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Genetic parameters, genome-wide association and gene networks for milk and reproductive traits in Guzerá cattle
Livestock Science ( IF 1.8 ) Pub Date : 2020-09-29 , DOI: 10.1016/j.livsci.2020.104273
José Teodoro Paiva , Maria Gabriela Campolina Diniz Peixoto , Frank Angelo Tomita Bruneli , Amanda Botelho Alvarenga , Hinayah Rojas Oliveira , Alessandra Alves Silva , Delvan Alves Silva , Renata Veroneze , Fabyano Fonseca Silva , Paulo Sávio Lopes

The profitability of dairy activity is influenced by the genetic selection of economically important traits. In this context, the correct estimation of genetic parameters and the knowledge regarding candidate genes involved in the expression of genetically associated traits may help develop appropriate breeding strategies for the Guzerá breed. In this study, genetic parameters and candidate genes were estimated for accumulated 305-day milk yield (305MY), age at n calving (ANC), and milk yield efficiency (MYE) in Guzerá cattle. The (co)variance components were estimated by the restricted maximum likelihood method, and single nucleotide polymorphisms (SNPs) effects were estimated using the weighted single-step genome-wide association approach. The numbers of SNPs and samples used after quality control were 29,869 and 870, respectively. Candidate genes identified in a GWAS were selected to build gene networks by using the ClueGO Cytoscape plug-in (kappa score level ≥ 0.4). Heritabilities estimated for 305MY, ANC, and MYE were moderate to high (0.23, 0.41, and 0.42, respectively). Genetic correlations were positive between 305MY × ANC and 305MY × MYE (0.10 and 0.81, respectively) and negative between MYE × ANC (-0.53). Based on the GWAS analysis, a total of 89 significant SNPs (threshold value of 5.77 on the –log10 scale) were found for 305MY, and no significant SNPs were found for the other traits. Based on the top 5 significant SNPs (i.e., significant SNPs that explained the largest proportion of additive genetic variance), the following positional candidate genes were found to be related to 305MY in Guzerá cattle: CIB4, OTOF, LOXL2, PPFIA2, NXN, MRM3, GEMIN4, DBIL5, and FAM57A. In addition, the gene network analysis revealed the candidate genes BCR, P2RY12, P2RY14, GPR87, IFT81, SYT1, IL16, and HOOK3, which shared important biological processes and functions (e.g., Rho guanine nucleotide exchange factor activity, G-protein coupled purinergic nucleotide receptor signaling, intraciliary transport involved in cilium assembly, calcium ion-dependent exocytosis, chemotaxis regulation, and microtubule anchoring at centrosome), for 305MY.



中文翻译:

古塞拉牛乳和生殖性状的遗传参数,全基因组关联和基因网络

乳制品活动的获利能力受经济上重要特征的基因选择影响。在这种情况下,对遗传参数的正确估计以及有关与遗传相关性状表达有关的候选基因的知识可能有助于为古泽拉(Guzerá)品种制定适当的育种策略。在这项研究中,遗传参数和候选基因进行了估计累计305天产奶量(305MY),年龄在ñ古塞拉牛的产犊量(ANC)和产奶效率(MYE)。(协)方差成分通过限制最大似然法进行估算,单核苷酸多态性(SNPs)效果通过加权单步全基因组关联方法进行估算。质量控制后使用的SNP和样品数量分别为29,869和870。通过使用ClueGO Cytoscape插件(kappa得分≥0.4),选择了在GWAS中识别的候选基因来构建基因网络。估计的305MY,ANC和MYE的遗传力为中等到较高(分别为0.23、0.41和0.42)。305MY×ANC和305MY×MYE之间的遗传相关为正(分别为0.10和0.81),而MYE×ANC之间的遗传相关为负(-0.53)。根据GWAS分析,共有89个重要SNP(阈值5.77 –对数为10的对数为305MY),其他性状均未发现明显的SNP。根据排名前5位的重要SNP(即解释最大的加性遗传变异的重要SNP),发现以下位置候选基因与Guzerá牛中的305MY相关:CIB4,OTOF,LOXL2,PPFIA2,NXN,MRM3 ,GEMIN4,DBIL5FAM57A。此外,基因网络分析显示候选基因BCR,P2RY12,P2RY14,GPR87,IFT81,SYT1,IL16HOOK3,它们具有重要的生物学过程和功能(例如,Rho鸟嘌呤核苷酸交换因子活性,G蛋白偶联的嘌呤能核苷酸受体信号传导,纤毛组装中的纤毛内转运,钙离子依赖性胞吐作用,趋化性调节和微管锚定在中心体上),为305MY。

更新日期:2020-10-05
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