运用SNP芯片评估马身猪保种群体的遗传结构

doi:10.11843/j.issn.0366-6964.2021.04.008

摘要/Abstract

摘要： 旨在研究马身猪保种群体的遗传多样性、亲缘关系和家系结构。本研究利用Illumina CAUPorince 50 K SNP芯片检测39头保种马身猪的单核苷酸多态性（single nucleotide polymorphism，SNP）；采用Plink软件计算最小等位基因频率、多态信息含量、观察杂合度和期望杂合度，分析保种群体的遗传多样性；采用Plink软件构建状态同源（identity by state，IBS）距离矩阵和分析连续性纯合片段（runs of homozygosity，ROH），采用Gmatix软件构建G矩阵，分析保种群体的亲缘关系；采用Mega X软件构建群体进化树，分析保种群体的家系结构。结果显示，39头保种马身猪中共检测到43 832个SNPs位点，平均基因型检出率为0.980 1；通过质控的SNPs位点有28 859个，其中72.4%具有多态性，该款SNP芯片适用于分析马身猪的遗传多样性。有效等位基因数为1.563 4，多态信息含量为0.412，最小等位基因频率为0.258，表明马身猪保种群体的遗传多样性比较丰富；平均观察杂合度为0.354 1，平均期望杂合度为0.349 9，说明马身猪保种群体出现了分化；平均IBS遗传距离为0.284 2，其中公猪为0.285 2，IBS距离矩阵和G矩阵结果均表明部分种猪之间存在亲缘关系；ROH共有8 131个，其中46.15%的长度在400～600 Mb之间，平均近交系数为0.237，说明保种群体的近交程度高；群体进化树结果表明，马身猪保种群体来源于3个家系，各家系的个体数量差异明显。马身猪保种群体的遗传多样性较丰富，但近交程度高，家系少，各家系的个体数量差异大，容易引起遗传多样性的丢失，因此，需从原种场引入新的血统，扩大保种群体数量，降低近交系数。

关键词: 马身猪, 保种群体, SNP芯片, 遗传多样性, 亲缘关系, 家系结构

Abstract: The study aimed to explore the genetic diversity, relationship and family structure of Mashen pigs conserved population. Illumina CAUPorince 50 K SNP chip was used to detect the single nucleotide polymorphism (SNP) in 39 Mashen pigs. The minor allele frequency, polymorphism information content, observed heterozygosity and expected heterozygosity were calculated by Plink software to analyze the genetic diversity of conserved population. The identity by state (IBS) distance matrix was constructed and runs of homozygosity (ROH) was analyzed by Plink software. The G matrix was constructed by Gmatix software. IBS, ROH and G matrix were used to analyze the genetic relationship of conserved population. The phylogenetic tree constructed by Mega X software was used to analyze the family structure of conserved population. The result showed that 43 832 SNPs were detected in 39 Mashen pigs, and the average genotype detection rate was 0.980 1. Twenty-eight thousand eight hundred and fifty-nine SNPs met the demand of quality control, and 72.4% of which were polymorphic sites, which indicated that the SNP chip was suitable for analyzing the genetic diversity of Mashen pigs. The effective allele number, polymorphism information content and minor allele frequency were 1.563 4, 0.412, and 0.258, respectively, which indicated that the genetic diversity of Mashen pigs conserved population was abundant. The average observed heterozygosity and expected heterozygosity were 0.354 1 and 0.349 9, which suggested the conserved population of Mashen pigs had differentiated. The IBS genetic distance of 39 Mashen pigs was 0.284 2, and the IBS genetic distance of 20 breeding boars was 0.285 2. The results of IBS distance matrix and G matrix both showed that some breeding pigs had relationship with each other. Eight thousand one hundred and thirty one ROHs were detected in conserved population of Mashen pigs, 46.15% of which were between 400 and 600 Mb in length. The average inbreeding coefficient of conserved population based on ROH was 0.237, which indicated the high degree of inbreeding in conserved population. The result of phylogenetic tree showed that all individuals belonged to 3 families and the number of each family was significantly different. The genetic diversity of conserved population in Mashen pigs is abundant, but the inbreeding coefficient is high, the family of conserved population is few, and the number of individuals in each family varies greatly, which can lead to the loss of genetic diversity. Therefore, importing the new blood from the original conservation farm of Mashen pigs, expanding population size and decreasing inbreeding coefficient are essential ways in the future.

