Genome-Wide Association Study and Selective Sweep Analysis Reveal the Genetic Architecture of Body Weights in a Chicken F(2) Resource Population.
Genome-Wide Association Study and Selective Sweep Analysis Reveal the Genetic Architecture of Body Weights in a Chicken F(2) Resource Population.
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DOI：
10.3389/fvets.2022.875454
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发表时间：
2022
影响因子：
3.2
通讯作者：
中科院分区：
文献类型：
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快速生长是肉鸡育种中最重要的经济性状之一。识别肉鸡生长性状的标记和基因不仅有利于标记辅助选择（MAS）/基因组选择（GS），而且为了解肉鸡生长性状的遗传结构提供了重要信息。本研究以肉仔鸡与中国地方品种白耳黄鸡杂交的F2资源群为研究对象，测定了1 ~ 12周龄的体重（BW 1 ~ BW 12）。对519只F2代鸡进行全基因组重测序，并结合全基因组关联分析（GWAS）和选择性扫描分析，对影响鸡体重的遗传结构进行了综合分析。结果，使用全基因组有效混合模型关联（GEMMA）包鉴定了1，539个对不同周龄体重具有显著影响的SNP。这些SNP分布在1号和4号染色体上。此外，BW 1-BW 12的选择窗口从1，581到2，265不等。基于GWAS和选择性扫描分析，还鉴定了总共42个对BW 1-BW 12具有显著影响的基因。其中，二酰基甘油激酶eta（DGKH）、淋巴细胞白血病缺失基因（DLEU 7）、叉头盒O 17（FOXO 1）、核粒细胞运载蛋白α 3亚基（KPNA 3）、钙结合蛋白39样（CAB 39 L）、钾电压门控通道相互作用蛋白4（KCNIP 4）和狭缝导向配体2（SLIT 2）等基因的基本功能被认为是影响肉鸡生长的重要基因。本研究结果可为肉鸡生长性状的遗传结构研究提供重要信息。
Rapid growth is one of the most important economic traits in broiler breeding programs. Identifying markers and genes for growth traits may not only benefit marker-assisted selection (MAS)/genomic selection (GS) but also provide important information for understanding the genetic architecture of growth traits in broilers. In the present study, an F2 resource population derived from a cross between the broiler and Baier yellow chicken (a Chinese local breed) was used and body weights from 1 to 12 weeks of age [body weight (BW) 1–BW12)] were measured. A total of 519 F2 birds were genome re-sequenced, and a combination of genome-wide association study (GWAS) and selective sweep analysis was carried out to characterize the genetic architecture affecting chicken body weight comprehensively. As a result, 1,539 SNPs with significant effects on body weights at different weeks of age were identified using a genome-wide efficient mixed-model association (GEMMA) package. These SNPs were distributed on chromosomes 1 and 4. Besides, windows under selection identified for BW1–BW12 varied from 1,581 to 2,265. A total of 42 genes were also identified with significant effects on BW1–BW12 based on both GWAS and selective sweep analysis. Among these genes, diacylglycerol kinase eta (DGKH), deleted in lymphocytic leukemia (DLEU7), forkhead box O17 (FOXO1), karyopherin subunit alpha 3 (KPNA3), calcium binding protein 39 like (CAB39L), potassium voltage-gated channel interacting protein 4 (KCNIP4), and slit guidance ligand 2 (SLIT2) were considered as important genes for broiler growth based on their basic functions. The results of this study may supply important information for understanding the genetic architecture of growth traits in broilers.