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Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds
Genetics Selection Evolution ( IF 4.1 ) Pub Date : 2021-09-22 , DOI: 10.1186/s12711-021-00671-w
Miguel Gozalo-Marcilla 1, 2 , Jaap Buntjer 1 , Martin Johnsson 1, 3 , Lorena Batista 1 , Federico Diez 1, 2 , Christian R Werner 1 , Ching-Yi Chen 4 , Gregor Gorjanc 1 , Richard J Mellanby 2 , John M Hickey 1 , Roger Ros-Freixedes 1, 5
Affiliation  

Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study for backfat thickness using data from eight lines of diverse genetic backgrounds. Data comprised 275,590 pigs from eight lines with diverse genetic backgrounds (breeds included Large White, Landrace, Pietrain, Hampshire, Duroc, and synthetic lines) genotyped and imputed for 71,324 single-nucleotide polymorphisms (SNPs). For each line, we estimated SNP associations using a univariate linear mixed model that accounted for genomic relationships. SNPs with significant associations were identified using a threshold of p < 10–6 and used to define genomic regions of interest. The proportion of genetic variance explained by a genomic region was estimated using a ridge regression model. We found significant associations with backfat thickness for 264 SNPs across 27 genomic regions. Six genomic regions were detected in three or more lines. The average estimate of the SNP-based heritability was 0.48, with estimates by line ranging from 0.30 to 0.58. The genomic regions jointly explained from 3.2 to 19.5% of the additive genetic variance of backfat thickness within a line. Individual genomic regions explained up to 8.0% of the additive genetic variance of backfat thickness within a line. Some of these 27 genomic regions also explained up to 1.6% of the additive genetic variance in lines for which the genomic region was not statistically significant. We identified 64 candidate genes with annotated functions that can be related to fat metabolism, including well-studied genes such as MC4R, IGF2, and LEPR, and more novel candidate genes such as DHCR7, FGF23, MEDAG, DGKI, and PTN. Our results confirm the polygenic architecture of backfat thickness and the role of genes involved in energy homeostasis, adipogenesis, fatty acid metabolism, and insulin signalling pathways for fat deposition in pigs. The results also suggest that several less well-understood metabolic pathways contribute to backfat development, such as those of phosphate, calcium, and vitamin D homeostasis.

中文翻译:

不同遗传背景猪系背膘厚度的遗传结构和主要基因

背膘厚度是猪肉生产的重要胴体成分特征,通常包括在猪育种计划中。在本文中,我们报告了使用来自不同遗传背景的八行数据的背膘厚度的大型全基因组关联研究的结果。数据包括来自具有不同遗传背景的八个品系(品种包括大白、长白、皮特兰、汉普郡、杜洛克和合成品系)的 275,590 头猪,对 71,324 个单核苷酸多态性 (SNP) 进行了基因分型和估算。对于每条线,我们使用解释基因组关系的单变量线性混合模型估计 SNP 关联。使用 p < 10–6 的阈值确定具有显着关联的 SNP,并用于定义感兴趣的基因组区域。使用岭回归模型估计由基因组区域解释的遗传方差的比例。我们发现 27 个基因组区域的 264 个 SNP 与背膘厚度显着相关。在三个或更多品系中检测到六个基因组区域。基于 SNP 的遗传力的平均估计值为 0.48,按行估计的范围为 0.30 至 0.58。基因组区域共同解释了一条线内背膘厚度的加性遗传方差的 3.2% 到 19.5%。单个基因组区域解释了一条线内高达 8.0% 的背膘厚度的附加遗传变异。这 27 个基因组区域中的一些也解释了基因组区域在统计上不显着的品系中高达 1.6% 的加性遗传变异。我们确定了 64 个具有注释功能的候选基因,这些候选基因可能与脂肪代谢相关,包括经过充分研究的基因,如 MC4R、IGF2 和 LEPR,以及更多新的候选基因,如 DHCR7、FGF23、MEDAG、DGKI 和 PTN。我们的研究结果证实了背膘厚度的多基因结构以及与能量稳态、脂肪生成、脂肪酸代谢和胰岛素信号通路有关的基因在猪脂肪沉积中的作用。结果还表明,一些不太了解的代谢途径有助于背膘发育,例如磷酸盐、钙和维生素 D 稳态的代谢途径。我们的研究结果证实了背膘厚度的多基因结构以及与能量稳态、脂肪生成、脂肪酸代谢和胰岛素信号通路有关的基因在猪脂肪沉积中的作用。结果还表明,一些不太了解的代谢途径有助于背膘发育,例如磷酸盐、钙和维生素 D 稳态的代谢途径。我们的研究结果证实了背膘厚度的多基因结构以及与能量稳态、脂肪生成、脂肪酸代谢和胰岛素信号通路有关的基因在猪脂肪沉积中的作用。结果还表明,一些不太了解的代谢途径有助于背膘发育,例如磷酸盐、钙和维生素 D 稳态的代谢途径。
更新日期:2021-09-23
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