Key words: Mashen pig, conserved population, SNP chip, genetic diversity, relationship, family structure

中图分类号:

S828.2

蔡春波, 张雪莲, 张万峰, 杨阳, 高鹏飞, 郭晓红, 李步高, 曹果清. 运用SNP芯片评估马身猪保种群体的遗传结构[J]. 畜牧兽医学报, 2021, 52(4): 920-931.

CAI Chunbo, ZHANG Xuelian, ZHANG Wanfeng, YANG Yang, GAO Pengfei, GUO Xiaohong, LI Bugao, CAO Guoqing. Evaluation of Genetic Structure in Mashen Pigs Conserved Population Based on SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(4): 920-931.

参考文献 38

[1]	BRAVO S,LARAMA G,QUIÑONES J,et al.Genetic diversity and phylogenetic relationship among Araucana creole sheep and Spanish sheep breeds[J].Small Rumin Res,2019,172:23-30.
[2]	YANG S L,WANG Z G,LIU B,et al.Genetic variation and relationships of eighteen Chinese indigenous pig breeds[J].Genet Sel Evol,2003,35:657.
[3]	XIAN Q,ZHANG Z,SUN H,et al.Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by se-quencing data[J].Anim Genet,2017,48(5):596-599.
[4]	ROHRER G A,FREKING B A,NONNEMAN D.Single nucleotide polymorphisms for pig identification and parentage exclusion[J].Anim Genet,2007,38(3):253-258.
[5]	SILIÓ L,RODRÍGUEZ M C,FERNÁNDEZ A,et al.Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics[J].J Anim Breed Genet,2013,130(5):349-360.
[6]	RAMOS A M,CROOIJMANS R P M A,AFFARA N A,et al.Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing tech-nology[J].PLoS One,2009,4(8):e6524.
[7]	刘冉冉,赵桂苹,文杰.鸡基因组育种和保种用SNP芯片研发及应用[J].中国家禽,2018,40(15):1-6.LIU R R,ZHAO G P,WEN J.Development of genome-wide SNP genotyping arrays for chicken breeding and conservation[J].China Poult,2018,40(15):1-6.(in Chinese)
[8]	LOPES M S,SILVA F F,HARLIZIUS B,et al.Improved estimation of inbreeding and kinship in pigs using optimized SNP panels[J].BMC Genet,2013,14:92.
[9]	王珏,刘成琨,刘德武,等.基于不同密度SNP芯片在杜洛克公猪中的全基因组选择效果分析[J].中国畜牧杂志,2019,55(12):75-79.WANG J,LIU C K,LIU D W,et al.Analysis of genomic selection based on SNP data of various density chips in Duroc male pig population[J].Chinese Journal of Animal Science,2019,55(12):75-79.(in Chinese)
[10]	WANG Z,CHEN Q,YANG Y,et al.Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data[J].Anim Genet,2015,46(6):697-701.
[11]	黄树文,张哲,陈赞谋,等.广东省现有5个地方猪种基于SNP芯片的遗传多样性分析[J].中国畜牧杂志,2018,54(6):33-37.HUANG S W,ZHANG Z,CHEN Z M,et al.Genetic diversity analysis of five cantonese indigenous pigs based on SNP chip[J].Chinese Journal of Animal Science,2018,54(6):33-37.(in Chinese)
[12]	GUO X H,QIN B Y,YANG X F,et al.Comparison of carcass traits,meat quality and expressions of MyHCs in muscles between Mashen and Large White pigs[J].Ital J Anim Sci,2019,18(1):1410-1418.
[13]	王泽艺,石建中,刘郑煜,等.马身猪和大白猪背最长肌Rac1基因发育性表达研究[J].山西农业大学学报:自然科学版,2016,36(11):827-831.WANG Z Y,SHI J Z,LIU Z Y,et al.Developmental expression of Rac1 gene in Longissimus dorsi in Mashen and large white pigs[J].Journal of Shanxi Agricultural University:Natural Science Edition,2016,36(11):827-831.(in Chinese)
