| 摘要: |
| 为从全基因组水平探索影响藏猪骨骼肌发育的遗传变异，本研究对5头迪庆藏猪进行全基因组重测序，并合并NCBI数据库中来自3个省的藏猪、与藏猪同样小体型及生长慢的巴马香猪、及体型大且生长快速的杜洛克和大白猪共70个猪只的全基因组重测序数据进行整合分析，获得全基因组SNP后结合选择信号检测与等位基因频率(AF)分析鉴定藏猪-香猪与杜洛克-大白猪的遗传差异；利用GO和KEGG功能富集分析藏猪骨骼肌转录组与蛋白组相关基因。结果发现:1)2 211个基因在藏猪-香猪与杜洛克-大白猪2个比较组中存在遗传差异，138个基因富集到骨骼肌发育相关的GO功能集及KEGG通路；2)9个基因(UCHL3、POSTN、COL12A1、PGK1、JPH1、GPT2、RBFOX1、FLNB和DCX)已报道参与藏猪60 d胚胎背最长肌发育调控，1个(CKM)参与6月龄藏猪背最长肌发育调控；3)10个基因共包含936个SNP，其中655个SNP位于基因间区，255个是内含子变异，少量SNP是外显子及调控区变异。本研究从全基因组水平鉴定了与藏猪骨骼肌发育相关基因及其遗传变异，为以后持续深入解析藏猪骨骼肌发育的遗传机制提供参考。 |
| 关键词: 藏猪 骨骼肌发育 全基因组SNP 选择信号 等位基因频率 |
| DOI：10.11841/j.issn.1007-4333.2023.03.08 |
| 投稿时间：2022-06-02 |
| 基金项目:云南省基础研究计划面上项目(202101AT070061)；云南省重大科技专项计划(202102AE090039) |
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| Analysis of genes related to skeletal muscle development in Tibetan pigs based on whole genome sequencing |
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XIONG Heli,ZHANG Yan,ZHANG Bin,XIANG Decai,Chang Yajie,Liu Shaona,ZHAO Zhiyong*
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| (Swine Science and Animal Nutrition Institute, Yunnan Animal Science and Veterinary Institute, Kunming 650224, China) |
| Abstract: |
| To explore the genetic variations related to skeletal muscle development in Tibetan pigs at the whole genome level, this study conducted the whole genome re-sequencing of 5 Diqing Tibetan pigs, and merged with 70 whole genome re-sequencing data in NCBI database of Tibetan pigs from three regions, Xiang pigs with the same body size and growth rates as Tibetan Pigs, and Duroc and Large white with large size and fast growth. After obtaining the whole genome SNP, the genetic differences between Tibetan-Xiang pigs and Duroc-Large white pigs were detected by selective sweep and allele frequency analysis of individuals with confirmed population relationship by population genetic analysis. By integrating genetic differences with GO and KEGG analysis, and previous studies on the transcriptome and proteome of skeletal muscle in Tibetan pigs to identify genes related to skeletal muscle development. The results showed that: 1)A total of 2 211 genes had genetic differences between Tibetan-Xiang pigs and Duroc-Large white pigs, and 138 genes were enriched to GO enrichments and KEGG pathways related to skeletal muscle development; 2)Nine of the 2 211 genes(UCHL3, POSTN, COL12A1, PGK1, JPH1, GPT2, RBFOX1, FLNB and DCX)were transcribed and translated into proteins in the longissimus dorsi muscle of 60 day embryos, one gene of CKM was the DEPs between the two comparison groups of 6-month-old finishing pigs; 3)The 10 genes contained 936 SNPs, of which 655 were located in intergenic region, 255 were intron variations, and a few located in exon and regulatory region. This study identified genetic variations and genes related to skeletal muscle development in Tibetan pigs, which would provide informative insights into further researches for the genetic mechanism of skeletal muscle development in Tibetan pigs. |
| Key words: Tibetan pig skeletal muscle whole genome SNPs selective sweep allele frequency |
