使用参数函数从荷斯坦奶牛的日产奶量中得出的泌乳曲线参数的基因组背景

摘要(中文译文)

泌乳曲线参数（LCP）因其与泌乳曲线形状的关系及其生物学解释，在奶牛育种规划的优化中至关重要。在此背景下，本研究的主要目标是对美国荷斯坦牛中基于3种非线性函数（Wood [WD]、Wilmink [WL]和Ali-Schaeffer [AS]）的随机回归模型得出的各种泌乳曲线参数进行全基因组关联研究和功能富集分析。我们使用了11,139头头胎和6,735头二胎母牛的2,754,840条和1,642,653条日产奶量记录，这些母牛出生于2012年至2019年间。共有14,464头动物使用60,277个SNP进行了基因分型。基于GBLUP方法，对随机回归系数估算了SNP效应、其所解释的总加性遗传方差比例及其近似P值。使用校正了独立染色体片段数量的改良Bonferroni多重检验校正来识别显著SNP。随后检查了位于显著SNP上游或下游100 kb范围内的基因和数量性状位点，并对每个泌乳曲线参数所识别的候选基因进行了功能富集分析。对于头胎母牛，分别鉴定出81、128和196个显著SNP对应于WD、WL和AS参数；而对于二胎母牛，相同参数分别鉴定出120、125和128个显著SNP。显著SNP位于18条常染色体上。一个基因组区域（BTA14: 1,801,116 bp）为所有参数函数（WD、WL和AS）所共有。位于BTA15和BTA19的基因组标记为WL参数所特有；而位于BTA3和BTA20的标记为AS参数所特有。位于BTA14的显著SNP捕获了超过1%的总加性遗传方差。二十个候选基因（即ARC、ADGRB1、C8orf90、CYP11B1、DENND3、GML、GPR20、JRK、LY6D、LY6E、LY6L、LYNX1、LYPD2、PSCA、PTK2、PTP4A3、SLURP1、SLC45A4、THEM6和TSNARE1）为所有参数函数所共有。对于头胎母牛的WD参数c（即泌乳高峰后的下降斜率参数）以及二胎母牛的AS参数d和f（与上升斜率相关的参数），未发现显著的基因本体论条目。既往报道已在这些基因组区域内鉴定出具有与细胞凋亡和基因表达调控、产奶量、临床乳房炎、乳糖、体细胞评分、脂肪产量和乳房形态相关的生物学功能的候选基因。本研究鉴定出多个与泌乳曲线参数相关的候选基因，增进了我们对美国荷斯坦牛泌乳曲线参数基因组结构的理解。

Abstract

Lactation curve parameters (LCP) are essential in the refinement of dairy cattle breeding programs due to their relationship with the shape of lactation curves and their biological interpretations. In this context, the primary objectives of this study were to perform genome-wide association studies and functional enrichment analyses of various LCP from random regression models based on 3 nonlinear functions (Wood [WD], Wilmink [WL], and Ali-Schaeffer [AS]) in American Holstein cattle. We used 2,754,840 and 1,642,653 daily milk yield records of 11,139 first- and 6,735 second-parity cows, respectively, born between 2012 and 2019. A total of 14,464 animals were also genotyped with 60,277 SNPs. The SNP effects, the proportion of the total additive genetic variance explained by them, and their approximate P-values, were estimated for the random regression coefficients based on the GBLUP method. Significant SNP were identified using a modified Bonferroni multiple testing correction that accounts for the number of independent chromosomal segments. Genes and quantitative trait loci located within 100 kb upstream or downstream of the significant SNP were then examined, and functional enrichment analyses were conducted on the candidate genes identified for each LCP. For first-parity cows, 81, 128, and 196 significant SNP were identified for the WD, WL, and AS parameters, respectively, whereas for second-parity cows, 120, 125, and 128 significant SNP were identified for the same parameters. The significant SNP were located on 18 autosomal chromosomes. One genomic region (BTA14: 1,801,116 bp) was common to all the parametric functions (WD, WL, and AS). The genomic markers located on BTA15 and BTA19 were unique to the WL parameters; whereas those located on BTA3 and BTA20 were unique to the AS parameters. There were significant SNP located on BTA14 capturing more than 1% of the total additive genetic variance. Twenty candidate genes (i.e., ARC, ADGRB1, C8orf90, CYP11B1, DENND3, GML, GPR20, JRK, LY6D, LY6E, LY6L, LYNX1, LYPD2, PSCA, PTK2, PTP4A3, SLURP1, SLC45A4, THEM6, and TSNARE1) were common to all the parametric functions. No significant gene ontology terms were found for the WD parameter c (i.e., decreasing slope parameter after the lactation peak yield) for first-parity cows, and for the AS parameters d and f (parameters associated with the increasing slope) for second-parity cows. Previous reports have identified candidate genes within these genomic regions that possess biological functions related to apoptotic and regulation of gene expression, milk production, clinical mastitis, milk lactose, SCS, fat yield, and udder morphology. This study enabled the identification of several candidate genes associated with LCP, enhancing our understanding of the genomic architecture underlying LCP in American Holstein cattle.

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