基于基因组SNP和ROH的剑白香猪群体遗传结构解析

doi:10.11843/j.issn.0366-6964.2023.10.011

摘要/Abstract

摘要： 旨在从分子水平分析剑白香猪的群体结构以及遗传多样性，对剑白香猪的种质资源鉴定和保护提供技术支持。本研究利用Porcine SNP50 BeadChip （Illumina，United States）芯片对138头剑白香猪的全基因组SNP进行扫描，通过对主成分、遗传距离、亲缘关系和公猪血统进行分析，研究剑白香猪的群体结构；通过ROH分析，确定剑白香猪的遗传多样性。结果显示，此剑白香猪群体无明显分层，但大致可以分为3个部分，群体内的遗传距离平均值约为0.273，所有公猪划分为4个血统；剑白香猪群体共检测出2 893个ROHs，平均每个个体约有21个ROHs，平均ROH长度约为7.18 Mb，平均近交系数（F_ROH）为0.27%，表明剑白香猪近交积累较少。通过多种分析表明，该群体家系数量适中，个别家系公畜数量较少，个体间亲缘关系中等，近交程度较低，群体的遗传多样性较高。本研究在基因组水平分析了剑白香猪的群体遗传结构和遗传多样性，为剑白香猪群体复壮和种业安全措施制定提供了分子依据。

关键词: 剑白香猪, 群体结构, ROH, SNP, 遗传多样性

Abstract: The purpose of this study was to analyze the population structure and genetic diversity of Jianbai Xiang pigs at the molecular level and to provide technical support for the identification and conservation of germplasm resources of Jianbai Xiang pigs. Using Porcine SNP50 BeadChip (Illumina, United States) to scan the whole genome SNP of 138 Jianbai Xiang pigs, the population structure of Jianbai Xiang pigs was studied by analyzing the principal component, genetic distance, genetic relationship and boar pedigree. The genetic diversity of the Jianbai Xiang pig was determined by ROH analysis. The results showed that there was no obvious stratification in this population, but it could be roughly divided into 3 parts. The average genetic distance within the population was about 0.273, and all boars were divided into 4 lineages. A total of 2 893 ROHs were detected in Jianbai Xiang pigs, with an average of 21 ROHs per individual. The average ROH length was 7.18 Mb and the average inbreeding coefficient (F_ROH) was 0.27%, indicating that the inbreeding accumulation of Jianbai Xiang pigs was small. A variety of analyses showed that the population had a moderate number of families, a small number of male animals in individual families, moderate genetic relationships between individuals, a low degree of inbreeding, and high genetic diversity. In this study, the population genetic structure and genetic diversity of Jianbai Xiang pigs were analyzed at the genome level, which provided the molecular basis for population rejuvenation and seed industry safety measures of Jianbai Xiang pigs.

Key words: Jianbai Xiang pig, population structure, ROH, SNP, genetic diversity

中图分类号:

S828.2

胡紫平, 王立刚, 宗文成, 侯任达, 苏艳芳, 牛乃琪, 王立贤, 王源, 张龙超. 基于基因组SNP和ROH的剑白香猪群体遗传结构解析[J]. 畜牧兽医学报, 2023, 54(10): 4117-4125.

HU Ziping, WANG Ligang, ZONG Wencheng, HOU Renda, SU Yanfang, NIU Naiqi, WANG Lixian, WANG Yuan, ZHNAG Longchao. Genetic Structure Analysis of Jianbai Xiang Pig Population Based on Genomic SNP and ROH[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4117-4125.

