Stronen Astrid V, Pertoldi Cino, Iacolina Laura, Kadarmideen Haja N, Kristensen Torsten N
Section of Biology and Environmental Science, Department of Chemistry and Bioscience Aalborg University Aalborg Denmark.
Department of Biology, Biotechnical Faculty University of Ljubljana Ljubljana Slovenia.
Evol Appl. 2019 Mar 12;12(6):1096-1113. doi: 10.1111/eva.12783. eCollection 2019 Jun.
Native domestic breeds represent important cultural heritage and genetic diversity relevant for production traits, environmental adaptation and food security. However, risks associated with low effective population size, such as inbreeding and genetic drift, have elevated concerns over whether unique within-breed lineages should be kept separate or managed as one population. As a conservation genomic case study of the genetic diversity represented by native breeds, we examined native and commercial cattle () breeds including the threatened Danish Jutland cattle. We examined population structure and genetic diversity within breeds and lineages genotyped across 770K single nucleotide polymorphism loci to determine (a) the amount and distribution of genetic diversity in native breeds, and (b) the role of genetic drift versus selection. We further investigated the presence of outlier loci to detect (c) signatures of environmental selection in native versus commercial breeds, and (d) native breed adaptation to various landscapes. Moreover, we included older cryopreserved samples to determine (e) whether cryopreservation allows (re)introduction of original genetic diversity. We investigated a final set of 195 individuals and 677K autosomal loci for genetic diversity within and among breeds, examined population structure with principal component analyses and a maximum-likelihood approach and searched for outlier loci suggesting artificial or natural selection. Our findings demonstrate the potential of genomics for identifying the uniqueness of native domestic breeds, and for maintaining their genetic diversity and long-term evolutionary potential through conservation plans balancing inbreeding with carefully designed outcrossing. One promising opportunity is the use of cryopreserved samples, which can provide important genetic diversity for populations with few individuals, while helping to preserve their traditional genetic characteristics. Outlier tests for native versus commercial breeds identified genes associated with climate adaptation, immunity and metabolism, and native breeds may carry genetic variation important for animal health and robustness in a changing climate.
本土家养品种代表了重要的文化遗产以及与生产性状、环境适应和粮食安全相关的遗传多样性。然而，与有效种群规模较小相关的风险，如近亲繁殖和遗传漂变，引发了人们对于独特的品种内谱系应分开保存还是作为一个种群进行管理的更多关注。作为对本土品种所代表的遗传多样性的保护基因组学案例研究，我们考察了本土和商业牛（）品种，包括濒危的丹麦日德兰牛。我们在跨越77万个单核苷酸多态性位点进行基因分型的品种和谱系内研究了种群结构和遗传多样性，以确定：（a）本土品种中遗传多样性的数量和分布；（b）遗传漂变与选择的作用。我们进一步研究了异常位点的存在情况，以检测：（c）本土品种与商业品种中环境选择的特征；（d）本土品种对各种景观的适应性。此外，我们纳入了保存时间较长且经过冷冻保存的样本，以确定：（e）冷冻保存是否允许（重新）引入原始遗传多样性。我们研究了195个个体和67.7万个常染色体位点的最终数据集，以了解品种内和品种间的遗传多样性，通过主成分分析和最大似然法研究种群结构，并寻找表明人工选择或自然选择的异常位点。我们的研究结果表明，基因组学在识别本土家养品种的独特性、通过平衡近亲繁殖与精心设计的远交的保护计划来维持其遗传多样性和长期进化潜力方面具有潜力。一个有前景的机会是使用冷冻保存的样本，这些样本可以为个体数量较少的种群提供重要的遗传多样性，同时有助于保留其传统遗传特征。对本土品种与商业品种的异常位点测试确定了与气候适应、免疫和代谢相关的基因，本土品种可能携带在气候变化中对动物健康和强健性很重要的遗传变异。
