四川盆地6个地方鸡群体遗传关系研究

doi:10.11843/j.issn.0366-6964.2022.02.005

摘要/Abstract

摘要： 随着交通便利与市场化杂交利用，我国地方鸡遗传资源面临血液混杂、品种来源和品种间的遗传关系不清晰的问题。为了给第三次全国畜禽遗传资源普查工作提供依据。本研究对位于中国大巴山脉和乌蒙山区的6个地方鸡群体（每个群体公、母各10只）共118个个体进行了简化基因组GBS测序，分析了核酸多态性（Pi）、观测杂合度（Ho）、期望杂合度（He）、多态信息含量（PIC）、观测等位基因数（Na）、有效等位基因数（Ne）、遗传分化（Fst）、遗传距离（DR）和基因流（Nm）等指标。研究发现，岩水鸡黑羽群体的遗传多样性较低（He=0.154；PIC=0.125），大宁河鸡遗传多样性最为丰富（He=0.197，PIC=0.162）。城口山地鸡和大宁河鸡之间的遗传分化最低（Fst=0.053），基因流最高（Nm=4.50），丰岩乌骨鸡和岩水鸡黑羽群体之间的遗传分化最高（Fst=0.183），对应的基因流最低（Nm=1.12）。系统发生树和主成分分析显示，岩水鸡白羽群体和黑羽群体聚为一类，城口山地鸡、大宁河鸡和旧院黑鸡聚为一类，丰岩乌骨鸡单独为一类。Structure分析表明，城口山地鸡与岩水鸡白羽群体血缘混杂。本研究探明了邻近区域地方品种的遗传关系，位于乌蒙山区的丰岩乌骨鸡与大巴山脉的旧院黑鸡、城口山地鸡、大宁河鸡、岩水鸡黑羽和白羽具有较远的遗传距离。本研究为地方品种的保护和开发利用提供了依据。

关键词: 地方鸡品种, 遗传多样性, 简化基因组, 基因流, 系统发生树

Abstract: With the convenience of transportation and market-oriented cross utilization, the genetic resources of local chickens in China are facing the problems of blood mixing and the unclear breed source and genetic relationship among breeds. The study aimed to provide a basis for the Third National Census of Livestock and Poultry Genetic Resources. A simplified genomic GBS sequencing was carried out on 118 individuals from 6 local chicken populations (10 males and 10 females in each population) located in Daba Mountains and Wumeng Mountains in China. The nucleotide polymorphism (Pi), observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), number of observed alleles (Na), number of effective alleles (Ne), genetic differentiation (Fst), genetic distance (DR) and gene flow (Nm) of these populations were analyzed. It was found that the genetic diversity of black feather population of Yanshui chicken was low (He=0.154; PIC=0.125), and the genetic diversity of Daninghe chicken was the most abundant (He=0.197, PIC=0.162). The genetic differentiation between Chengkou mountain chicken and Daninghe chicken was the lowest (Fst =0.053), the gene flow was the highest (Nm=4.50), the genetic differentiation between Fengyan black bone chicken and black feather population of Yanshui chicken was the highest (Fst=0.183), and the corresponding gene flow was the lowest (Nm=1.12). Phylogenetic tree and principal component analysis showed that the white feather population and black feather population of Yanshui chicken were clustered into one class. Chengkou mountain chicken, Daninghe chicken and Jiuyuan black chicken were clustered into one class, while Fengyan black bone chicken was a separate class. Structure analysis showed that the blood of Chengkou mountain chicken and white feather population of Yanshui chicken was mixed. This study proved the genetic relationship of local breeds in adjacent areas. Fengyan black bone chicken located in Wumeng Mountain has a long genetic distance from Jiuyuan black chicken, Chengkou mountain chicken, Daninghe chicken, black feather and white feather populations of Yanshui chicken in Daba Mountain. This study provides a basis for the protection, development and utilization of local chicken breeds.

Key words: local chicken breeds, genetic diversity, simplified genome, gene flow, phylogenetic tree

中图分类号:

S831.2

尤桂爽, 易兴友, 蒋美山, 李中伟, 谭和林, 曹池, 舒刚, 田尧夫, 朱庆, 赵小玲. 四川盆地6个地方鸡群体遗传关系研究[J]. 畜牧兽医学报, 2022, 53(2): 370-380.

YOU Guishuang, YI Xingyou, JIANG Meishan, LI Zhongwei, TAN Helin, CAO Chi, SHU Gang, TIAN Yaofu, ZHU Qing, ZHAO Xiaoling. Study on the Genetic Relationship of Six Local Chicken Populations from Sichuan Basin[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(2): 370-380.

