使用高密度SNP芯片评估的欧洲本地猪品种的基因组多样性，连锁不平衡和选择特征。,Scientific Reports

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使用高密度SNP芯片评估的欧洲本地猪品种的基因组多样性，连锁不平衡和选择特征。
Scientific Reports ( IF 3.8 ) Pub Date : 2019-09-19 , DOI: 10.1038/s41598-019-49830-6
M Muñoz ₁ , R Bozzi ₂ , J García-Casco ₁ , Y Núñez ₁ , A Ribani ₃ , O Franci ₂ , F García ₁ , M Škrlep ₄ , G Schiavo ₃ , S Bovo ₃ , V J Utzeri ₃ , R Charneca ₅ , J M Martins ₅ , R Quintanilla ₆ , J Tibau ₆ , V Margeta ₇ , I Djurkin-Kušec ₇ , M J Mercat ₈ , J Riquet ₉ , J Estellé ₁₀ , C Zimmer ₁₁ , V Razmaite ₁₂ , J P Araujo ₁₃ , Č Radović ₁₄ , R Savić ₁₅ , D Karolyi ₁₆ , M Gallo ₁₇ , M Čandek-Potokar ₄ , A I Fernández ₁ , L Fontanesi ₃ , C Óvilo ₁

Affiliation

Departamento Mejora Genética Animal, INIA, Madrid, Spain.
DAGRI, Animal Science Section, Università degli Studi di Firenze, Firenze, Italy.
Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy.
Kmetijski inštitut Slovenije, Hacquetova ulica 17, SI-1000, Ljubljana, Slovenia.
Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal.
IRTA, Programa de Genética y Mejora Animal, Barcelona, Spain.
Faculty of Agrobiotechnical Sciences Osijek, University of Osijek, Osijek, Croatia.
IFIP - Institut du Porc, Le Rheu, France.
INRA, Génétique Physiologie et Système d'Elevage, Castanet-Tolosan, France.
GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Wolpertshausen, Germany.
Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, Lithuania.
Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Ponte de Lima, Portugal.
Institute for Animal Husbandry-Pig Research Department, Autoput for Zagreb 16, 11080, Belgrade-Zemun, Serbia.
University of Belgrade, Faculty of agriculture, Nemanjina 6, 11080, Belgrade-Zemun, Serbia.
Department of Animal Science, University of Zagreb, Faculty of Agriculture, Zagreb, Croatia.
Associazione Nazionale Allevatori Suini (ANAS), Roma, Italy.

本地品种的遗传特征对于保持其基因组变异性，推进保护政策并促进其推广和可持续性至关重要。使用高密度SNP芯片评估了20个欧洲本地猪品种和少量西班牙野生猪的基因组多样性。使用GeneSeek Genomic Profiler（GGP）70 K HD猪基因分型芯片对总共992个DNA样品进行了分析。基因型数据用于计算遗传多样性，种群分化和结构，遗传距离，连锁不平衡和有效种群大小。我们的结果指出了几种变种，例如Turopolje，Apulo Calabrese，Casertana，Mora Romagnola和立陶宛本土花le，它们的遗传多样性最低，杂合度低且有效种群很小，表明需要加强保护战略。主成分分析表明，同一品种的个体聚集，很少有其他品种与其他品种明显隔离。几个品种部分重叠，表明遗传接近，在伊比利亚和阿连特雅纳品种中尤为明显。西班牙野猪与其他西方种群之间的关系也很狭窄，这与野生动物和家养动物之间的经常性混杂相一致。我们还基于FST离群值测试在整个选择范围内的基因组中搜索了基因座。在潜在的选定基因组区域中检测到了可能是适应特定环境和生产系统以及表型性状差异的潜在候选基因。主成分分析表明，同一品种的个体聚集，很少有其他品种与其他品种明显隔离。几个品种部分重叠，表明遗传接近，在伊比利亚和阿连特雅纳品种中尤为明显。西班牙野猪与其他西方种群之间的关系也很狭窄，这与野生动物和家养动物之间的经常性混杂相一致。我们还基于FST离群值测试在整个选择范围内的基因组中搜索了基因座。在潜在的选定基因组区域中检测到了可能是适应特定环境和生产系统以及表型性状差异的潜在候选基因。主成分分析表明，同一品种的个体聚集，很少有其他品种与其他品种明显隔离。几个品种部分重叠，表明遗传接近，在伊比利亚和阿连特雅纳品种中尤为明显。西班牙野猪与其他西方种群之间的关系也很狭窄，这与野生动物和家养动物之间的经常性混杂相一致。我们还基于FST离群值测试在整个选择范围内的基因组中搜索了基因座。在潜在的选定基因组区域中检测到了可能是适应特定环境和生产系统以及表型性状差异的潜在候选基因。几个品种部分重叠，表明遗传接近，在伊比利亚和阿连特雅纳品种中尤为明显。西班牙野猪与其他西方种群之间的关系也很狭窄，这与野生动物和家养动物之间的经常性混杂相一致。我们还基于FST离群值测试在整个选择范围内的基因组中搜索了基因座。在潜在的选定基因组区域中检测到了可能是适应特定环境和生产系统以及表型性状差异的潜在候选基因。几个品种部分重叠，表明遗传接近，在伊比利亚和阿连特雅纳品种中尤为明显。西班牙野猪与其他西方种群之间的关系也很狭窄，这与野生动物和家养动物之间的经常性混杂相一致。我们还基于FST离群值测试在整个选择范围内的基因组中搜索了基因座。在潜在的选定基因组区域中检测到了可能是适应特定环境和生产系统以及表型性状差异的潜在候选基因。与野生动物和家养动物之间的经常性混和相一致。我们还基于FST离群值测试在整个选择范围内的基因组中搜索了基因座。在潜在的选定基因组区域中检测到了可能是适应特定环境和生产系统以及表型性状差异的潜在候选基因。与野生动物和家养动物之间的反复混合相一致。我们还基于FST离群值测试在整个选择范围内的基因组中搜索了基因座。在潜在的选定基因组区域中检测到了可能是适应特定环境和生产系统以及表型性状差异的潜在候选基因。

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Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip.

Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.

更新日期：2019-09-19

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