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（mitochondrial genomes），已被栽培胡萝卜育种者用作遗传资源，但目前对其在自然中的多样性程度所知甚少。尤为值得关注的是，线粒体基因atp9的推定终止密码子区域存在一处单核苷酸多态性（Single Nucleotide Polymorphism，SNP），该位点此前已被证实与雄性不育、雄性可育的表型变异相关联。本研究针对采自美国东部24个种群的野胡萝卜个体，对其线粒体基因atp1、atp9及细胞色素c氧化酶亚基1（cox1）开展了序列分型或聚合酶链式反应-限制性片段长度多态性（Polymerase Chain Reaction-Restriction Fragment Length Polymorphism，PCR/RFLP）基因分型。在被调查的128个个体中，超过半数在该物种通常被认为是atp9终止密码子的位点上，携带的是CAA或AAA基因型，而非TAA基因型。研究同时发现，无论是花组织还是叶组织，均未检测到CAA终止密码子发生线粒体RNA编辑（胞嘧啶向尿嘧啶（C→U）编辑）的证据。本研究数据证实了植物线粒体基因组中基因内重组的存在——相较于更为常见的基因间重组。atp9区域其他位置以及另外两个被检测基因中的插入缺失（Insertion-Deletion，Indel）和单核苷酸多态性变异，与三种atp9终止密码子基因型呈现非随机关联；不过进一步分析表明，重组事件提升了多位点基因型的多样性。总体而言，种群间的线粒体遗传多样性仅呈现适度的种群结构分化，其固定指数（Fst）为0.34。