Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy.
Dipartimento di Scienze Veterinarie, Università di Pisa, Pisa, Italy.
PLoS One. 2021 Jan 15;16(1):e0232436. doi: 10.1371/journal.pone.0232436. eCollection 2021.
The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (25 goats/breed), whose genotypes were available from the AdaptMap project [Argentata (ARG), Bionda dell'Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of breed traceability via discriminant analysis on principal components (DAPC) based on cross-validation. ROH analyses was used to assess the genetic diversity of GRF, while admixture and DAPC to evaluate its relationship to the other breeds. For GRF, common ROH (more than 45% in GRF samples) was detected on CHR 12 at, roughly 50.25-50.94Mbp (ARS1 assembly), which spans the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area of common ROH was also present in DIT, while a broader region (49.25-51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis revealed a small region of common ancestry from GRF shared by BIO, VSS, ARG and CCG breeds. The DAPC model yielded 100% assignment success for GRF. Overall, our results support the identification of GRF as a distinct native Italian goat breed. This work can contribute to planning conservation programmes to save GRF from extinction and will improve the understanding of the socio-agro-economic factors related with the farming of GRF.
本研究旨在调查加福尼亚诺（GRF）山羊的遗传多样性，该品种目前正面临灭绝的风险。为此，对 48 只 GRF 山羊进行了 Illumina CaprineSNP50 BeadChip 基因分型，并与来自 AdaptMap 项目的 214 只属于其他 9 个意大利品种的山羊（每个品种约 25 只）进行了分析[Argentata (ARG)、Bionda dell'Adamello (BIO)、Ciociara Grigia (CCG)、Di Teramo (DIT)、Garganica (GAR)、Girgentana (GGT)、Orobica (ORO)、Valdostana (VAL) 和 Valpassiria (VSS)]。在以下方面进行了比较分析：i) 纯合子片段（ROH），ii) 混合祖先，iii) 通过基于交叉验证的主成分判别分析（DAPC）进行品种溯源的准确性。ROH 分析用于评估 GRF 的遗传多样性，而混合和 DAPC 用于评估其与其他品种的关系。对于 GRF，在 CHR 12 上检测到共同的 ROH（在 GRF 样本中超过 45%），大致在 50.25-50.94Mbp（ARS1 组装），跨越着丝粒蛋白 J（centromere protein）和白细胞介素 17D（interleukin 17D）基因。DIT 中也存在相同的共同 ROH 区域，而 ARG、CCG 和 GGT 之间则共享一个更广泛的区域（~49.25-51.94Mbp）。混合分析显示，BIO、VSS、ARG 和 CCG 品种与 GRF 共有一小部分共同祖先。DAPC 模型对 GRF 的分配成功率达到 100%。总的来说，我们的结果支持将 GRF 鉴定为一个独特的意大利本土山羊品种。这项工作有助于制定保护计划，以防止 GRF 灭绝，并将提高对与 GRF 养殖相关的社会经济因素的理解。
