基于全基因组SNP标记分析中国地方鸡品种的遗传多样性和种群结构

doi:10.11843/j.issn.0366-6964.2023.02.013

Abstract

Abstract: The aim of this study was to analyze the genetic diversity and population structure of Chinese native chicken breeds. A total of 157 chickens from 8 Chinese native breeds and 233 commercial chickens were genotyped using Affymetrix Axiom 600K high-density chicken chip. Each breed's genetic diversity was calculated with observed heterozygosity, expected heterozygosity, minor allele frequency, inbreeding coefficient and nucleotide diversity. Population structure was analyzed with neighbor-joining phylogenetic analysis, principal component analysis, population structure analysis and multidimensional scaling (MDS). Identity by state (IBS) and pairwise differentiation coefficient (Fst) were used to study the genetic relationship between and within breeds. Runs of homozygosity (ROH) analysis was used to obtain more accurate inbreeding coefficients. The results showed that the observed heterozygosity of each population was higher than the corresponding expected heterozygosity. Minor allele frequencies ranged from 0.175 to 0.236. Inbreeding coefficients ranged from 0.018 to 0.205. Nucleotide diversity ranged from 0 to 6×10^-4. The obvious genetic differentiation was observed between breeds according to the phylogenetic tree and principal component analysis. MDS analysis revealed a relatively close genetic relationship between Chinese native chickens and purebred broiler lines. IBS genetic distance ranged from 0.092 9 to 0.319 9. The populations had a moderate genetic differentiation based on the pairwise Fst data (0.09-0.22). Furthermore, 5 242 ROHs with lengths ranging from 1 Mb to 41.51 Mb were discovered. The ROH-based inbreeding coefficient (F_ROH) ranged between 0.010 and 0.150. These results revealed that the overall genetic diversity of local chickens is richer. Langshan chicken and Wannan three-yellow chicken had the most genetic diversity. High-levels inbreeding occurred in Fighting chickens, Gushi chickens and Chahua chicken, which might had ever been suffered from inbreeding events. Different breeds existed high genetic differentiation. The results of this study will aid in designing and implementing conservation strategies, which will promote the utilization and conservation of genetic resources.

Key words: Chinese native chicken, genome-wide SNP, genetic diversity, population structure, ROH analysis

CLC Number:

S831.2

GAO Chaoqun, CAO Ranran, DU Wenping, HU Xiaoyu, LEI Yanru, LI Wenting, KANG Xiangtao. Genetic Diversity and Population Structure Analysis of Chinese Native Chicken Breeds using Genome-wide SNPs[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 554-562.

