Data from: Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota)

Mitochondrial genomes extracted from wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is a SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study either sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9 and cox1 found in D. carota individuals collected from 24 populations in the eastern U.S. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intra-genic recombination, as opposed the more common inter-genic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other two genes surveyed, were non-randomly associated with the three atp9 stop codon variants, though further analysis suggested that multi-locus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an Fst of 0.34.从野胡萝卜（Daucus carota）野生种群中提取的线粒体基因组，已被栽培胡萝卜育种者作为遗传资源加以利用，但目前对其在自然中的多样性程度尚知之甚少。尤为值得关注的是，线粒体基因atp9的推定终止密码子处存在一处单核苷酸多态性（SNP），该位点此前已被证实与雄性不育及雄性可育表型变异相关。本研究针对美国东部24个种群中采集的野胡萝卜（D. carota）个体的线粒体基因atp1、atp9与cox1，获取了序列或PCR/RFLP基因型数据。在被检测的128个个体中，超过半数的个体在该物种通常被认为行使atp9终止密码子功能的位点上，携带CAA或AAA基因型，而非TAA基因型。我们同时发现，无论是花组织还是叶组织中，均未检测到CAA终止密码子发生线粒体RNA编辑（mitochondrial RNA editing，胞嘧啶向尿嘧啶转变）的证据。本研究数据集提供了基因内重组的证据，这与植物线粒体基因组中更为普遍的基因间重组形成对比。atp9基因其他区域以及本次检测的另外两个基因中存在的插入缺失（Indel）与单核苷酸多态性（SNP）变异，与atp9终止密码子的三种变异类型呈非随机关联；不过进一步分析表明，多位点基因型多样性因重组作用而得到增强。总体而言，种群间线粒体遗传多样性的结构仅为中等程度，其群体分化系数（Fst）为0.34。