基于SNP芯片分析青峪猪保种群体的遗传结构

doi:10.11843/j.issn.0366-6964.2020.02.007

Abstract

Abstract: In order to better understand the genetic structure changes of Qingyu pig in the process of generation replacement, and better protect and utilize the genetic resources of Qingyu pig, the 50K SNP chip was used to measure SNP of 141 healthy adult individuals (26 boars, 115 sows) in Qingyu pig population. The pedigree of Qingyu pig population and each generation was corrected by various analysis softwares, and then the genetic diversity, genetic distance and genetic structure changes were analyzed. The results showed that the closed population was composed of 3 overlapping generations, the effective size of the population was 12, and the whole population could be divided into 6 families with boar and 1 family without boar. Among them, the effective size of the 3rd generation was the least, only three. The proportion of polymorphism markers decreased with the increase of generation. The average genetic distance of 141 Qingyu pigs was (0.260 4±0.025 2), and that of 26 boars was (0.263 3±0.023 7). With the increase of reproductive generations, the genetic distance of each generation population had a slight upward trend, and the genetic relationship and genetic distance between some breeding pigs were relatively closer; in 141 Qingyu pig population, 1 481 long homozygous segments (ROH) were detected, 78.01% of which were within 200 Mb. The inbreeding coefficient based on the ROH value showed that the average inbreeding coefficient of the whole population was 0.055, and the inbreeding coefficient of each generation continuously rose, reaching 0.075 by the 3rd generation. In conclusion, the study on the genetic structure of Qingyu pig population at the molecular level shows that there is a loss of population genetic diversity in the process of closed subsequent breeding, and it is necessary to strengthen the selection mating system or introduce external blood to ensure the long-term preservation of the genetic resources of Qingyu pig.

Key words: SNP chip, Qingyu pig, population genetic structure

CLC Number:

S828.2

LIU Bin, SHEN Linyuan, CHEN Ying, LI Qiang, LIAO Kun, GUO Zhixian, ZHANG Shunhua, ZHU Li. 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.

