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Abstract：
BACKGROUND: Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns.
RESULTS: We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow.
CONCLUSIONS: Our results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.
RESULTS: We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow.
CONCLUSIONS: Our results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.
摘要：
背景：伊比利亚原始品种在非常有限的地理空间内表现出明显的表型多样性。虽然大多数商业牛的基因组数据正在积累，这些原始品种仍然缺乏。全基因组数据是了解历史品种形成的后果以及早期混合事件在观察到的多样性模式中的假定作用的关键。
结果：我们对属于八个伊比利亚本地品种的48个基因组进行了测序，发现单个品种在遗传上非常不同，FST值在4％至16％之间，并且核苷酸多样性水平相似或大于欧洲同行，即泽西和荷斯坦。所有八个品种都显示出来自非洲牛磺酸牛的显着基因流或混合，并包括来自多个来源的mtDNA和Y染色体单倍型。此外，在所有分析的牛磺酸品种中，我们检测到X染色体相对于常染色体的分化非常低，可能反映男性偏向的基因流。
结论：我们的结果表明，混合的整体复杂历史导致了具有看似有限的地理范围的品种的基因组多样性出乎意料的高水平，这些品种远离牛磺酸牛的主要驯化中心在近东。这可能是地中海国家贸易传统和育种实践相结合的结果。我们还发现，在所有研究的牛磺酸和野马品种中，常染色体与性染色体的分化水平可能受到与雄性偏向基因流相关的广泛育种实践的影响。
结果：我们对属于八个伊比利亚本地品种的48个基因组进行了测序，发现单个品种在遗传上非常不同，FST值在4％至16％之间，并且核苷酸多样性水平相似或大于欧洲同行，即泽西和荷斯坦。所有八个品种都显示出来自非洲牛磺酸牛的显着基因流或混合，并包括来自多个来源的mtDNA和Y染色体单倍型。此外，在所有分析的牛磺酸品种中，我们检测到X染色体相对于常染色体的分化非常低，可能反映男性偏向的基因流。
结论：我们的结果表明，混合的整体复杂历史导致了具有看似有限的地理范围的品种的基因组多样性出乎意料的高水平，这些品种远离牛磺酸牛的主要驯化中心在近东。这可能是地中海国家贸易传统和育种实践相结合的结果。我们还发现，在所有研究的牛磺酸和野马品种中，常染色体与性染色体的分化水平可能受到与雄性偏向基因流相关的广泛育种实践的影响。