参考文献 40

[1]	国家畜禽遗传资源委员会.中国畜禽遗传资源志[M].北京:中国农业出版社,2011.China National Commission of Animal Genetic Resources.Animal genetic resources in China[M].Beijing:China Agriculture Press,2011.(in Chinese)
[2]	汤青萍,陈宽维,李慧芳,等.应用微卫星标记对12个中国地方乌骨鸡品种遗传多样性的研究[J].畜牧兽医学报,2005,36(8):755-760.TANG Q P,CHEN K W,LI H F,et al.Analysis of the genetic diversity of 12 Chinese Indigenous Black-bone chicken breeds using microsatellite marker[J].Acta Veterinaria et Zootechnica Sinica,2005,36(8):755-760.(in Chinese)
[3]	刘嘉,李富贵,桂涛涛,等.旧院黑鸡及其三系配套组合的外貌特征及肉用性能分析[J].西北农业学报,2019,28(2):161-168.LIU J,LI F G,GUI T T,et al.Appearance characteristics and meat performances analysis of Jiuyuan black chicken and three-line hybrid combinations[J].Acta Agriculturae Boreali-occidentalis Sinica,2019,28(2):161-168.(in Chinese)
[4]	易兴友,曹池,陈建华,等.开州岩水鸡品种资源调查[J].中国畜牧业,2021(14):53-55..YI X Y,CAO C,CHEN J H,et al.Investigation on breed resources of Kaizhou Yanshui chicken[J].China Animal Industry,2021(14):53-55.(in Chinese)
[5]	《中国畜禽遗传资源状况》编委会.中国畜禽遗传资源状况[M].北京:中国农业出版社,2004.Editorial Board of the Status of Livestock and Poultry Genetic Resources in China.Report on domestic animal genetic resources in China[M].Beijing:China Agriculture Press,2004.(in Chinese)
[6]	WEIGEND S,VEF E,WESCH G,et al.Conception for conserving genetic resources in poultry in Germany[J].Arch Gefügelk,1995,59(6):327-334.
[7]	ELSHIRE R J,GLAUBITZ J C,SUN Q,et al.A robust,simple Genotyping-By-Sequencing (GBS) approach for high diversity species[J].PLoS One,2011,6(5):e19379.
[8]	POLAND J A,RIFE T W.Genotyping-by-sequencing for plant breeding and genetics[J].Plant Genome,2012,5(3):92-102.
[9]	PÉRTILLE F,GUERRERO-BOSAGNA C,DA SILVA V H,et al.High-throughput and cost-effective chicken genotyping using next-generation sequencing[J].Sci Rep,2016,6:26929.
[10]	CHEN Q,MA Y F,YANG Y M,et al.Genotyping by genome reducing and sequencing for outbred animals[J].PLoS One,2013, 8(7):e67500.
[11]	DE DONATO M,PETERS S O,MAITCHELL S E,et al.Genotyping-by-sequencing (GBS):a novel,efficient and cost-effective genotyping method for cattle using next-generation sequencing[J].PLoS One,2013,8(5):e62137.
[12]	董世武,王天骄,刘华淼,等.基于GBS技术对梅花鹿、马鹿及其杂交后代基因组SNP特征的分析[J].畜牧兽医学报,2019,50(12):2422-2430.DONG S W,WANG T J,LIU H M,et al.Analysis of genomic SNP characteristics of sika deer,red deer and their hybrid progenies based on GBS technology[J].Acta Veterinaria et Zootechnica Sinica,2019,50(12):2422-2430.(in Chinese)
[13]	KATSUMURA T,ODA S,MITANI H,et al.Medaka population genome structure and demographic history described via genotyping-by-sequencing[J].G3(Bethesda),2019,9(1):217-228.
[14]	DORANT Y,BENESTAN L,ROUGEMONT Q,et al.Comparing Pool-seq,rapture,and GBS genotyping for inferring weak population structure:the American lobster (Homarus americanus) as a case study[J].Ecol Evol,2019,9(11):6606-6623.
[15]	GANDOMKAR H,SHEKARABI S P H,ALIABDOLHAY H,et al.Characterization of novel genotyping-by-sequencing (GBS)-based simple sequence repeats (SSRs) and their application for population genomics of Capoeta aculeata (Valenciennes, 1844)[J].Mol Biol Rep,2021,48(9):6471-6480.
[16]	VAN DER AUWERA G A,CARNEIRO M O,HARTL C,et al.From FastQ data to high-confidence variant calls:the genome analysis toolkit best practices pipeline[J].Curr Protoc Bioinform,2013,43(1110):11.10.1-11.10.33.
[17]	ALEXANDER D H,NOVEMBRE J,LANGE K.Fast model-based estimation of ancestry in unrelated individuals[J].Genome Res,2009,19(9):1655-1664.
[18]	MALOMANE D K,SIMIANER H,WEIGEND A,et al.The SYNBREED chicken diversity panel:a global resource to assess chicken diversity at high genomic resolution[J].BMC Genomics,2019,20(1):345.
[19]	李国辉,魏清宇,张会永,等.基于RAD-seq技术分析边鸡保种群体的遗传进化[J].农业生物技术学报,2019,27(12):2198-2206.LI G H,WEI Q Y,ZHANG H Y,et al.The analysis on genetic evolution of Bian chicken (Gallus gallus) population based on RAD-seq technology[J].Journal of Agricultural Biotechnology,2019,27(12):2198-2206.(in Chinese)
