Data_Sheet_1_Genetic Parameters and Genome-Wide Association Studies of Eight Longevity Traits Representing Either Full or Partial Lifespan in Chinese Holsteins.docx

Due to the complexity of longevity trait in dairy cattle, two groups of trait definitions are widely used to measure longevity, either covering the full lifespan or representing only a part of it to achieve an early selection. Usually, only one group of longevity definition is used in breeding program for one population, and genetic studies on the comparisons of two groups of trait definitions are scarce. Based on the data of eight traits well representing the both groups of trait definitions, the current study investigated genetic parameters and genetic architectures of longevity in Holsteins. Heritabilities and correlations of eight longevity traits were estimated using single-trait and multi-trait animal models, with the data from 103,479 cows. Among the cows with phenotypes, 2,630 cows were genotyped with the 150K-SNP panel. A single-trait fixed and random Circuitous Probability Unification model was performed to detect candidate genes for eight longevity traits. Generally, all eight longevity traits had low heritabilities, ranging from 0.038 for total productive life and herd life to 0.090 for days from the first calving to the end of first lactation or culling. High genetic correlations were observed among the traits within the same definition group: from 0.946 to 0.997 for three traits reflecting full lifespan and from 0.666 to 0.997 for five traits reflecting partial productive life. Genetic correlations between two groups of traits ranged from 0.648 to 0.963, and increased gradually with the extension of lactations number regarding the partial productive life traits. A total of 55 SNPs located on 25 chromosomes were found genome-wide significantly associated with longevity, in which 12 SNPs were associated with more than one trait, even across traits of different definition groups. This is the first study to investigate the genetic architecture of longevity representing both full and the partial lifespan simultaneously, which will assist the selection of an appropriate trait definition for genetic improvement of longevity. Because of high genetic correlations with the full lifespan traits and higher heritability, the partial productive life trait measured as the days from the first calving to the end of the third lactation or culling could be a good alternative for early selection on longevity. The candidate genes identified by this study, such as RPRM, GRIA3, GTF2H5, CA5A, CACNA2D1, FGF10, and DNAJA3, could be used to pinpoint causative mutations for longevity and further benefit the genomic improvement of longevity in dairy cattle.

鉴于奶牛长寿性状的复杂性，当前学界广泛采用两类性状定义方式评估奶牛长寿性：一类覆盖全生命周期，另一类仅涵盖部分生命周期以实现早期选育。通常，单个群体的育种项目仅使用一类长寿性状定义，而针对两类性状定义的比较遗传学研究仍较为匮乏。本研究基于能够分别代表两类长寿性状定义的8个性状的表型数据，对荷斯坦奶牛（Holstein）的长寿性遗传参数及遗传结构展开探究。研究利用103479头奶牛的表型数据，通过单性状与多性状动物模型估算8个长寿性状的遗传力及遗传相关。其中，2630头有表型记录的奶牛使用150K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片完成了基因分型。针对8个长寿性状，本研究采用单性状固定效应-随机效应迂回概率统一模型（Circuitous Probability Unification model）检测候选基因。总体而言，8个长寿性状的遗传力均较低，范围为总生产寿命和牛群寿命的0.038，至首次产犊至首泌乳期结束或淘汰的天数的0.090。同一定义类别的性状间呈现较高的遗传相关：反映全生命周期的3个性状间遗传相关介于0.946至0.997之间，反映部分生产寿命的5个性状间遗传相关介于0.666至0.997之间。两类性状间的遗传相关范围为0.648至0.963，且随着部分生产寿命性状对应的泌乳次数增加，两类性状间的遗传相关逐渐升高。全基因组范围内共检测到25条染色体上的55个SNP与长寿性状呈显著关联，其中12个SNP可同时与多个性状相关，甚至可关联不同定义类别的性状。本研究是首个同时探究覆盖全生命周期与部分生命周期两类长寿性状遗传结构的研究，其结果将为长寿性遗传改良中合适性状定义的选择提供参考。由于与全生命周期性状间存在较高遗传相关且自身遗传力更高，以"首次产犊至第三泌乳期结束或淘汰的天数"衡量的部分生产寿命性状，可作为奶牛长寿性早期选育的优良替代性状。本研究鉴定的候选基因，如RPRM、GRIA3、GTF2H5、CA5A、CACNA2D1、FGF10及DNAJA3，可用于定位长寿性状的致因突变，进而助力奶牛长寿性的基因组改良。