全基因组选择信号解析剑白香猪和从江香猪的遗传差异

Deciphering Genome-wide Selection Signals Reveals Genetic Differences between Jianbai and Congjiang Xiang Pigs

旨在通过全基因组选择信号分析揭示剑白香猪和从江香猪的遗传差异,提高对从江香猪和剑白香猪种群的保护状况、遗传多样性、群体结构和和适应性进化的认识。本研究随机选取2岁龄从江香猪和剑白香猪各5头,并分为两组。通过全基因组重测序对从江香猪和剑白香猪测序,将测序数据利用bwa软件比对到猪参考基因组Sscrofa 11.1上,随后使用GATK软件进行变异检测和SNP、INDEL过滤提取。同时,利用Plink和SNeP软件进行群体遗传多样性分析,包括群体有效大小、多态位点比例、观测杂合度、期望杂合度。使用vcftools软件分析群体选择信号,并通过KEGG和GO分析受选择区域基因。经过SNP和INDEL分析,发现从江香猪和剑白香猪群体共有的SNPs位点数为16158002个,从江香猪特有的为6863992个,剑白香猪特有的为4275660个;共有的INDEls位点数为3275375个,从江香猪特有的为1674081个,剑白香猪特有的为1114248个。从采样起算,从江香猪和剑白香猪的群体在13代前的有效大小均为18头。其中,从江香猪的多态性位点比例更高,达到了0.8757,而二者群体的观测杂合度均高于期望杂合度。剑白香猪和从江香猪的核苷酸多样性均小于0.5%,群体内选择检验Tajima’s D值均大于0,ROD值为0.5531,Fst值为0.7362。KEGG和GO富集分析表明,剑白香猪和从江香猪的遗传差异涉及多种通路和基因功能。包括涉及轴突引导、ECM与受体的相互作用、局部粘附、PI3K-Akt信号通路、硫辛酸代谢、cGMP-PKG信号通路、MAPK信号传导途径、核苷酸切除修复、阿佩林信号通路、心律失常性右室心肌病等通路。剑白香猪和从江香猪群体之间存在一定的群体多态性损失,群体分歧度较高,两亚群间存在明显的种群分化,并且二者基因组内存在大量的中等频率等位基因,需要提高从江香猪和剑白香猪群体内的遗传多样性,减少外来血缘引入导致纯种度降低的风险。

The purpose was to unveil the genetic disparities between the Jianbai and Congjiang Xiang pigs breeds,enhance the understanding of their conservation status,genetic diversity,population structure,and adaptive evolution through whole-genome selection signal analysis.The 2-year-old Congjiang and Jianbai Xiang pigs were randomly selected and divided into two groups of 5 pigs each.Whole-genome resequencing was performed on Jianbai and Congjiang Xiang pigs,and the sequencing data was aligned to the pig reference genome Sscrofa 11.1 using the bwa software.Subsequently,the GATK software was used for variant detection and filtering of SNPs and INDELs.Additionally,population genetic diversity analysis,including effective population size,proportion of polymorphic loci,observed heterozygosity,and expected heterozygosity,was carried out using Plink and SNeP software.The population selection signals were analyzed using the vcftools software,and the selected genomic regions were subjected to KEGG and GO pathway analyses.After SNP and INDEL analysis,it was found that there were 16158002 common SNPs in the populations of Jianbai and Congjiang Xiang pigs,with 6863992 SNPs unique to Congjiang and 4275660 unique to Jianbai.The common INDELs were 3275375,with 1674081 INDELs unique to Congjiang and 1114248 unique to Jianbai.Starting from the sampling time point,the effective population size of both Congjiang and Jianxiang pig populations could be traced back to 18 individuals 13 generations ago.The Congjiang breed displayed a higher proportion of polymorphic loci,with a value of 0.8757,whereas both populations had observed heterozygosity values exceeding the expected heterozygosity.Nucleotide diversity was less than 0.5%for both breeds,and Tajima’s D was greater than 0,with ROD values of 0.5531 and Fst values of 0.7362.KEGG and GO enrichment analyses showed that the genetic differences between Jianbai and Congjiang Xiang pigs involved multiple pathways and gene functions,including axon guidance,ECM-receptor interaction,focal adhesion,PI3K-Akt signaling pathway,lipoic acid metabolism,cGMP-PKG signaling pathway,MAPK signaling pathway,nucleotide excision repair,aspirin signaling pathway,and arrhythmogenic right ventricular cardiomyopathy.There are a certain loss of population polymorphism and a high degree of population divergence between the Jianbai and Congjiang pig populations.There is clear population differentiation between the two breeds,and both genomes exhibit a substantial number of alleles at intermediate frequencies.It is necessary to enhance the genetic diversity within the Congjiang and Jianbai Xiang pig populations and reduce the risk of decreased purity due to the introduction of foreign lineages.