Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds.
Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds.
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DOI：
10.1186/s12711-021-00671-w
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发表时间：
2021-09-22
期刊：
影响因子：
--
通讯作者：
Ros-Freixedes R
中科院分区：
文献类型：
--
作者：
Gozalo-Marcilla M;Buntjer J;Johnsson M;Batista L;Diez F;Werner CR;Chen CY;Gorjanc G;Mellanby RJ;Hickey JM;Ros-Freixedes R
背膘厚是猪肉生产的重要胴体组成性状，通常包括在猪育种计划中。在本文中，我们报告了一个大的全基因组关联研究的结果，背膘厚度使用的数据来自不同的遗传背景的八行。数据包括275，590头来自8个不同遗传背景的猪系（品种包括大白色、长白猪、皮特兰猪、汉普郡猪、杜洛克猪和合成系）的基因型，并估算了71，324个单核苷酸多态性（SNP）。对于每个品系，我们使用考虑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的阈值鉴定具有显著关联的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。我们在27个基因组区域发现了264个SNP与背膘厚度的显著相关性。在三个或更多个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，各品系的估计值范围为0.30至0.58。基因组区域共同解释了3.2%至19.5%的加性遗传方差的背膘厚线内。单个基因组区域可以解释同一品系内背膘厚的加性遗传方差的8.0%。这27个基因组区域中的一些也解释了高达1.6%的基因组区域不具有统计学显著性的品系的加性遗传方差。我们确定了64个具有注释功能的候选基因，这些基因可能与脂肪代谢相关，包括已充分研究的基因，如MC 4 R，IGF 2和LEPR，以及更多新的候选基因，如DHCR 7，FGF 23，MEDAG，DGKI和PTN。我们的研究结果证实了背膘厚度的多基因结构和参与能量稳态、脂肪形成、脂肪酸代谢和胰岛素信号通路的基因在猪脂肪沉积中的作用。研究结果还表明，一些不太清楚的代谢途径有助于背膘的发展，如磷酸盐，钙和维生素D的稳态。在线版本包含补充材料，可通过10.1186/s12711-021-00671-w获得。
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. The online version contains supplementary material available at 10.1186/s12711-021-00671-w.
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影响因子：
10.6
作者：
Ballatori, Nazzareno;Christian, Whitney V.;Wheeler, Sadie G.;Hammond, Christine L.
通讯作者：
Hammond, Christine L.
影响因子：
3.7
作者：
Blaj I;Tetens J;Preuß S;Bennewitz J;Thaller G
通讯作者：
Thaller G
影响因子：
64.5
作者：
Boyle EA;Li YI;Pritchard JK
通讯作者：
Pritchard JK
影响因子：
2.4
作者：
Just F;Reyer H;Muráni E;Ponsuksili S;Oster M;Wimmers K
通讯作者：
Wimmers K
影响因子：
1.8
作者：
Galve, A.;Burgos, C.;Lopez-Buesa, P.
通讯作者：
Lopez-Buesa, P.