Animal and Poultry Breeding Department, Desert Research Center, Cairo, Egypt.
Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
BMC Genomics. 2023 Sep 26;24(1):573. doi: 10.1186/s12864-023-09679-6.
Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (F) and fixation index (F) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average F was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest F was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean F was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high F values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both F and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.
了解家畜的基因组特征对于成功的繁殖计划和保护至关重要。然而，埃及当地的山羊品种在这方面的信息却很匮乏。在当前的研究中，我们鉴定了具有选择特征的基因组区域，并检测了埃及努比亚山羊、大马士革山羊、巴尔克山羊和布尔山羊品种的纯合子（ROH）、基因组近交系数（F）和固定指数（F）。共有 46268 个 SNP 标记和 337 只动物用于基因组分析。平均而言，在各自品种的常染色体基因组中，每个个体检测到 145.44、42.02、87.90 和 126.95 个 ROH。累积的 ROH 长度范围从大马士革的 46.5 Mb 到埃及努比亚的 360 Mb。在所有品种中，最短的 ROH 片段（<2 Mb）最为常见，而最长的 ROH 片段（>16 Mb）仅在埃及努比亚山羊中发现。埃及努比亚山羊的平均 F 值最高（0.12），其次是布尔山羊（0.11），而大马士革山羊和巴尔克山羊的 F 值最低（~0.05 和 ~0.03）。估计的平均 F 值为 0.14（埃及努比亚山羊和布尔山羊）、0.077（埃及努比亚山羊和巴尔克山羊）、0.075（埃及努比亚山羊和大马士革山羊）、0.071（巴尔克山羊和布尔山羊）、0.064（大马士革山羊和布尔山羊）和 0.015（大马士革山羊和巴尔克山羊），用于每对品种。有趣的是，在包含 ALPK1 和 KCNIP4 的染色体 6 上观察到了多个导致 F 值较高的 SNP。同时具有 F 和 ROH 的基因组区域与免疫（IL4R、PHF23、GABARAP、GPS2 和 CD68）、生殖（SPATA2L、TNFSF12、TMEM95 和 RNF17）、胚胎发育（TCF25 和 SOX15）和适应（MC1R、KDR 和 KIT）相关的基因，表明这些基因可能对当地环境条件有潜在的遗传适应。我们的研究结果有助于理解不同山羊品种的遗传结构，并可能为埃及当地山羊品种的有效保护和繁殖计划提供有价值的信息。
