Inbreeding depression can adversely affect traits related to fitness, reproduction and productive performance. Although current research suggests that inbreeding levels are generally low in most goat breeds, the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data. We genotyped 1040 goats with the Goat SNP50 BeadChip. This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns. We detected 38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1, 2, 4, 6, 14, 16 and 17. Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes. Four regions on chromosomes 8 and 25 were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count. Notably, these regions contain several genes related with immunity, such as SYK, IL27, CCL19 and CCL21. Moreover, one region on chromosome 2 was significantly associated with inbreeding depression for milk yield. Although genomic inbreeding levels are low in Murciano-Granadina goats, significant evidence of inbreeding depression for the logarithm of the somatic cell count, a phenotype closely associated with udder health and milk yield, have been detected in this population. Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis, which is one of the main causes of dairy goat culling.

中文翻译：

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Murciano-Granadina山羊纯合性和近交抑制的基因组模式

近交衰退会对与健康、繁殖和生产性能相关的性状产生不利影响。尽管目前的研究表明，大多数山羊品种的近交水平普遍较低，但仅在少数基于家谱数据的研究中调查了近交衰退对经济利益表型的影响。我们使用 Goat SNP50 BeadChip 对 1040 只山羊进行了基因分型。该信息用于估计不同的分子近交系数并表征纯合性和纯合性模式的运行。我们检测到 38 个纯合性增加的基因组区域以及 8 个定位到染色体 1、2、4、6、14、16 和 17 的 ROH 热点。分析了 817 只具有乳品性状可用记录的山羊，以评估近交的潜在后果对牛奶表型的抑制。对于体细胞计数的自然对数，8 号和 25 号染色体上的四个区域与近交衰退显着相关。值得注意的是，这些区域包含几个与免疫相关的基因，如 SYK、IL27、CCL19 和 CCL21。此外，2号染色体上的一个区域与产奶量的近交衰退显着相关。尽管 Murciano-Granadina 山羊的基因组近交水平较低，但在该群体中已检测到体细胞计数的对数（一种与乳房健康和产奶量密切相关的表型）近交抑制的重要证据。减少近亲繁殖有望通过提高产奶量和减少乳腺炎的发病率来增加经济收益，而乳腺炎是奶山羊扑杀的主要原因之一。