Chokoe T C, Hadebe K, Muchadeyi F C, Nephawe K A, Dzomba E F, Mphahlele T D, Matelele T C, Mtileni B J
Farm Animal Genetic Resources, Department of Agriculture, Land Reform and Rural Development, Pretoria, South Africa.
School of Agriculture & Environmental Sciences, University of Limpopo, Polokwane, South Africa.
Front Genet. 2022 Aug 9;13:909472. doi: 10.3389/fgene.2022.909472. eCollection 2022.
Indigenous goats form the majority of populations in smallholder, low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support of communal farming. Effective population size ( ), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current of Gauteng was the lowest at 371 animals, while the historical across populations suggests that the ancestor has decreased by 53.86%, 44.58%, 42.16%, and 41.16% in Free State (FS), North West (NW), Limpopo (LP), and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship ( > 5 Mb) were highest in FS (0.08 ± 0.09) and lowest in the Eastern Cape (EC) (0.02 ± 0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as and were identified (occurring in over 20% of the samples) in FS ( = 37), GP ( = 42), and NW ( = 2) populations only. The mean length of ROH across populations was 7.76 Mb and ranged from 1.61 Mb in KwaZulu-Natal (KZN) to 98.05 Mb (GP and NW). The distribution of ROH according to their size showed that the majority ( = 1949) of the detected ROH were > 5 Mb in length compared to the other categories. Assuming two hypothetical ancestral populations, the populations from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP share a common origin but have substantial admixture from the EC and NW populations. The findings revealed that the occurrence of high and autozygosity varied largely across breeds in communal indigenous goat populations at recent and ancient events when a genome-wide single-nucleotide polymorphism (SNP) marker was used. The use of Illumina goat SNP50K BeadChip shows that there was a migration route of communal indigenous goat populations from the northern part (LP) of South Africa to the eastern areas of the KZN that confirmed their historical relatedness and coincides with the migration periods of the Bantu nation.
本土山羊在小规模、低投入、低产出的生产系统中占大多数，由于它们对不同生产环境的适应性以及对社区养殖的支持，被视为重要的遗传资源。有效种群大小（ ）、近亲繁殖水平和纯合子连续区域（ROHs）是探索遗传多样性和了解种群历史的有效工具，有助于支持遗传资源利用和保护的育种策略。在各个种群中，豪登省目前的有效种群大小最低，为371只动物，而各群体的历史有效种群大小表明，在过去的971代中，自由邦（FS）、西北省（NW）、林波波省（LP）和豪登省（GP）的祖先有效种群大小分别减少了53.86%、44.58%、42.16%和41.16%。与古老亲缘关系相关的基因组近亲繁殖水平（ > 5 Mb）在自由邦最高（0.08 ± 0.09），在东开普省（EC）最低（0.02 ± 0.02）。仅在自由邦（ = 37）、豪登省（ = 42）和西北省（ = 2）种群中鉴定出总共871个ROH岛区域，其中包括重要的环境适应和耐热性基因，如 和 （出现在超过20%的样本中）。各群体中ROH的平均长度为7.76 Mb，范围从夸祖鲁 - 纳塔尔省（KZN）的1.61 Mb到98.05 Mb（豪登省和西北省）。根据大小分布的ROH表明，与其他类别相比，检测到的大多数ROH（ = 1949）长度大于5 Mb。假设两个假设的祖先种群，揭示了来自夸祖鲁 - 纳塔尔省和林波波省的种群，支持主成分1。夸祖鲁 - 纳塔尔省和林波波省的基因组有共同起源，但有来自东开普省和西北省种群的大量混合。研究结果表明，当使用全基因组单核苷酸多态性（SNP）标记时，在近期和古代事件中，本土山羊群体中高 和纯合性的出现因品种而异。Illumina山羊SNP50K芯片的使用表明，本土山羊群体存在从南非北部（林波波省）到夸祖鲁 - 纳塔尔省东部地区的迁移路线，证实了它们的历史相关性，并且与班图民族的迁移时期相吻合。
