Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations.

中文翻译：

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意大利山羊品种的纯合子运行：低投入系统中管理实践的影响

气候和农业系统，其中一些被认为是低投入农业系统，意大利北部和南部的山羊种群之间存在差异，并导致了不同的管理实践。这些过程在近亲繁殖和选择区域方面影响了基因组的形成，并导致了北方和南方种群之间的差异。近交和选择特征都可以通过对纯合子运行 (ROH) 的分析来确定，这提供了有用的信息来帮助不同农村地区管理该物种。我们分析了来自意大利山羊联盟 2 数据集的 902 只山羊的 ROH 分布和近亲繁殖 (FROH)。我们评估了来自意大利北部 (NRD) 和中南部 (CSD) 的山羊品种在个体 ROH 数量和长度方面的差异。然后，我们使用三种方法确定了区分这两组的选择特征：ROH、ΔROH 和平均 FST。ROH 分析表明，一些意大利山羊品种的近亲繁殖系数较低，这归因于它们的管理和历史。ROH 在经历非最佳管理或种群规模较小的品种中更长。在几个小品种中，ROH 长度等级是平衡的，反映了更准确的交配计划。NRD 和 CSD 群体之间气候和管理的差异导致了不同的 ROH 长度和数量：在孤立山谷中繁殖的 NRD 种群呈现出更多和更短的 ROH 段，而 CSD 种群具有更少和更长的 ROH，这可能是因为它们在水平迁移实践中经历了更多的混合事件，然后是最近的标准化。我们在 NRD 组中与生育相关的 11 号染色体上的选择特征中确定了 4 个基因，在 CSD 组中与 5 号和 6 号染色体上的 23 个基因有关。最后，我们在 12 号染色体上确定了 17 个基因，这些基因与两组中的环境适应和体型大小相关，具有高纯合性。这些结果显示了不同的管理实践如何影响两个意大利山羊群体的基因组近亲繁殖水平，并且可能有助于在低投入系统中进行管理，同时保护小种群的多样性。我们在 NRD 组中与生育相关的 11 号染色体上的选择特征中确定了 4 个基因，在 CSD 组中与 5 号和 6 号染色体上的 23 个基因有关。最后，我们在 12 号染色体上确定了 17 个基因，这些基因与两组中的环境适应和体型大小相关，具有高纯合性。这些结果显示了不同的管理实践如何影响两个意大利山羊群体的基因组近亲繁殖水平，并且可能有助于在低投入系统中进行管理，同时保护小种群的多样性。我们在 NRD 组中与生育相关的 11 号染色体上的选择特征中确定了 4 个基因，在 CSD 组中与 5 号和 6 号染色体上的 23 个基因有关。最后，我们在 12 号染色体上确定了 17 个基因，这些基因与两组中的环境适应和体型大小相关，具有高纯合性。这些结果显示了不同的管理实践如何影响两个意大利山羊群体的基因组近亲繁殖水平，并且可能有助于在低投入系统中进行管理，同时保护小种群的多样性。