Whole genome SNPs discovery in Nero Siciliano pig

Abstract Autochthonous pig breeds represent an important genetic reserve to be utilized mainly for the production of typical products. To explore its genetic variability, here we present for the first time whole genome sequencing data and SNPs discovered in a male domestic Nero Siciliano pig compared to the last pig reference genome Sus scrofa11.1.A total of 346.8 million paired reads were generated by sequencing. After quality control, 99.03% of the reads were mapped to the reference genome, and over 11 million variants were detected.Additionally, we evaluated sequence diversity in 21 fitness-related loci selected based on their biological function and/or their proximity to relevant QTLs. We focused on genes that have been related to environmental adaptation and reproductive traits in previous studies regarding local breeds. A total of 6,747 variants were identified resulting in a rate of 1 variant every ~276 bases. Among these variants 1,132 were novel to the dbSNP151 database. This study represents a first step in the genetic characterization of Nero Siciliano pig and also provides a platform for future comparative studies between this and other swine breeds.摘要 地方猪品种是重要的遗传资源库，主要可用于特色产品的生产。为探究其遗传变异特征，本研究首次公开了一头雄性家养西西里黑猪（Nero Siciliano pig）的全基因组测序数据，以及以最新猪参考基因组Sus scrofa11.1为参照所鉴定得到的单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）。测序共产生3.468亿条双端读段（paired reads），经质量控制后，99.03%的读段可比对至参考基因组，共鉴定得到超过1100万个变异位点。此外，本研究对21个与适应性相关的位点进行了序列多样性分析，这些位点均基于其生物学功能或与相关数量性状位点（Quantitative Trait Locus, QTL）的临近性筛选得到。本研究聚焦于既往针对地方猪品种的研究中与环境适应性及繁殖性状相关的基因，共鉴定得到6747个变异位点，平均每约276个碱基就存在1个变异。其中1132个变异位点为dbSNP151数据库中未收录的新变异。本研究是西西里黑猪遗传特征解析的第一步，同时也为该品种与其他猪品种的后续比较研究提供了研究平台。