Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Milan, Italy.
Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy.
Genet Sel Evol. 2021 Dec 11;53(1):92. doi: 10.1186/s12711-021-00685-4.
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 (F) 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 F. 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.
意大利北部和南部的山羊群体所处的气候和农业系统（其中有一些被认为是低投入的农业系统）有所不同，这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，导致了北部和南部群体之间的差异。通过分析纯合区域（ROH）可以确定近亲繁殖和选择的特征，这为管理不同农村地区的该物种提供了有用的信息。
我们分析了意大利山羊联盟 2 数据集的 902 只山羊的 ROH 分布和近亲繁殖系数（F）。我们评估了意大利北部（NRD）和中南部（CSD）地区山羊品种之间个体 ROH 数量和长度的差异。然后，我们使用三种方法（ROH、ΔROH 和平均 F）来识别区分这两个群体的选择特征。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。在非最佳管理或种群规模较小的品种中，ROH 更长。在几个小品种中，ROH 长度类别是平衡的，这反映了更准确的交配计划。NRD 和 CSD 群体之间的气候和管理差异导致了不同的 ROH 长度和数量：在孤立山谷中饲养的 NRD 群体呈现出更多和更短的 ROH 片段，而 CSD 群体则具有更少和更长的 ROH，这可能是因为它们在水平迁徙实践中经历了更多的混合事件，随后进行了更近期的标准化。我们在 NRD 群体的 11 号染色体上确定了与繁殖有关的四个选择特征中的基因，在 CSD 群体的 5 号和 6 号染色体上确定了与生长有关的 23 个基因。最后，我们在 12 号染色体上确定了 17 个与环境适应和体型有关的基因，在这两个群体中都存在高度的纯合性。
这些结果表明，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，并可能有助于在低投入系统中协助管理，同时保护小种群的多样性。
