华东地区地方鸡品种mtDNA控制区遗传多样性

Genetic diversity of local chicken breeds in East China based on mitochondrial DNA D-loop region

为了探明我国华东地区地方鸡品种的遗传多样性和群体遗传结构,追溯其母系起源和进化过程,利用PCR技术扩增了11个地方鸡品种的线粒体DNA(mtDNA)控制区(D-loop)序列,并结合NCBI数据库中已发表的红色原鸡(Gallus gallus)D-loop区全序列,分析了它们的遗传多样性与亲缘关系,构建了11个品种与红色原鸡系统发生邻接树。结果表明:11个地方品种mtDNA D-loop区全长为1,231或1,232 bp,其中1,231 bp的序列有196条,1,232 bp的序列有123条,经过比对发现,两者在859 bp处存在单碱基缺失。11个地方品种319个个体共计检测到变异位点37个,总体单倍型多样度核苷酸多样度和平均核苷酸差异分别为0.901±0.009、0.00573±0.000001和6.833。按照鸡mtDNA单倍型分类通用标准,共包含35种单倍型,可以分为A、B、C和E共4个分支(单倍型群),分别包括11、10、9和5个单倍型。中介网络图中11个鸡品种也很明显地分成了4个支系,分别含有100、118、47和54条序列。系统发育树分为4个大枝,海南亚种(G.gallus jabouillei)自成一枝;C单倍型群与4个亚种的红色原鸡聚为一枝;E单倍型群与2个亚种红色原鸡聚为一枝;A和B单倍型群只与滇南亚种(G.gallus spadiceus)聚为一枝。11个品种中,除了狼山和丝羽乌骨鸡2个标准化品种外,都有很高的遗传多样性,可开发选择潜力很大。没有发现线粒体品种特异性DNA序列。华东地区地方品种至少有4个母系起源,部分品种可能受到了欧美高产品系的渗入。

The objective of this study was to determine the origin and evolution of chickens in Eastem China by assessing the genetic diversities and structures of 11 local chicken breeds. The complete D-loop re- gion of mitochondrial DNA （mtDNA） of 319 chickens from 11 local breeds were sequenced and analyzed together with published data for the red junglefowl. These sequences were then used in a neighbor-joining method to construct the phylogenetic tree of these breeds and the red junglefowl. The D-loop regions of the local breeds were characterized by 1,231 and 1,232 bp; the 1,231 bp haplotype had 196 sequences, while the 1,232 bp haplotype had 123 sequences, with a base C deficiency from the 859 bp site in the 1,231 bp haplo- type. A total of 37 mutation sites were detected in the 319 individuals. The average haplotype diversity, nu- cleotide diversity, and nucleotide difference were 0.901 ±： 0.009, 0.005 73 ± 0.000001 and 6.833, respec- tively. A total of 35 haplotypes were identified which belonged to four previously published clades, i.e. Clades A, B, C, and E, which contained 11, 10, 9, and 5 haptotypes, respectively. Median-joining network profiles of the haplotype indicated the 11 local breeds were divided into four maternal clades containing 100, 118, 47, and 54 sequences. The cluster of five subspecies of the red junglefowl and 11 local breeds were di-vided into four distinct groups. Gallus gallusjabouillei was grouped alone. Haplotype C and four subspecies ofjtmglefowl were clustered in one group. Haplotype E and two subspecies ofjunglefowl were clustered in another group. Haplotypes A, B, and Gallus gallus spadiceus were clustered in another group. Chickens from eastern China revealed abtmdant genetic diversity in the mtDNA D-loop region, except for the Langshan and Silky breeds. No breed-specific matrilineal clade was observed. We conclude that chicken breeds from east- ern China likely share four common maternal lineages, and that some chicken populations may have been mixed with exotic lineage chickens.