References 31

[1]	杨红杰,彭华,王林云.从我国猪肉消费趋势展望地方猪种发展前景[J].中国畜牧杂志,2014,50(16):6-10.YNG H J,PENG H,WANG L Y.Future prospects for the development of Chinese in digenous pig breeds with perspective of pork consumption trends[J].Chinese Journal of Animal Science,2014,50(16):6-10.(in Chinese)
[2]	FANG M,HU X,JIANG T,et al.The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers[J].Anim Genet,2005,36(1):7-13.
[3]	于福清.我国地方猪种资源最新状况与保护利用建议[J].农村养殖技术,2012(12):21-23.Y F Q.The latest situation of local pig resources in China and suggestions for protection and utilization[J].Journal of Rural Animal-Breeding Technology,2012(12):21-23.(in Chinese)
[4]	郑雪君,杨婷婷.中国地方猪品种的保护与利用分析[J].中国畜牧杂志,2015,51(16):24-27.ZENG X J,YANG T T.Analysis on the conservation and utilization of Chinese local pig breeds[J].Chinese Journal of Animal Science,2015,51(16):24-27.(in Chinese)
[5]	廖坤,高成忠,何忠平,等.湖川山地猪(青峪猪)的种质特性及其保护[J].中国猪业,2013,8(S1):154-156.LAO K,GAO C Z,HE Z P,et al.Germplasm characteristics and protection of Huchuan mountain pig (Qingyu pig)[J].China Swine Industry,2013,8(S1):154-156.(in Chinese)
[6]	沈林園,朱砺,廖坤,等.青峪猪的胴体性状、肉质特性及营养成分分析[J].营养学报,2014,36(5):516-518.SEN L Y,ZHU L,LIAO K,et al.Slaughter performance,meat qulity and nutritional composition analysis of Qingyu Pig[J].Acta Nutrimenta Sinica,2014,36(5):516-518.(in Chinese)
[7]	唐立群,肖层林,王伟平.SNP分子标记的研究及其应用进展[J].中国农学通报,2012,28(12):154-158.TNG L Q,XIAO C L,WANG W P.Research and application progress of SNP markers[J].Chinese Agricultural Science Bulletin,2012,28(12):154-158.(in Chinese)
[8]	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.
[9]	曲娟娟,于敏,董蕾,等.SNP在动植物遗传育种中的应用[J].东北农业大学学报,2011,42(12):9-13.Q J J,YU M,DONG L,et al.Applications of SNP in animal and plant genetic breeding[J].Journal of Northeast Agricultural University,2011,42(12):9-13.(in Chinese)
[10]	BOSSE M,MEGENS H J,MADSEN O,et al.Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations[J].Genome Res,2015,25(7):970-981.
[11]	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.
[12]	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.HANG 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)
[13]	PURCELL S,NEALE B,TODD-BROWN K,et al.PLINK:a tool set for whole-genome association and population-based linkage analyses[J].Am J Hum Genet,2007,81(3):559-575.
[14]	KUMAR S,STECHER G,TAMURA K.MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets[J].Mol Biol Evol,2016,33(7):1870-1874.
[15]	孙浩,王振,张哲,等.基于基因组测序数据的梅山猪保种现状分析[J].上海交通大学学报:农业科学版,2017,35(4):65-70.SN H,WANG Z,ZHANG Z,et al.Exploring the current situation of conservation of Meishan pigs based on genome sequencing data[J].Journal of Shanghai Jiaotong University:Agricultural Science,2017,35(4):65-70.(in Chinese)
[16]	BARBATO M,OROZCO-TERWENGEL P,TAPIO M,et al.SNeP:a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data[J].Front Genet,2015,6:109.
[17]	WANG L,SØRENSEN P,JANSS L,et al.Genome-wide and local pattern of linkage disequilibrium and persistence of phase for 3 Danish pig breeds[J].BMC Genet,2013,14:115.
[18]	罗元宇.华南地方猪连锁不平衡分析及有效群体大小估计[D].广州:华南农业大学,2016.LO Y Y.Analysis of lingkage disequilibrium and estimation of effective population size in Southern Chinese indigenous pig breeds[D].Guangzhou:South China Agricultural University,2016.(in Chinese)
[19]	TRASPOV A,DENG W J,KOSTYUNINA O,et al.Erratum to:population structure and genome characterization of local pig breeds in Russia,Belorussia,Kazakhstan and Ukraine[J].Genet Sel Evol,2016,48:16.
[20]	SANCRISTOBAL M,CHEVALET C,HALEY C S,et al.Genetic diversity within and between European pig breeds using microsatellite markers[J].Anim Genet,2006,37(3):189-198.
[21]	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.
[22]	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-Aust J Anim Sci,2004,17(9):1219-1222.
[23]	张天时,王清印,刘萍,等.中国对虾(Fenneropenaeus chinensis)人工选育群体不同世代的微卫星分析[J].海洋与湖沼,2005,36(1):72-80.ZANG T S,WANG Q Y,LIU P,et al.Genetic diversity analysis on selected populations of shrimp Fenneropenaeus chinensis by microsatellites[J].Oceanologia et Limnologia Sinica,2005,36(1):72-80.(in Chinese)
[24]	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.WNG 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)
[25]	牛荣,商海涛,魏泓,等.版纳小耳猪近交系5家系35个微卫星座位的遗传分析[J].遗传学报,2001,28(6):518-526.NU R,SHANG H T,WEI H,et al.Genetic analysis of 35 microsatellite loci in 5 lineages of Xishuangbanna miniature pig inbred line[J].Acta Genetica Sinica,2001,28(6):518-526.(in Chinese)
[26]	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.
[27]	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.
[28]	刘德武,杨关福,李加琪,等.用RAPD标记分析6个品种猪的群体遗传结构[J].畜牧兽医学报,2002,33(1):18-22.LU D W,YANG G F,LI J Q,et al.Analysing genetic construction of six pig breeds using RAPD marker[J].Acta Veterinaria et Zootechnica Sinica,2002,33(1):18-22.(in Chinese)
[29]	吴林慧,孙琦,王荔茹,等.恩施黑猪基因组群体遗传学参数的估计与选择信号研究[J].畜牧兽医学报,2019,50(3):485-494.W L H,SUN Q,WANG L R,et al.A study of the population genetics parameters and selection signatures in Enshi black pig[J].Acta Veterinaria et Zootechnica Sinica,2019,50(3):485-494.(in Chinese)
[30]	孙华,宋忠旭,彭先文,等.湖北白猪优质系血源组成比例及其系谱结构分析[J].湖北农业科学,2014,53(24):6061-6063.SN H,SONG Z X,PENG X W,et al.Blood percentage and pedigree analyses of Hubei white swine with high quality line[J].Hubei Agricultural Sciences,2014,53(24):6061-6063.(in Chinese)
[31]	于国升.深县猪现有群体生产性能遗传分析[D].保定:河北农业大学,2018.Y G S.Genetic analysis of production performance of existing population in Shenxian pig[D].Baoding:Hebei Agricultural University,2018.(in Chinese)

Analysis of Genetic Structure of Conservation Population in Qingyu Pig Based on SNP Chip

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