参考文献 34

[1]	魏菁, 张子群, 王琦, 等.中国地方猪种种质资源的保护与利用探讨[J].畜禽业, 2021, 32(3):43-44.WEI J, ZHANG Z Q, WANG Q, et al.Conservation and utilization of germplasm resources of local pig breeds in China[J].Livestock and Poultry Industry, 2021, 32(3):43-44.(in Chinese)
[2]	李平华, 马翔, 张叶秋, 等.影响二花脸猪高产仔性能的生理及遗传机制研究进展[J].遗传, 2017, 39(11):1016-1024.LI P H, MA X, ZHANG Y Q, et al.Progress in the physiological and genetic mechanisms underlying the high prolificacy of the Erhualian pig[J].Hereditas (Beijing), 2017, 39(11):1016-1024.(in Chinese)
[3]	LI X J, QIAO R M, YE J W, et al.Integrated miRNA and mRNA transcriptomes of spleen profiles between Yorkshire and Queshan black pigs[J].Gene, 2019, 688:204-214.
[4]	孟珊, 杨阳, 李睿霄, 等.lncRNA-6617调控猪肌内前体脂肪细胞分化的筛选与功能研究[J].畜牧兽医学报, 2022, 53(6):1712-1722.MENG S, YANG Y, LI R X, et al.Screening and functional study of lncRNA-6617 regulating porcine intramuscular preadipocytes differentiation[J].Acta Veterinaria et Zootechnica Sinica, 2022, 53(6):1712-1722.(in Chinese)
[5]	聂林峰, 樊彦红, 张庆宇, 等.中国地方猪种对世界养猪业的贡献、利用现状和展望[J].畜牧与兽医, 2017, 49(10):126-130.NIE L F, FAN Y H, ZHANG Q Y, et al.Chinese indigenous pig's utilization status, prospects and its contribution to the world's pig breeding[J].Animal Husbandry & Veterinary Medicine, 2017, 49(10):126-130.(in Chinese)
[6]	AI H S, HUANG L S, REN J.Genetic diversity, linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers[J].PLoS One, 2013, 8(2):e56001.
[7]	CHEN Z T, YE X W, ZHANG Z, et al.Genetic diversity and selection signatures of four indigenous pig breeds from eastern China[J].Anim Genet, 2022, 53(4):506-509.
[8]	GAO Z D, ZHANG Y B, LI Z, et al.Genomic breed composition of Ningxiang pig via different SNP panels[J].J Anim Physiol Anim Nutr (Berl), 2022, 106(4):783-791.
[9]	XU P, WANG X P, NI L G, et al.Genome-wide genotyping uncovers genetic diversity, phylogeny, signatures of selection, and population structure of Chinese Jiangquhai pigs in a global perspective[J].J Anim Sci, 2019, 97(4):1491-1500.
[10]	WU X D, ZHOU R, WANG Y L, et al.Genome-wide scan for runs of homozygosity in Asian wild boars and Anqing six-end-white pigs[J].Anim Genet, 2022, 53(6):867-871.
[11]	WANG X P, ZHANG H, HUANG M, et al.Whole-genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs[J].Evol Appl, 2021, 14(2):383-398.
[12]	WANG X, WANG C, HUANG M, et al.Genetic diversity, population structure and phylogenetic relationships of three indigenous pig breeds from Jiangxi Province, China, in a worldwide panel of pigs[J]. Anim Genet, 2018, 49(4):275-283.
[13]	MENG F B, CAI J C, WANG C N, et al.Single nucleotide polymorphism-based analysis of the genetic structure of the Min pig conserved population[J].Anim Biosci, 2022, 35(12):1839-1849.
[14]	覃海, 陈伟, 毕欢, 等.基于转录组测序对剑白香猪黑色素生成相关基因的筛选与分析[J].中国兽医学报, 2022, 42(11):2261-2271, 2283.QIN H, CHEN W, BI H, et al.Screening and analysis of Genes related to melanin production in Jianbai Xiang pig based on Transcriptome sequencing[J].Chinese Journal of Veterinary Science, 2022, 42(11):2261-2271, 2283.(in Chinese)
[15]	ZHANG R, YANG M, HOU X H, et al.Characterization and difference of lipids and metabolites from Jianhe White Xiang and Large White pork by high-performance liquid chromatography-tandem mass spectrometry[J].Food Res Int, 2022, 162:111946.