References 45

[1]	GUO Y, OU J H, ZAN Y J, et al.Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history[J].Evol Appl, 2022, 15(4):553-564.
[2]	MIAO Y W, PENG M S, WU G S, et al.Chicken domestication:an updated perspective based on mitochondrial genomes[J].Heredity (Edinb), 2013, 110(3):277-282.
[3]	XIONG X, ZHANG L X, HAO Y, et al.How urbanization and ecological conditions affect urban diet-linked GHG emissions:new evidence from China[J].Resour Conserv Recycl, 2022, 176:105903.
[4]	WANG M S, THAKUR M, PENG M S, et al.863 genomes reveal the origin and domestication of chicken[J].Cell Res, 2020, 30(8):693-701.
[5]	ABDULWAHID A M, ZHAO J B.China as a center of origin and domestication of chicken:a review[J].Agric Rev, 2022, 43(2):170-177.
[6]	LUO W, LUO C L, WANG M, et al.Genome diversity of Chinese indigenous chicken and the selective signatures in Chinese gamecock chicken[J].Sci Rep, 2020, 10(1):14532.
[7]	NIE C S, ALMEIDA P, JIA Y X, et al.Genome-wide single-nucleotide polymorphism data unveil admixture of Chinese indigenous chicken breeds with commercial breeds[J].Genome Biol Evol, 2019, 11(7):1847-1856.
[8]	TIXIER-BOICHARD M, LEENSTRA F, FLOCK D K, et al.A century of poultry genetics[J].Worlds Poult Sci J, 2012, 68(2):307-321.
[9]	YANG X, LIU C L, YANG B G, et al.Investigating genetic diversity and population phylogeny of five Chongqing local chicken populations autosomal using microsatellites[J].Anim Biotechnol, 2021, 33(6):1190-1197.
[10]	AZIMU W, MANATBAY B, LI Y, et al.Genetic diversity and population structure analysis of eight local chicken breeds of Southern Xinjiang[J].Br Poult Sci, 2018, 59(6):629-635.
[11]	CHEN G H, BAO W B, SHU J T, et al.Assessment of population structure and genetic diversity of 15 Chinese indigenous chicken breeds using microsatellite markers[J].Asian-Australas J Anim Sci, 2008, 21(3):331-339.
[12]	HABIMANA R, OKENO T O, NGENO K, et al.Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers[J].PLoS One, 2020, 15(4):e0225084.
[13]	RASHID M A, MANJULA P, FARUQUE S, et al.Genetic diversity and population structure of indigenous chicken of Bangladesh using microsatellite markers[J].Asian-Australas J Anim Sci, 2020, 33(11):1732-1740.
[14]	ROH H J, KIM S C, CHO C Y, et al.Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers[J]. Asian-Australas J Anim Sci, 2020, 33(12):1896-1904.
[15]	SABRY A, RAMADAN S, HASSAN M M, et al.Assessment of genetic diversity among Egyptian and Saudi chicken ecotypes and local Egyptian chicken breeds using microsatellite markers[J].J Environ Biol, 2021, 42:33-39.
[16]	TADANO R, NISHIBORI M, NAGASAKA N, et al.Assessing genetic diversity and population structure for commercial chicken lines based on forty microsatellite analyses[J].Poult Sci, 2007, 86(11):2301-2308.
[17]	任芳.怒江缺须盆唇鱼种群遗传结构及遗传多样性分析[D].贵阳:贵州大学, 2021.REN F.Population genetic diversity and genetic structure analysis of the placocheilus cryptonemus in the Nujiang River[D].Guiyang:Guizhou University, 2021.(in Chinese)
[18]	ZHANG J X, NIE C S, LI X H, et al.Genome-wide population genetic analysis of commercial, indigenous, game, and wild chickens using 600K SNP microarray data[J].Front Genet, 2020, 11:543294.
[19]	CENDRON F, PERINI F, MASTRANGELO S, et al.Genome-wide SNP analysis reveals the population structure and the conservation status of 23 Italian chicken breeds[J].Animals, 2020, 10(8):1441.
[20]	MEYERMANS R, GORSSEN W, WIJNROCX K, et al.Unraveling the genetic diversity of Belgian Milk Sheep using medium-density SNP genotypes[J].Anim Genet, 2020, 51(2):258-265.
[21]	TRUJANO-CHAVEZ M Z, RUÍZ-FLORES A, LÓPEZ-ORDAZ R, et al.Genetic diversity in reproductive traits of Braunvieh cattle determined with SNP markers[J].Vet Med Sci, 2022, 8(4):1709-1720.
[22]	ZORC M, ŠKORPUT D, GVOZDANOVIĆ K, et al.Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia[J].Genet Sel Evol, 2022, 54(1):30.
