基于SNP芯片分析贵州地方鸡品种(类群)的遗传多样性

Genetic diversity of local chicken breeds(groups)in Guizhou based on SNP chip

【目的】了解贵州地方鸡品种遗传多样性及确定品种间的遗传关系,为贵州地方鸡品种(类群)资源的保护和创新利用提供参考依据。【方法】采集香炉山鸡(SL)、瑶山鸡(YS)、黔东南小香鸡(XX)和威宁鸡(WN)共66份血液样本,基于京芯一号鸡55K SNP芯片对4个贵州地方鸡品种(类群)进行SNP位点检测,采用Plink v1.90、VCFtools v0.1.17和Admixture v1.3分别进行遗传多样性、群体结构及亲缘关系分析。【结果】4个贵州地方鸡品种(类群)的有效群体含量(Ne)介于3.1~3.2,且期望杂合度(He)均低于观察杂合度(Ho),多态信息含量(PIC)排序为威宁鸡(0.8583)>瑶山鸡(0.8350)>黔东南小香鸡(0.8123)>香炉山鸡(0.8001),均大于0.50,呈高度多态性,遗传多样性丰富。基于状态同源(IBS)遗传距离矩阵构建的系统发育进化树显示,香炉山鸡的分支最长、威宁鸡的分支最短。主成分分析(PCA)结果表明,4个贵州地方鸡品种(类群)间的界限分明,且各品种(类群)间无相互渗透现象;在Admixture祖代分析中,祖先集群数量(K)=2时,群体分群效果最佳,说明4个贵州地方鸡品种(类群)有2个共同的祖先。4个贵州地方鸡品种(类群)间的群体分化系数(Fst)接近0.05,说明群体间并未产生明显分化。4个贵州地方鸡品种(类群)的G矩阵亲缘关系分析结果和IBS遗传距离分析结果一致,香炉山鸡群个体间的亲缘关系和遗传距离最近,而威宁鸡群个体间的亲缘关系和遗传距离最远。【结论】4个贵州地方鸡品种(类群)遗传多样性较丰富,且品种(类群)间的界限明显,无相互渗透现象,但亲缘关系中有部分品种(类群)间存在近交风险,因此今后的育种工作应进一步改良香炉山鸡和黔东南小香鸡的配种方式,并适当增加群体数量及公母比例,以避免近交衰退。

【Objective】This study aimed to analyze the genetic diversity of Guizhou local chicken breeds(groups)and determine the genetic relationship among breeds,so as to provide reference for the protection and innovative utilization of Guizhou local chicken breeds resources.【Method】A total of 66 blood samples were collected from four Guizhou local chicken breeds(groups)[Xianglushan chicken(SL),Yaoshan chicken(YS),Qiandongnan Xiaoxiang chicken(XX)and Weining chicken(WN)].SNP loci detection for the four Guizhou local chicken breeds(groups)was conducted based on Jingxin No.1 chicken 55 K SNP chip.The genetic diversity,population structure and genetic relationship of the four Guizhou local chicken breeds(groups)were analyzed using Plink v1.90,VCFtools v0.1.17 and Admixture v1.3,respectively.【Result】The effective population content(Ne)among the four Guizhou local chicken breeds(groups)ranged from 3.1 to 3.2,and the expected heterozygosity(He)was all lower than the observed heterozygosity(Ho).The polymorphism information content(PIC)rankings were as follows:Weining chicken(0.8583)>Yaoshan chicken(0.8350)>Qiandongnan Xiaoxiang chicken(0.8123)>Lushan chicken(0.8001),all above 0.50,indicating that the four Guizhou local chicken breeds(groups)were highly polymorphic and rich in genetic diversity.The phylogenetic tree based on the identity by state(IBS)genetic distance matrix showed that Xianglushan chicken had the longest branch and Weining chicken had the shortest branch.The results of principal component analysis(PCA)showed that the boundaries between the four Guizhou local chicken breeds(groups)were clear,and there was no mutual penetration between the breeds(groups).In the Admixture progenitor analysis,the optimal group clustering occurred when the number of ancestor clusters(K)=2,indicating that Xianglushan chicken,Yaoshan chicken,Qiandongnan chicken and Weining chicken had two common ancestors.The population differentiation coefficient(Fst)among the four Guizhou local chicken breeds(groups)was close to 0.05,indicating that there was no obvious differentiation among the groups.The results of G matrix kinship analysis of four Guizhou local chicken breeds(groups)were consistent with the results of IBS genetic distance analysis.The interindividual kinship and genetic distance between Xianglushan chicken individuals were the closest,whereas those between Weining chicken individual were the farthest.【Conclusion】The four Guizhou local chicken breeds(groups)exhibit rich genetic diversity with clear boundaries between breeds(groups),and there is no mutual penetration phenomenon.However,there is risk of inbreeding among some breeds(groups)in the kinship.Therefore,it is neccesary to improve breeding methods of Xianglushan chickens and Qiandongnan Xiaoxiang chickens in the future breeding work,appropriately increase the number of groups and the male-to-female ratio to avoid inbreeding decline.