Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Cork, Fermoy, Ireland.
School of Mathematics and Statistics, University College Dublin, Belfield, Dublin 4, Ireland.
BMC Genomics. 2021 Oct 23;22(1):757. doi: 10.1186/s12864-021-08075-2.
The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process.
A total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit.
The present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.
牛的胴体价值是胴体重量和质量的函数。鉴于胴体质量对生产者的经济重要性，它通常被纳入牛肉育种目标。详细了解有助于提高胴体质量的遗传变异对于最大限度地提高育种效率以提高胴体质量非常有用。本研究的目的有两个：首先，使用 923 头荷斯坦-弗里森、945 头夏洛来和 974 头利木赞公牛群体中的拷贝数变异 (CNV) 数据对胴体重量、胴体结构和胴体脂肪进行全基因组关联分析；其次，使用 712,555 个单核苷酸多态性 (SNP) 的 Log R 比值 (LRR) 值对同一牛群进行胴体性状的单独关联分析。SNP 的 LRR 值是 SNP 在基因分型过程中产生的信号强度的度量。
共检测到 13969、3954 和 2805 个可检测到的 CNV 与荷斯坦-弗里森、夏洛来和利木赞的三个胴体性状相关。在至少一个牛品种中，有 16 个 CNV 的拷贝数和 34 个 SNP 的 LRR 与三个胴体性状中的至少一个相关。除了三个 SNP 之外，在 CNV 关联分析或 SNP LRR 关联分析中检测到的数量性状基因座都没有在基于 SNP 等位基因计数的传统关联分析中检测到。与胴体性状相关的许多 CNV 和 SNP 位于与剪接体和核糖体结构和功能相关的基因附近；特别是，编码剪接体亚基的 U6 和编码核糖体亚基的 5S rRNA。
本研究表明，CNV 数据和 SNP LRR 数据可用于检测与牛胴体性状相关的基因组区域，提供了比仅使用 SNP 等位基因计数在全基因组关联分析中通常采用的方法更多的数量性状基因座信息。
