Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark.
Department of Breeding and Genetics, Nofima AS, PO Box 210, N-1431 Ås, Norway.
J Dairy Sci. 2022 Feb;105(2):1357-1368. doi: 10.3168/jds.2021-20410. Epub 2021 Nov 17.
Selecting for lower methane emitting cows requires insight into the most biologically relevant phenotypes for methane emission, which are close to the breeding goal. Several methane phenotypes have been suggested over the last decade. However, the (dis)similarity of their underlying genetic architecture and correlation structures are poorly understood. Therefore, the objective of this study was to test association of SNP and genomic regions through GWAS on 8 CH emission traits in Danish Holstein cattle. The traits studied were methane concentration (MeC; ppm), methane production (MeP ; g/d), 2 definitions of residual methane (RMETc and RMETp: MeC and MeP regressed on metabolic body weight and energy-corrected milk, respectively), 2 definitions of methane intensity (MeI; MeIc = MeC/ECM and MeIp = MeP/ECM); 2 definitions of methane yield per kilogram of dry matter intake (MeY; MeYc = MeC/dry matter intake and MeYp = MeP/dry matter intake). A total of 1,962 cows with genotypes (Illumina BovineSNP50 Chip or Eurogenomic custom SNP chip) and repeated records of the above-mentioned 8 methane traits were analyzed. Strong associations were found with 3 traits (MeC, MeP, and MeYc) on chromosome 13 and with 5 traits (MeC, MeP, MeIp, MeYp, and MeYc) on chromosome 26. For MeIc, MeIp, RMETc, MeYc, and MeYp, some suggestive association signals were identified on chromosome 1. Genomic segments of 1 Mbp (n = 2,525) were tested for their association with these traits, which identified between 33 to 54 significantly associated regions. In a pairwise comparison, MeC and MeP were the traits that shared the highest number of significant segments (17). The same trend was observed when comparing SNP significantly associated with the traits MeC and MeP shared from 23 to 25 SNP (most of which were located in chromosomes 11, 13, and 26). Based on our results on GWAS and genetic correlations, we conclude that MeC is (genetically) more closely linked to MeP than any of the other methane traits analyzed.
选择甲烷排放量较低的奶牛需要深入了解与甲烷排放最相关的生物学表型，这些表型接近选育目标。在过去的十年中，已经提出了几种甲烷表型。然而，它们潜在的遗传结构和相关结构的相似性和差异性尚未被充分理解。因此，本研究的目的是通过 GWAS 检测丹麦荷斯坦奶牛 8 个 CH 排放性状的 SNP 和基因组区域的关联。所研究的性状包括甲烷浓度（MeC；ppm）、甲烷产量（MeP；g/d）、2 种剩余甲烷（RMETc 和 RMETp：分别回归代谢体重和能量校正奶的 MeC 和 MeP）、2 种甲烷强度（MeI；MeIc = MeC/ECM 和 MeIp = MeP/ECM）、2 种每千克干物质摄入的甲烷产量（MeY；MeYc = MeC/干物质摄入和 MeYp = MeP/干物质摄入）。共分析了 1962 头具有基因型（Illumina BovineSNP50 芯片或 Eurogenomic 定制 SNP 芯片）和上述 8 种甲烷性状重复记录的奶牛。在第 13 号染色体上发现了与 3 个性状（MeC、MeP 和 MeYc）和第 26 号染色体上与 5 个性状（MeC、MeP、MeIp、MeYp 和 MeYc）的强关联。对于 MeIc、MeIp、RMETc、MeYc 和 MeYp，在第 1 号染色体上鉴定出了一些提示性关联信号。对 1 Mbp（n = 2525）的基因组片段进行了与这些性状的关联测试，鉴定出了 33 到 54 个显著相关区域。在成对比较中，MeC 和 MeP 是共享最多显著片段的性状（17 个）。当比较与性状 MeC 和 MeP 显著相关的 SNP 时，也观察到了相同的趋势，这些 SNP 共享 23 到 25 个 SNP（其中大部分位于 11、13 和 26 号染色体上）。基于我们在 GWAS 和遗传相关性方面的结果，我们得出结论，与分析的其他甲烷性状相比，MeC 在遗传上与 MeP 的关联更为密切。
