Comprehensive Genomic Analysis and Selection Signature Detection in Endangered Beigang Pigs Whole-Genome sequencing Data. And this is the Dataset for research.

The Beigang pig, identified as one of the endangered breeds during Chinese indigenous pigs genetic resource survey, is notable for their remarkable roughage tolerance and high reproductive capacity, according to historical records. Morphologically, Beigang pig shares similarities with most indigenous pigs in Eastern China, particularly their large ears, which serves as a valuable reference for research the genetic mechanisms underlying large ears in pigs. However, there is currently a lack of clear understanding regarding the genetic structure and inbreeding levels of the Beigang pig population. This study utilized whole-genome sequencing data from 145 Beigang pigs and integrated genetic information from commercial pigs and indigenous pigs in Eastern China to conduct an comprehensive analysis of the Beigang pig’s genetic structure. Two selection signal detection methods, Runs of Homozygosity (ROH) and Fixation Index (FST), were employed to explores the differences in genome between Beigang pig and other pigs. Additionally, FarmGtex gene expression prediction were used to uncover the genetic mechanisms controlling ear size in Beigang pigs. The results indicated that the Beigang pig holds a unique status among Chinese indigenous pigs, exhibiting a high degree of genetic diversity and a low level of inbreeding within its population. Furthermore, this research identified five homozygous variant sites in the WIF1 gene as important candidate loci potentially influencing ear size in Beigang pigs.

据历史记载，北港猪是中国地方猪遗传资源调查中认定的濒危猪种之一，以极强的粗饲料耐受性和高繁殖性能著称。形态学上，北港猪与中国东部多数地方猪种具有相似特征，尤以大耳朵为典型，这为解析猪大耳朵性状的遗传机制提供了重要参考。然而，目前学界对北港猪种群的遗传结构及近交程度尚缺乏清晰认知。本研究利用145头北港猪的全基因组测序数据，整合商业猪种与中国东部地方猪种的遗传信息，对北港猪的遗传结构开展全面分析。本研究采用两种选择信号检测方法：纯合子片段（Runs of Homozygosity, ROH）与固定指数（Fixation Index, FST），解析北港猪与其他猪种的基因组差异。此外，本研究借助FarmGtex基因表达预测工具，揭示调控北港猪耳大小的遗传机制。研究结果显示，北港猪在中国地方猪种中具有独特地位，其种群遗传多样性较高且近交程度较低。此外，本研究在WIF1基因中筛选出5个纯合变异位点，这些位点可作为调控北港猪耳大小的潜在重要候选位点。

搜集汇总

背景与挑战

背景概述

该数据集包含145头濒危北港猪的全基因组测序数据，用于研究其遗传结构和选择信号特征，特别是发现了与耳型大小相关的WIF1基因候选位点。研究结果表明北港猪在中国本土猪种中具有独特的遗传多样性和低近交水平。