[23]	ABLONDI M, DADOUSIS C, VASINI M, et al.Genetic diversity and signatures of selection in a native Italian horse breed based on SNP data[J].Animals, 2020, 10(6):1005.
[24]	KRANIS A, GHEYAS A A, BOSCHIERO C, et al.Development of a high density 600K SNP genotyping array for chicken[J].BMC Genomics, 2013, 14:59.
[25]	WARREN W C, HILLIER L W, TOMLINSON C, et al.A new chicken genome assembly provides insight into avian genome structure[J].G3 (Bethesda), 2017, 7(1):109-117.
[26]	CHANG C C, CHOW C C, TELLIER L C A M, et al.Second-generation PLINK:rising to the challenge of larger and richer datasets[J].GigaScience, 2015, 4(1):7.
[27]	DANECEK P, AUTON A, ABECASIS G, et al.The variant call format and VCFtools[J].Bioinformatics, 2011, 27(15):2156-2158.
[28]	ALEXANDER D H, NOVEMBRE J, LANGE K.Fast model-based estimation of ancestry in unrelated individuals[J].Genome Res, 2009, 19(9):1655-1664.
[29]	HARTL D L, KALVEMARK A S, KHOO S, et al.Assess educ[M].Sunderland, MA:Sinauer Associates, 1980.
[30]	CENDRON F, MASTRANGELO S, TOLONE M, et al.Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds[J].Poult Sci, 2021, 100(2):441-451.
[31]	GORSSEN W, MEYERMANS R, BUYS N, et al.SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Piétrain pigs[J].Anim Genet, 2020, 51(1):32-42.
[32]	FERENČAKOVIĆ M, HAMZIĆ E, GREDLER B, et al.Estimates of autozygosity derived from runs of homozygosity:empirical evidence from selected cattle populations[J].J Anim Breed Genet, 2013, 130(4):286-293.
[33]	CAVILL E L, GOPALAKRISHNAN S, PUETZ L C, et al.Conservation genomics of the endangered Seychelles Magpie-Robin (Copsychus sechellarum):a unique insight into the history of a precious endemic bird[J].Ibis, 2022, 164(2):396-410.
[34]	SHI L Y, WANG L G, LIU J X, et al.Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population[J].J Anim Sci Biotechnol, 2020, 11:46.
[35]	BERTOLINI F, CARDOSO T F, MARRAS G, et al.Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats[J].Genet Sel Evol, 2018, 50(1):59.
[36]	GUTIÉRREZ-REINOSO M A, APONTE P M, GARCÍA-HERREROS M.A review of inbreeding depression in dairy cattle:current status, emerging control strategies, and future prospects[J].J Dairy Res, 2022, 89(1):3-12.
[37]	武艳平, 魏岳, 康昭风, 等.基于全基因组SNP分析8个地方鸡品种的遗传多样性[J].畜牧兽医学报, 2022, 53(2):646-653.WU Y P, WEI Y, KANG Z F, et al.Genetic diversity analysis of 8 local chicken breeds based on whole genome SNP[J].Acta Veterinaria et Zootechnica Sinica, 2022, 53(2):646-653.(in Chinese)
[38]	ZHANG M M, HAN W, TANG H, et al.Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs[J].BMC Genomics, 2018, 19(1):598.
[39]	YANG N, JIANG R S.Recent advances in breeding for quality chickens[J].Worlds Poult Sci J, 2005, 61(3):373-381.
[40]	BORTOLUZZI C, CROOIJMANS R P M A, BOSSE M, et al.The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity[J].Heredity (Edinb), 2018, 121(6):564-578.
[41]	KIM E S, COLE J B, HUSON H, et al.Effect of artificial selection on runs of homozygosity in U.S. Holstein cattle[J].PLoS One, 2013, 8(11):e80813.
[42]	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.
[43]	ONZIMA R B, UPADHYAY M R, DOEKES H P, et al.Genome-wide characterization of selection signatures and runs of homozygosity in Ugandan goat breeds[J].Front Genet, 2018, 9:318.
[44]	FLEMING D S, KOLTES J E, MARKEY A D, et al.Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array[J].BMC Genomics, 2016, 17:407.
[45]	STRILLACCI M G, VEGA-MURILLO V E, ROMÁN-PONCE S I, et al.Looking at genetic structure and selection signatures of the Mexican chicken population using single nucleotide polymorphism markers[J].Poult Sci, 2018, 97(3):791-802.

Genetic Diversity and Population Structure Analysis of Chinese Native Chicken Breeds using Genome-wide SNPs

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