Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil.
Unit of Animal Genomics, GIGA-R, University of Liège, Liège, Belgium.
BMC Genomics. 2021 May 17;22(1):354. doi: 10.1186/s12864-021-07676-1.
Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age.
We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels.
Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens.
拷贝数变异（CNVs）是结构基因组变异的主要类型，它们不仅在人类中，而且在牲畜中，是复杂性状遗传结构和表型变异的基础。我们沿着鸡基因组鉴定了 CNVs，并分析了它们与性能性状的关联。使用 Affymetrix®高密度 SNP 芯片数据对肉鸡群体进行全基因组 CNV 推断。将 CNVs 串联成片段，并使用线性混合模型考虑基因组关系矩阵进行关联分析，用于出生体重、21、35、41 和 42 日龄体重、35 至 41 日龄采食量、35 至 41 日龄饲料转化率和 35 至 41 日龄体重增加。
我们鉴定了 23214 个常染色体 CNVs，合并为 5042 个独特的 CNV 区域（CNVRs），覆盖了鸡常染色体基因组的 12.84%。一个显著的 CNV 片段与 GGA3 上的 BWG 相关（q 值=0.00443）；一个显著的 CNV 片段与 GGA3 上的 BW35（q 值=0.00571）、BW41（q 值=0.00180）和 BW42（q 值=0.00130）相关，一个显著的 CNV 片段与 GGA5 上的 BW 相关（q 值=0.00432）。所有显著的 CNV 片段均通过 qPCR 验证，观察到验证率为 92.59%。这些 CNV 片段位于附近的基因，如 KCNJ11、MyoD1 和 SOX6，这些基因已知与生长和发育有关。此外，基因集分析揭示了与肌肉生理学、细胞过程调节和钾通道相关的术语。
总的来说，这项基于 CNV 的全基因组关联研究揭示了可能调节鸡性能性状的潜在候选基因。我们的研究结果为未来研究特定基因在调节鸡性能中的作用提供了基础。