[14]	ZHAO Y Y,GAO P F,LI W,et al.Study on the developmental expression of Lbx1 gene in Longissimus dorsi of Mashen and Large White pigs[J].Ital J Anim Sci,2015,14(1):3720.
[15]	张旗,郭晓红,高鹏飞,等.马身猪MEF2A基因4种可变剪接体的克隆和生物信息学分析[J].中国畜牧兽医,2017,44(4):965-972.ZHANG Q,GUO X H,GAO P F,et al.Cloning and bioinformatics analysis of 4 alternative splice variants of MEF2A gene in Mashen pig[J].China Animal Husbandry and Veterinary Medicine,2017,44(4):965-972.(in Chinese)
[16]	GUO X H,LI M,GAO P F,et al.Novel splice isoforms of pig myoneurin and their diverse mRNA expression patterns[J].Asian-Australas J Anim Sci,2018,31(10):1581-1590.
[17]	张雪莲,晋大鹏,吴怡琦,等.猪NR1H3基因可变剪接体的克隆及表达特性研究[J].畜牧兽医学报,2020,51(1):43-54.ZHANG X L,JIN D P,WU Y Q,et al.Molecular cloning of alternative splice variants of NR1H3 gene and their expression patterns in pig[J].Acta Veterinaria et Zootechnica Sinica,2020,51(1):43-54.(in Chinese)
[18]	成志敏,张宁芳,王媛媛,等.基于RNA-Seq技术筛选影响猪肌纤维性状的候选基因[J].畜牧兽医学报,2019,50(5):918-929.CHENG Z M,ZHANG N F,WANG Y Y,et al.Screening of candidate genes for muscle fiber characteristics in pig using RNA-Seq[J].Acta Veterinaria et Zootechnica Sinica,2019,50(5):918-929.(in Chinese)
[19]	GAO P F,GUO X H,DU M,et al.LncRNA profiling of skeletal muscles in Large White pigs and Mashen pigs during development[J].J Anim Sci,2017,95(10):4239-4250.
[20]	郭晓红,郭玉龙,刘亚丹,等.仔猪不同发育阶段结肠微生物菌群特征分析[J].畜牧兽医学报,2019,50(9):1759-1774.GUO X H,GUO Y L,LIU Y D,et al.Characteristics of intestinal microflora of colon at different developmental stages in piglets[J].Acta Veterinaria et Zootechnica Sinica,2019,50(9):1759-1774.(in Chinese)
[21]	WAN Y,WANG F L,YUAN J H,et al.Effects of dietary fat on gut microbiota and faecal metabolites,and their relationship with cardiometabolic risk factors:a 6-month randomised controlled-feeding trial[J].Gut,2019,68(8):1417-1429.
[22]	ZHU J Q,KONG Y,YU J,et al.Consumption of drinking water N-nitrosamines mixture alters gut microbiome and increases the obesity risk in young male rats[J].Environ Pollut,2019,248:388-396.
[23]	曹果清,薛尚君,杨文平,等.山西白猪高产仔母系繁殖性能测定[J].中国畜牧兽医,2009,36(4):111-114.CAO G Q,XUE S J,YANG W P,et al.Study on the reproductive performance of specialized dam line with high farrowing rate of Shanxi White pig[J].China Animal Husbandry and Veterinary Medicine,2009,36(4):111-114.(in Chinese)
[24]	郭晓红,王效京,张敏,等.晋汾白猪繁殖性能的研究[J].山西农业大学学报:自然科学版,2013,33(4):280-283.GUO X H,WANG X J,ZHANG M,et al.Study on the reproductive performance of Jinfen White pig[J].Journal of Shanxi Agricultural University:Natural Science Edition,2013,33(4):280-283.(in Chinese)
