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

• Published in: The Journal of heredity 2012-05, Vol.103 (3), p.418-425
• Main Authors: Mandel, Jennifer R, McAssey, Edward V, Roland, Katherine M, McCauley, David E
• Format: Article
• Language: English
• Subjects: Codon, Terminator; Crops; Cyclooxygenase-1; Cytosine; Data processing; Daucus; Daucus carota; Daucus carota - genetics; Electron Transport Complex IV - genetics; Evolution, Molecular; Genes, Mitochondrial; Genetic diversity; Genetic resources; Genetic Variation; Genomes; Genotype; Genotypes; Heredity; Leaves; Mitochondria; Mitochondrial Proton-Translocating ATPases - genetics; Phenotype; Plant Proteins - genetics; Polymerase chain reaction; Polymorphism, Restriction Fragment Length; Polymorphism, Single Nucleotide; Recombination; Recombination, Genetic; Ribonucleic acid; RNA; RNA Editing; RNA, Plant - genetics; Sequence Analysis, DNA; Single-nucleotide polymorphism; Stop codon; Studies; Uridine
• ISSN: 0022-1503; 1465-7333
• DOI: 10.1093/jhered/esr142

Mitochondrial genomes extracted from the 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 an 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 the 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 United States. 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 intragenic recombination, as opposed to the more common intergenic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other 2 genes surveyed, were nonrandomly associated with the 3 atp9 stop codon variants, though further analysis suggested that multilocus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an F(ST) of 0.34.