on the previous research on genome wide selection sweep, this study will choose Tongcheng, Yichang Wild pigs and Large White to investigate the molecular mechanism on muscle fiber type composition for selection adaption from both genome and transcriptome level. Expression profiling of soleus and gastrocnemius muscle tissues from the studied pigs will be analyzed using RNA-seq technique, and then transcriptome difference are clarified. More SNPs will be increased within candidate genome region and selection sweep analysis will be implemented for fine mapping. Furthermore, allelic expression imbalance and gene function analysis approaches will be executed for biological function verification of candidate genes. The selection evolution pattern, molecular characterization and mechanisms of candidate gene and pathways will be demonstrated by means of population genetics and evolution genome statistical methods. The findings will be expect to help reveal the complex phenotypic evolution in pigs and contribute to better understanding of adaptability formation under artificial selection.

猪是经长期人工选择、且进化及驯化历程较为清晰的肉用家养动物，高产肉性能是其重要机能发生改变的表征之一。肌纤维（包括红肌和白肌纤维）是骨骼肌基本组成单位，其数量和直径决定着产肉能力高低。长期圈养及对产肉性能的高强度选择使得红肌/白肌纤维类型构成发生显著改变，在野猪、地方猪和培育猪之间呈现出巨大差异。本研究拟在前期成果基础上，选取我国地方通城猪，以宜昌野猪和瘦肉型大白猪为对照，从基因组和转录组水平对猪肌纤维类型构成变异的适应性分子机理进行探讨。通过RNA-seq技术对三个猪种的比目鱼肌（以红肌为主）和腓肠肌（以白肌为主）组织表达检测分析，揭示转录组比较差异；增补候选基因组区域SNP 密度，通过基因组选择清扫分析以精细确定候选基因；利用等位基因表达不平衡和基因功能研究技术，初步阐明候选基因生物学功能；综合群体遗传学和进化基因组学统计分析手段，探讨相关基因及通路的选择进化模式、分子作用规律及机制。