[16]	杨前勇.地方品种遗传多样性和群体结构的分析与统计方法[J].江西畜牧兽医杂志, 2017(5):1-4.YANG Q Y.Analysis and statistical methods of genetic diversity and population structure of local breeds[J].Jiangxi Journal of Animal Husbandry and Veterinary Medicine, 2017(5):1-4.(in Chinese)
[17]	刘晨龙, 卢丹, 周泉勇, 等.利用高密度SNP芯片分析杭猪的群体遗传结构[J].畜牧兽医学报, 2022, 53(8):2502-2513.LIU C L, LU D, ZHOU Q Y, et al.Analysis of population genetic structure of hang pigs by high density SNP chip[J].Acta Veterinaria et Zootechnica Sinica, 2022, 53(8):2502-2513.(in Chinese)
[18]	PERIPOLLI E, MUNARI D P, SILVA M V G B, et al.Runs of homozygosity:current knowledge and applications in livestock[J].Anim Genet, 2017, 48(3):255-271.
[19]	ZHANG Q Q, CALUS M P, GULDBRANDTSEN B, et al.Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds[J].BMC Genet, 2015, 16:88.
[20]	袁娇, 徐国强, 周翔, 等.基于SNP芯片监测通城猪的保种效果[J].畜牧兽医学报, 2022, 53(8):2514-2523.YUAN J, XU G Q, ZHOU X, et al.SNP chip-based monitoring of population conservation effect of Tongcheng pigs[J].Acta Veterinaria et Zootechnica Sinica, 2022, 53(8):2514-2523.(in Chinese)
[21]	陶璇, 杨雪梅, 梁艳, 等.基于SNP芯片的丫杈猪保种群体遗传结构研究[J].畜牧兽医学报, 2023, 54(6):2308-2319.TAO X, YANG X M, LIANG Y, et al.Analysis of genetic structure of conservation population in yacha pig based on SNP chip[J].Acta Veterinaria et Zootechnica Sinica, 2023, 54(6):2308-2319.(in Chinese)
[22]	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)
[23]	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)
[24]	蔡春波, 张雪莲, 张万峰, 等.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 C B, ZHANG X L, ZHANG W F, et al.Evaluation of genetic structure in mashen pigs conserved population based on SNP chip[J].Acta Veterinaria et Zootechnica Sinica, 2021, 52(4):920-931.(in Chinese)
[25]	MARRAS G, GASPA G, SORBOLINI S, et al.Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy[J].Anim Genet, 2015, 46(2):110-121.
[26]	ZHAN H W, ZHANG S X, ZHANG K L, et al.Genome-wide patterns of homozygosity and relevant characterizations on the population structure in Piétrain pigs[J].Genes (Basel), 2020, 11(5):577.
[27]	AI H S, FANG X D, YANG B, et al.Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing[J].Nat Genet, 2015, 47(3):217-225.
[28]	PERIPOLLI E, MUNARI D P, SILVA M V G B, et al.Runs of homozygosity:current knowledge and applications in livestock[J].Anim Genet, 2017, 48(3):255-271.
[29]	XU Z, SUN H, ZHANG Z, et al.Assessment of autozygosity derived from runs of homozygosity in Jinhua pigs disclosed by sequencing data[J].Front Genet, 2019, 10:274.
[30]	REBELATO A B, CAETANO A R.Runs of homozygosity for autozygosity estimation and genomic analysis in production animals[J].Pesq Agropec Bras, 2018, 53(9):975-984.
[31]	WANG Y, DONG R L, LI X, et al.Analysis of the genetic diversity and family structure of the Licha black pig population on Jiaodong Peninsula, Shandong province, China[J].Animals (Basel), 2022, 12(8):1045.
[32]	YUAN J, ZHOU X, XU G Q, et al.Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip[J].Front Genet, 2022, 13:910521.
[33]	LIU B, SHEN L Y, GUO Z X, et al.Single nucleotide polymorphism-based analysis of the genetic structure of Liangshan pig population[J].Anim Biosci, 2021, 34(7):1105-1115.
[34]	戴丽荷, 褚晓红, 陈晓宇, 等.利用SNP标记分析淳安花猪群体遗传多样性和群体结构[J].养猪, 2021(6):59-64.DAI L H, CHU X H, CHEN X Y, et al.Analysis of genetic diversity and genetic structure in chun'an spotted pigs conserved population based on SNP chip[J].Swine Production, 2021(6):59-64.(in Chinese)