Guan Xiaojing, Geng Tuoyu, Silva Pradeepa, Smith Edward J
Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
J Hered. 2007 Nov-Dec;98(7):723-6. doi: 10.1093/jhered/esm094. Epub 2007 Nov 5.
Although it is known to be useful for certain genotype:phenotype assignments, our knowledge of the nature and extent of variation in the entire chicken (Gallus gallus) mitochondrial genome (mtGenome) is limited. Here, we used experimental and in silico tools to identify nucleotide variants in the mtGenome, including the coding and non-coding (D-loop) regions. The distribution of the experimentally identified mitochondrial DNA variants in meat- (broilers) and egg-type (White Leghorn) chickens was also assessed. A total of 113 single-nucleotide polymorphisms (SNPs) were identified. The in silico analysis revealed a total of 91 SNPs, with 70 in the coding region and 21 in the non-coding region. Of the 41 experimentally identified SNPs, 27 were in the D-loop. Together, the experimentally identified SNPs in the non-coding region formed 11 haplotypes, whereas the 14 SNPs in the coding region formed 6. Though, 9 of the D-loop region haplotypes were observed only in broilers, 3 of the 6 haplotypes from the coding region occurred at a significantly higher frequency in broilers. To our knowledge, this investigation represents the first whole-mtGenome scan for variation and an evaluation, though limited in sample size, of the haplotype distribution in meat- and egg-type populations, using the SNPs and haplotypes identified.
虽然已知其对某些基因型与表型的匹配有用，但我们对整个鸡（原鸡）线粒体基因组（mtGenome）变异的性质和程度的了解有限。在此，我们使用实验工具和计算机分析工具来鉴定mtGenome中的核苷酸变异，包括编码区和非编码区（D-loop）。我们还评估了实验鉴定出的线粒体DNA变异在肉用型（肉鸡）和蛋用型（白来航鸡）鸡中的分布情况。总共鉴定出113个单核苷酸多态性（SNP）。计算机分析总共揭示了91个SNP，其中70个在编码区，21个在非编码区。在实验鉴定出的41个SNP中，有27个位于D-loop区。非编码区实验鉴定出的SNP共同构成了11种单倍型，而编码区的14个SNP构成了6种单倍型。虽然D-loop区的9种单倍型仅在肉鸡中观察到，但编码区6种单倍型中的3种在肉鸡中的出现频率显著更高。据我们所知，本研究首次对整个mtGenome进行变异扫描，并利用鉴定出的SNP和单倍型，对肉用型和蛋用型群体中的单倍型分布进行了评估，尽管样本量有限。
