基于全基因组重测序挖掘大白- 长白二元母猪产仔数性状候选基因

屈子啸; 杨帅朋; 朱向星; 唐冬生

文章摘要

屈子啸，杨帅朋，朱向星，唐冬生.基于全基因组重测序挖掘大白- 长白二元母猪产仔数性状候选基因[J].广东农业科学,2023,50(3):120-128

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Mining Candidate Genes for Litter Size Traits in Large White - Landrace Crossbred Sows Based on Whole Genome Resequencing

DOI：10.16768/j.issn.1004-874X.2023.03.014

中文关键词: 大白-长白二元母猪产仔数基因组重测序候选基因遗传选育

英文关键词: Large White - Landrace binary sows litter size genome resequencing candidate gene genetic selection

基金项目:广东省重点领域研发计划-重大科技专项（2022B0202110002，2018B020203003）；广东省动物分子设计与精准育种重点实验室开放课题（2018A05）

作者	单位
屈子啸，杨帅朋，朱向星，唐冬生	佛山科学技术学院生命科学与工程学院 / 广东省动物分子设计育种与精准育种重点实验室，广东佛山 528000

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中文摘要:

【目的】产仔数是种用母猪的重要经济指标，挖掘调控母猪产仔数性状相关的候选基因，探索调控二元母猪为代表的商品猪繁殖力遗传机制，为进一步应用分子选育奠定基础。【方法】采用全基因组重测序对极端高产与极端低产的两组大长二元母猪进行比较分析，并利用选择消除分析方法取 Fst 和 θπ 信号交集为高选择区域，进行基因注释和候选基因筛选。【结果】在两组样本中共发现 8 040 367 个 SNP，50.6％的 SNP 位于基因间区域，45.2％的 SNP 位于内含子区域，在外显子区域、非编码区 3' 端、5' 端的 SNP 分别仅占 1.0％、1.1％、0.6％，其中位于基因组外显子区域的 SNP 中，有 28 879 个为非同义变异，占比 35.0%。提取位于外显子区域、内含子区域、非编码区 3' 端和 5' 端的 SNP 位点进行基因注释，共筛选到两组样本间的差异基因有 1 136 个。对差异基因进行 KEGG 与 GO 富集分析，筛选得到可能影响生殖性能和产仔数性状相关的候选基因共 10 个，包括EPHA4、SMAD7、GLI2、LRP1B、WT1、BAX、BCAT2、IL1B、FAF1，基因功能主要涉及胚胎发育、细胞凋亡等。【结论】大长二元母猪在产仔数性状上经历了显著的人工选择，初步挖掘出影响二元母猪产仔数性状的候选基因，这些基因在猪繁殖性能相关的生理活动中发挥作用，主要在母猪卵细胞成熟凋亡时期及妊娠初期参与调控。

英文摘要:

【Objective】The litter size is an important economic index for breeding sows. The candidate genes related to the regulation of litter size traits in sows were explored, and the genetic mechanism of commercial pig fertility represented by binary hybrid sows was investigated, in order to lay a foundation for further application of molecular breeding. 【Method】 Comparative analysis was conducted on two groups of extremely high and extremely low yielding Large White - Landrace sows by using whole genome resequencing, and selection elimination analysis was used to obtain Fst and θπ signal intersection as a high selection region for gene annotation and candidate gene screening.【Result】A total of 8 040 367 SNPs were found in two groups of samples, 50.6% of which were located in the intergenic region, 45.2% in the intron region, and only 1.0%, 1.1%, and 0.6% in the exon region, non-coding region 3' end, and 5' end, respectively. Among the SNP located in the exon region of the genome, 28 879 were non-synonymous variants, accounting for 35.0%. Extracting SNP loci located in the exon region, intron region, and non-coding regions at the 3' and 5' ends for gene annotation, a total of 1 136 differentially expressed genes were screened between the two groups of samples. KEGG and GO enrichment analysis on differential genes were conducted, and a total of 10 candidate genes that may affect reproductive performance and litter size traits were screened out, including EPHA4, SMAD7, GLI2, LRP1B, WT1, BAX, BCAT2, IL1B and FAF1. The gene functions mainly involved embryonic development, cell apoptosis, and etc【Conclusion】The Large White - Landrace binary sows have experienced significant artificial selection on the litter size trait, and the candidate genes affecting the litter size trait of binary sows have been preliminarily excavated. These genes play a role in the physiological activities related to pig reproductive performance, and mainly in the period of apoptosis of sow egg cells and the beginning of pregnancy to particpate in regulation.

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