[20]	SOGLIA D,SARTORE S,MAIONE S,et al.Growth performance analysis of two Italian slow-growing chicken breeds:Bianca di Saluzzo and Bionda Piemontese[J].Animals,2020,10(6):969.
[21]	HILLEL J,GROENEN M A M,TIXIER-BOICHARD M,et al.Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools[J].Genet Select Evolut,2003,35(6):533-557.
[22]	KIRIKCI K,CAM M A,MERCAN L.Genetic diversity and relationship among indigenous Turkish Karayaka sheep subpopulations[J].Arch Anim Breed,2020,63(2):269-275.
[23]	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.
[24]	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.
[25]	CHEN G H,WU X S,WANG D Q,et al.Cluster analysis of 12 Chinese native chicken populations using microsatellite markers[J].Asian Austral J Anim Sci,2004,17(8):1047-1052.
[26]	VIALE E,ZANETTI E,ÖZDEMIR D,et al.Development and validation of a novel SNP panel for the genetic characterization of Italian chicken breeds by next-generation sequencing discovery and array genotyping[J].Poult Sci,2017,96(11):3858-3866.
[27]	ABDALHAG M A,ZHANG T,FAN Q C,et al.Single nucleotide polymorphisms associated with growth traits in Jinghai yellow chickens[J].Genet Mol Res,2015,14(4):16169-16177.
[28]	ZANETTI E,DE MARCHI M,DALVIT C,et al.Genetic characterization of local Italian breeds of chickens undergoing in situ conservation[J].Poult Sci,2010,89(3):420-427.
[29]	王洪志,李国辉,张贤,等.基于RAD-seq简化基因组测序评价鹿苑鸡不同保种群保种现状[J].畜牧兽医学报,2017,48(5):818-825.WANG H Z,LI G H,ZHANG X,et al.Conservation status evaluation of Two Luyuan chicken populations based on RAD-seq simplified genome sequencing technology[J].Acta Veterinaria et Zootechnica Sinica,2017,48(5):818-825.(in Chinese)
[30]	FU X T,DOU J Z,MAO J X,et al.RAD typing:an integrated package for accurate de novo codominant and dominant RAD genotyping in mapping populations[J].PLoS One,2013,8(11):e79960.
[31]	KANGINAKUDRU S,METTA M,JAKATI R D,et al.Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken[J].BMC Evolut Biol,2008,8:174.
[32]	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 Austral J Anim Sci,2008,21(3):331-339.
[33]	MWACHARO J M,BJØRNSTAD G,MOBEGI V,et al.Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa[J].Mol Phylog Evolut,2011,58(2):374-382.
[34]	RASHID M A,MANJULA P,FARUQUE S,et al.Genetic diversity and population structure of indigenous chicken of Bangladesh using microsatellite markers[J].Asian Austral J Anim Sci,2020,33(11):1732-1740.
[35]	HASSEN H,NESER F W C,DE KOCK A,et al.Study on the genetic diversity of native chickens in northwest Ethiopia using microsatellite markers[J].Afr J Biotechnol,2009,8(7):1347-1353.
[36]	SEO D W,HOQUE M R,CHOI N R,et al.Discrimination of Korean native chicken lines using fifteen selected microsatellite markers[J].Asian Austral J Anim Sci,2013,26(3):316-322.
[37]	YAMAMOTO Y.Genetic diversity and genetic relationship of Bangladeshi native chickens[C]//International Poultry Show & Seminar.World's Poultry Science Association-Bangladesh Branch,2011.
[38]	高玉时,李慧芳,陈国宏,等.地方鸡种微卫星DNA指纹图谱建立与遗传多样性研究[J].云南农业大学学报, 2005,20(3):313-318.GAO Y S,LI H F,CHEN G H,et al.Construction of microsatellite DNA fingerprinting and analysis of genetic diversity of native chicken breeds[J].Journal of Yunnan Agricultural University,2005,20(3):313-318.(in Chinese)
[39]	GAO Y S,TU Y J,TONG H B,et al.AFLP fingerprinting analysis of genetic polymorphism of 12 indigenous chicken breeds[J].Chin J Agric Biotechnol,2006,4(1):33-38.
[40]	杨秀荣,蒋和生,徐文文,等.广西地方鸡品种群体遗传结构及其遗传关系分析[J].中国家禽,2019,41(3):6-9.YANG X R,JIANG H S,XU W W,et al.Genetic structure and relationship analysis in Guangxi native chicken breeds[J].China Poult,2019,41(3):6-9.(in Chinese)