苏姜猪mtDNA D-loop序列的遗传多样性分析

doi:10.16431/j.cnki.1671-7236.2023.04.019

摘要/Abstract

摘要： 【目的】通过对苏姜猪线粒体DNA (mtDNA) D-loop高变区Ⅰ的序列扩增测序,探究苏姜猪种群的种质资源特性和遗传多样性。【方法】采集苏姜猪核心群100头经产母猪耳组织,提取DNA后扩增苏姜猪核心群母猪mtDNA D-loop高变区Ⅰ的基因片段并测序,运用NCBI在线BLAST对测序序列与参考序列进行比对、校正并寻找同源序列,确定mtDNA D-loop高变区Ⅰ序列的长度和位置;使用DnaSP v.5.10.1软件统计获得群体中核苷酸多态位点和变异位点数量,分析单倍型多样度(Hd)、核苷酸多样性(Pi)、平均核苷酸差异度(K)等参数;使用Mega 7.0软件对不同单倍型进行基于Kimura’s 2-prarmetermodel的遗传距离计算,采用邻接法(Neighbor-Joining,NJ)对苏姜猪的4个单倍型、17个中国地方猪种、欧洲家猪(登录号:AF034253.1)的mtDNA D-loop高变区Ⅰ序列构建系统发育树。【结果】对100头苏姜猪的mtDNA D-loop序列高变区Ⅰ进行扩增测序,获得长度为429 bp的有效序列,获得的序列中,AT含量为63.1%,GC含量为36.9%;中性检验Tajima’s D值为-1.80517(P＜0.05),证实苏姜猪种群显著性偏离中性检验;被测序列中检测到19个变异位点,定义了4个单倍型,单倍型多样度为0.578,核苷酸多样性为0.0032;种群内4个单倍型之间的平均遗传距离在0.004~0.031之间。系统发育树结果显示,群体分为国内和国外2个类群,苏姜猪4个单倍型都聚集在国内分支上,其中单倍型H2和二花脸猪聚为一类,单倍型H4和姜曲海、皖南花猪等聚为一类。【结论】苏姜猪种群mtDNA D-loop高变区Ⅰ多态位点比例高,单倍型多样度高,核苷酸多样性低;苏姜猪群体内优势单倍型的遗传距离较近,占比较高,反映出苏姜猪群体母系来源较少。

关键词: 苏姜猪; 线粒体DNA D-loop区; 遗传变异; 单倍型多样度; 核苷酸多样性

Abstract: 【Objective】 By obtaining and comparing the partial sequence of mtDNA D-loop hypervariable region Ⅰ of Sujiang pig,the germplasm resource characteristics and genetic diversity of Sujiang pig population were revealed.【Method】 Ear tissues of 100 parturient sows from the core group of Sujiang pigs were collected and DNA were extracted.And gene fragments of mtDNA D-loop hypervariable region Ⅰ of sows in the core group of Sujiang pigs were amplified and sequenced.The NCBI online BLAST was used to compare and calibrate the sequencing and reference sequences,and homologous sequences were found to determine the length and location of the sequence of high variable region Ⅰ of mtDNA D-loop.DnaSP v.5.10.1 software was used to calculate the number of nucleotide polymorphic sites and mutation sites in the population and the haplotype diversity (Hd),nucleotide polymorphism (Pi),average nucleotide difference (K) and other parameters were analyzed.The genetic distance of the sample was calculated based on Kimura’s 2-prarmetermodel using Mega 7.0 software and the genetic distance between different haplotypes of Sujiang pig mtDNA D-loop region sequences were obtained.The phylogenetic tree was constructed by using Neighbor-Joining (NJ) on the mtDNA D-loop hypervariable region Ⅰ sequences of 4 haplotypes of Sujiang pig,17 Chinese pig breeds and European domestic pigs (accession No.:AF034253.1).【Result】 The highly variable region Ⅰ of mtDNA D-loop sequence of 100 Sujiang pigs was amplified and sequenced,and the effective sequence with a length of 429 bp was obtained,in which the content of AT was 63.1%,and the content of GC was 36.9%,neutral test Tajima’s D value was -1.80517 (P＜0.05).It was confirmed that Sujiang pig population significantly deviated from neutral test.A total of 19 mutation sites were detected in the sequencing column,and 4 haplotypes were defined,Hd was 0.578,Pi was 0.0032, and the average genetic distance between the four haplotypes in the population ranged from 0.004 to 0.031.Phylogenetic tree results showed that the joining group were divided into two groups:Domestic and foreign.The four haplotypes of Sujiang pig were clustered in the domestic branch,among which haplotype H2 and Erhuface pig were clustered in the same group,and haplotype H4 was clustered in the same group with Jiangquhai and Wannanhua pig.【Conclusion】 The proportion of polymorphic sites in the high variation region Ⅰ of mtDNA D-loop in Sujiang pig population was high,Hd was high,and Pi was low.The genetic distance of dominant haplotypes in Sujiang pig population was relatively close,and the proportion of dominant haplotypes was high,which reflected that there were fewer maternal sources in Sujiang pig population.

Key words: Sujiang pig; mtDNA D-loop; genetic variation; haplotype diversity; nucleotide diversity

中图分类号:

S828

韩大勇, 周春宝, 倪黎纲, 陈章言, 赵锦明. 苏姜猪mtDNA D-loop序列的遗传多样性分析[J]. 中国畜牧兽医, 2023, 50(4): 1472-1479.

HAN Dayong, ZHOU Chunbao, NI Ligang, CHEN Zhangyan, ZHAO Jinming. Genetic Diversity of mtDNA D-loop Sequence in Sujiang Pig[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1472-1479.

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