Pryce Jennie E, Haile-Mariam Mekonnen, Goddard Michael E, Hayes Ben J
Biosciences Research Division, Department of Environment and Primary Industries Victoria, 5 Ring Road, Bundoora 3083, Australia.
Genet Sel Evol. 2014 Nov 18;46(1):71. doi: 10.1186/s12711-014-0071-7.
Inbreeding reduces the fitness of individuals by increasing the frequency of homozygous deleterious recessive alleles. Some insight into the genetic architecture of fitness, and other complex traits, can be gained by using single nucleotide polymorphism (SNP) data to identify regions of the genome which lead to reduction in performance when identical by descent (IBD). Here, we compared the effect of genome-wide and location-specific homozygosity on fertility and milk production traits in dairy cattle.
Genotype data from more than 43 000 SNPs were available for 8853 Holstein and 4138 Jersey dairy cows that were part of a much larger dataset that had pedigree records (338 696 Holstein and 64 049 Jersey animals). Measures of inbreeding were based on: (1) pedigree data; (2) genotypes to determine the realised proportion of the genome that is IBD; (3) the proportion of the total genome that is homozygous and (4) runs of homozygosity (ROH) which are stretches of the genome that are homozygous.
A 1% increase in inbreeding based either on pedigree or genomic data was associated with a decrease in milk, fat and protein yields of around 0.4 to 0.6% of the phenotypic mean, and an increase in calving interval (i.e. a deterioration in fertility) of 0.02 to 0.05% of the phenotypic mean. A genome-wide association study using ROH of more than 50 SNPs revealed genomic regions that resulted in depression of up to 12.5 d and 260 L for calving interval and milk yield, respectively, when completely homozygous.
Genomic measures can be used instead of pedigree-based inbreeding to estimate inbreeding depression. Both the diagonal elements of the genomic relationship matrix and the proportion of homozygous SNPs can be used to measure inbreeding. Longer ROH (>3 Mb) were found to be associated with a reduction in milk yield and captured recent inbreeding independently and in addition to overall homozygosity. Inbreeding depression can be reduced by minimizing overall inbreeding but maybe also by avoiding the production of offspring that are homozygous for deleterious alleles at specific genomic regions that are associated with inbreeding depression.
近亲繁殖通过增加纯合有害隐性等位基因的频率来降低个体的适应性。通过使用单核苷酸多态性（SNP）数据来识别基因组中当同源纯合（IBD）时导致性能下降的区域，可以深入了解适应性和其他复杂性状的遗传结构。在此，我们比较了全基因组和特定位置纯合性对奶牛繁殖力和产奶性状的影响。
来自超过43000个SNP的基因型数据可用于8853头荷斯坦奶牛和4138头泽西奶牛，这些奶牛是一个包含系谱记录的更大数据集（338696头荷斯坦奶牛和64049头泽西奶牛）的一部分。近亲繁殖的测量基于：（1）系谱数据；（2）基因型以确定基因组中IBD的实际比例；（3）全基因组中纯合的比例；（4）纯合片段（ROH），即基因组中纯合的片段。
基于系谱或基因组数据的近亲繁殖增加1%，与牛奶、脂肪和蛋白质产量下降约表型均值的0.4%至0.6%相关，并且产犊间隔增加（即繁殖力下降）约表型均值的0.02%至0.05%。一项使用超过50个SNP的ROH进行的全基因组关联研究揭示了基因组区域，当完全纯合时，这些区域分别导致产犊间隔延长多达12.5天和产奶量减少260升。
可以使用基因组测量方法代替基于系谱的近亲繁殖来估计近亲繁殖衰退。基因组关系矩阵的对角元素和纯合SNP的比例均可用于测量近亲繁殖。发现较长的ROH（>3 Mb）与产奶量降低相关，并且除了总体纯合性之外，还能独立捕获近期的近亲繁殖。通过尽量减少总体近亲繁殖，或者也可以通过避免产生在与近亲繁殖衰退相关的特定基因组区域中有害等位基因纯合的后代，可以降低近亲繁殖衰退。
