Shin Donghyun, Won Kyung-Hye, Song Ki-Duk
Department of Animal Biotechnology, Chonbuk National University, Jeonju 54896, Korea.
The Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju 54896, Korea.
Asian-Australas J Anim Sci. 2018 Dec;31(12):1980-1990. doi: 10.5713/ajas.18.0122. Epub 2018 May 31.
The aim of this study was to discover the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) that were found in selective sweep regions of the Landrace genome.
Whole-genome re-sequencing data were obtained from 40 pigs, including 14 Landrace, 16 Yorkshire, and 10 wild boars, which were generated with the Illumina HiSeq 2000 platform. The nsSNPs in the selective sweep regions of the Landrace genome were identified, and the impacts of these variations on protein function were predicted to reveal their potential association with traits of the Landrace breed, such as reproductive capacity.
Total of 53,998 nsSNPs in the mapped regions of pigs were identified, and among them, 345 nsSNPs were found in the selective sweep regions of the Landrace genome which were reported previously. The genes featuring these nsSNPs fell into various functional categories, such as reproductive capacity or growth and development during the perinatal period. The impacts of amino acid sequence changes by nsSNPs on protein function were predicted using two in silico SNP prediction algorithms, i.e., sorting intolerant from tolerant and polymorphism phenotyping v2, to reveal their potential roles in biological processes that might be associated with the reproductive capacity of the Landrace breed.
The findings elucidated the domestication history of the Landrace breed and illustrated how Landrace domestication led to patterns of genetic variation related to superior reproductive capacity. Our novel findings will help understand the process of Landrace domestication at the genome level and provide SNPs that are informative for breeding.
本研究旨在发现长白猪基因组选择清除区域中非同义单核苷酸多态性（nsSNPs）的功能影响。
从40头猪中获取全基因组重测序数据，包括14头长白猪、16头大白猪和10头野猪，这些数据是使用Illumina HiSeq 2000平台生成的。鉴定长白猪基因组选择清除区域中的nsSNPs，并预测这些变异对蛋白质功能的影响，以揭示它们与长白猪品种性状（如繁殖能力）的潜在关联。
在猪的映射区域共鉴定出53,998个nsSNPs，其中345个nsSNPs存在于先前报道的长白猪基因组选择清除区域中。具有这些nsSNPs的基因属于各种功能类别，如繁殖能力或围产期的生长发育。使用两种计算机模拟SNP预测算法，即从耐受中筛选不耐受和多态性表型分析v2，预测nsSNPs引起的氨基酸序列变化对蛋白质功能的影响，以揭示它们在可能与长白猪品种繁殖能力相关的生物学过程中的潜在作用。
这些发现阐明了长白猪品种的驯化历史，并说明了长白猪驯化如何导致与优良繁殖能力相关的遗传变异模式。我们的新发现将有助于在基因组水平上理解长白猪的驯化过程，并提供对育种有参考价值的SNPs。
