Numerous genomic scans for positive selection have been performed in livestock species within the last decade, but often a detailed characterization of the detected regions (gene or trait under selection, timing of selection events) is lacking. Cryopreserved resources stored in reproductive or DNA gene banks offer a great opportunity to improve this characterization by providing direct access to recent allele frequency dynamics, thereby differentiating between signatures from recent breeding objectives and those related to more ancient selection constraints. Improved characterization can also be achieved by using next-generation sequencing data, which helps narrowing the size of the detected regions while reducing the number of associated candidate genes. We estimated genetic diversity and detected signatures of recent selection in French Large White pigs by sequencing the genomes of 36 animals from three distinct cryopreserved samples: two recent samples from dam (LWD) and sire (LWS) lines, which had diverged from 1995 and were selected under partly different objectives, and an older sample from 1977 prior to the divergence. French LWD and LWS lines have lost approximately 5% of the SNPs that segregated in the 1977 ancestral population. Thirty-eight genomic regions under recent selection were detected in these lines and the corresponding selection events were further classified as convergent between lines (18 regions), divergent between lines (10 regions), specific to the dam line (6 regions) or specific to the sire line (4 regions). Several biological functions were found to be significantly enriched among the genes included in these regions: body size, body weight and growth regardless of the category, early life survival and calcium metabolism more specifically in the signatures in the dam line and lipid and glycogen metabolism more specifically in the signatures in the sire line. Recent selection on IGF2 was confirmed and several other regions were linked to a single candidate gene (ARHGAP10, BMPR1B, GNA14, KATNA1, LPIN1, PKP1, PTH, SEMA3E or ZC3HAV1, among others). These results illustrate that sequencing the genome of animals at several recent time points generates considerable insight into the traits, genes and variants under recent selection in a population. This approach could be applied to other livestock populations, e.g. by exploiting the rich biological resources stored in cryobanks.

中文翻译：

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在两个不同的采样时间对来自法国大白猪的冷冻资源进行全基因组测序，揭示了母系和父系之间趋同和趋异选择的强烈特征

在过去十年中，已经对牲畜物种进行了大量用于阳性选择的基因组扫描，但通常缺乏对检测到的区域（选择中的基因或性状、选择事件的时间）的详细描述。储存在生殖或 DNA 基因库中的低温保存资源提供了一个很好的机会，通过提供对最近等位基因频率动态的直接访问来改善这种特征，从而区分最近育种目标的特征和与更古老的选择限制相关的特征。还可以通过使用下一代测序数据来改进表征，这有助于缩小检测区域的大小，同时减少相关候选基因的数量。我们通过对来自三个不同冷冻保存样本的 36 只动物的基因组进行测序，估计了法国大白猪的遗传多样性并检测了最近选择的特征：两个来自大坝 (LWD) 和父系 (LWS) 品系的最近样本，它们从 1995 年开始分化，在部分不同的目标下选择的，以及在分歧之前的 1977 年的较旧样本。法国 LWD 和 LWS 品系丢失了大约 5% 的 SNP，这些 SNP 在 1977 年的祖先种群中分离。在这些品系中检测到最近选择的 38 个基因组区域，相应的选择事件进一步分类为品系之间会聚（18 个区域）、品系之间发散（10 个区域）、大坝品系特有（6 个区域）或特定于父系（4 个区域）。发现这些区域中包含的基因显着丰富了几种生物学功能：体型、体重和生长（不分类别）、早年存活和钙代谢（更具体地在母系特征中）以及脂质和糖原代谢更多特别是在父系的签名中。最近对 IGF2 的选择得到确认，其他几个区域与单个候选基因（ARHGAP10、BMPR1B、GNA14、KATNA1、LPIN1、PKP1、PTH、SEMA3E 或 ZC3HAV1 等）相关联。这些结果表明，在最近几个时间点对动物的基因组进行测序可以对种群中最近选择的性状、基因和变异产生相当大的洞察力。这种方法可以应用于其他牲畜种群，例如