[25]	PRAMOD S,KUMARASAMY P,ROSALYN A,et al.Molecular characterization of Vembur sheep (Ovis aries) of south India based on microsatellites[J].Indian J Sci Technol,2009,2(11):55-58.
[26]	FAN B,WANG Z G,LI Y J,et al.Genetic variation analysis within and among Chinese indigenous swine populations using microsatellite markers[J].Anim Genet,2002,33(6):422-427.
[27]	WANG X,CAO H H,GENG S M,et al.Genetic diversity of 10 indigenous pig breeds in China by using microsatellite markers[J].Asian-Australas J Anim Sci,2004,17(9):1219-1222.
[28]	张跟喜,丁馥香,王金玉,等.利用微卫星标记分析边鸡遗传多样性及保种效果[J].农业生物技术学报,2010,18(5):944-950.ZHANG G X,DING F X,WANG J Y,et al.Analysis on genetic diversity and conserved effect of Bian chicken using microsatellite markers[J].Journal of Agricultural Biotechnology,2010,18(5):944-950.(in Chinese)
[29]	HAUSER L,BAIRD M,HILBOM R,et al.An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population[J].Mol Ecol Resour,2011,11(Suppl 1):150-161.
[30]	AI H S,YANG B,LI J,et al.Population history and genomic signatures for high-altitude adaptation in Tibetan pigs[J].BMC Genomics,2014,15:834.
[31]	MUÑOZ M,BOZZI R,GARCÍA-CASCO J,et al.Genomic diversity,linkage disequilibrium and selec-tion signatures in European local pig breeds assessed with a high density SNP chip[J].Sci Rep,2019,9:13546.
[32]	DIAO S Q,HUANG S W,XU Z T,et al.Genetic diversity of indigenous pigs from South China area revealed by SNP array[J].Animals,2019,9(6):361.
[33]	刘彬,沈林園,陈映,等.基于SNP芯片分析青峪猪保种群体的遗传结构[J].畜牧兽医学报,2020,51(2):260-269.LIU B,SHEN L Y,CHEN Y,et al.Analysis of genetic structure of conservation population in Qingyu pig based on SNP chip[J].Acta Veterinaria et Zootechnica Sinica,2020,51(2):260-269.(in Chinese)
[34]	曹果清,李步高,石建中,等.应用21个微卫星标记监测马身猪遗传多样性变化趋势[J].畜牧兽医学报,2010,41(8):932-938.CAO G Q,LI B G,SHI J Z,et al.Genetic monitoring on genetic diversity of Mashen pig using 21 microsatellite markers[J].Acta Veterinaria et Zootechnica Sinica,2010,41(8):932-938.(in Chinese)
[35]	KIRIN M,MCQUILLAN R,FRANKLIN C S,et al.Genomic runs of homozygosity record population history and consanguinity[J].PLoS One,2010,5(11):e13996.
[36]	BOSSE M,MEGENS H J,MADSEN O,et al.Regions of homozygosity in the porcine genome:consequence of demography and the recombination landscape[J].PLoS Genet,2012,8(11):e1003100.
[37]	王晨,马宁,郭春和,等.基于SNP芯片分析的蓝塘猪遗传群体结构[J].广东农业科学,2018,45(6):110-115.WANG C,MA N,GUO C H,et al.Population structure of Lantang pig evaluated using SNP chip[J].Guangdong Agricultural Sciences,2018,45(6):110-115.(in Chinese)
[38]	李正杰,周先坤,王浥尘,等.阿坝藏族羌族自治州若尔盖地区藏猪mtDNA D-Loop的遗传多样性分析[J].畜牧兽医学报,2019,50(12):2387-2399.LI Z J,ZHOU X K,WANG Y C,et al.Genetic diversity of Tibetan pig mitochondrial DNA D-loop in Ruoergai area of A'ba Tibetan and Qiang Autonomous Prefecture[J].Acta Veterinaria et Zootechnica Sinica,2019,50(12):2387-2399.(in Chinese)