Inbreeding increases homozygosity, which in turn increases the frequency of harmful recessive alleles, resulting in inbreeding depression. Inbreeding depression on fertility reduces the profitability of dairy farming by decreasing the lifetime milk production of cows and by increasing insemination and veterinary costs. Continuous homozygous segments, called runs of homozygosity (ROH), are currently considered to provide an effective measure of genomic inbreeding. The aim of this study was to estimate the effect of increased intrachromosomal homozygosity for female fertility in the Finnish Ayrshire population using ROH and haplotype analysis. Genotypes were obtained from 13,712 females with the Illumina BovineLD v.2 BeadChip low-density panel (Illumina Inc., San Diego, CA) and imputed to 50K density. After quality control, 40,554 single nucleotide polymorphisms remained for the analysis. Phenotypic data consisted of records for nonreturn rate, intervals from first to last insemination (IFL), and intervals from calving to first insemination. The raw phenotypic values were preadjusted for systematic effects before statistical analyses. The ROH-based inbreeding coefficients (F_ROH) were used as covariates in the mixed model equation to estimate the association between inbreeding and inbreeding depression on female fertility. First, we estimated the effect of increased chromosomal F_ROH. We detected significant inbreeding depression on IFL. Based on our results, a 10% increase in F_ROH on chromosomes 2, 18, and 22 were associated with IFL of heifers lengthening by 1.6, 0.9, and 0.7 d, respectively. Similarly, a 10% increase in F_ROH on chromosome 15 was associated with IFL of second-parity cows increasing by 2.3 d. Next, we located the regions within the chromosomes showing inbreeding depression. Our analysis revealed regions near the beginning of chromosome 2 and toward the ends of chromosomes 15, 18, and 22 that were associated with inbreeding depression on IFL. Last, we performed a haplotype analysis for the detected regions. The most promising haplotypes of each region were associated with IFL of heifers increasing by 4.4, 3.2, and 4.1 d on chromosomes 2, 18, and 22, respectively. The haplotype on chromosome 15 associated with IFL of second-parity cows increasing by 7.6 d. Overall, the breeding program requires inbreeding control, as increased genomic inbreeding in our study was associated with reduced reproductive ability in Finnish Ayrshire cattle.

近交会增加纯合性，这反过来会增加有害隐性等位基因的频率，导致近交衰退。近亲繁殖力降低会降低奶牛的终生奶产量，并增加授精和兽医费用，从而降低了奶牛养殖的利润。连续的纯合区段，称为纯合运行（ROH），目前被认为可提供有效的基因组近交措施。这项研究的目的是使用ROH和单倍型分析来评估增加的染色体内纯合性对芬兰Ayrshire人口中女性生育力的影响。使用Illumina BovineLD v.2 BeadChip低密度检测板（Illumina Inc.，圣地亚哥，加利福尼亚）从13,712位女性中获得基因型，并推算至50K密度。经过质量控制40 保留554个单核苷酸多态性用于分析。表型数据包括单向输精率，第一次受精到最后一次受精的间隔以及从产犊到第一次受精的间隔。在进行统计分析之前，对原始表型值进行了系统影响的预调整。基于ROH的近交系数（F_ROH）被用作混合模型方程式的协变量，以估计近亲繁殖和近亲衰退对女性生育力的关联。首先，我们估计了增加的染色体F _ROH的影响。我们在IFL上检测到明显的近交衰退。根据我们的结果，第_2、18和22号染色体上F _ROH增加10％与小母牛的IFL分别延长1.6 d，0.9 d和0.7 d有关。同样，F _ROH增加10％第15号染色体上的突变与第二胎母牛的IFL有关，增加了2.3 d。接下来，我们在染色体内定位了显示近交抑制的区域。我们的分析揭示了与IFL近交衰退相关的2号染色体起点附近，15号，18号和22号染色体末端的区域。最后，我们对检测到的区域进行了单倍型分析。每个区域最有希望的单倍型与小母牛的IFL相关，分别在2号，18号和22号染色体上增加了4.4、3.2和4.1 d。与第二胎的母牛的IFL相关的15号染色体上的单倍型增加了7.6 d。总体而言，育种计划需要近交控制，因为我们研究中基因组近交的增加与芬兰艾尔郡牛繁殖能力的降低有关。