Dataset Information

Pervasive Mitochondrial Sequence Heteroplasmy in Natural Populations of Wild Carrot, Daucus carota spp. carota L.

ABSTRACT: Exceptions to the generally accepted rules that plant mitochondrial genomes are strictly maternally inherited and that within-individual sequence diversity in those genomes, i.e., heteroplasmy, should be minimal are becoming increasingly apparent especially with regard to sequence-level heteroplasmy. These findings raise questions about the potential significance of such heteroplasmy for plant mitochondrial genome evolution. Still studies quantifying the amount and consequences of sequence heteroplasmy in natural populations are rare. In this study, we report pervasive sequence heteroplasmy in natural populations of wild carrot, a close relative of the cultivated crop. In order to assay directly for this heteroplasmy, we implemented a quantitative PCR assay that can detect and quantify intra-individual SNP variation in two mitochondrial genes (Cox1 and Atp9). We found heteroplasmy in > 60% of all wild carrot populations surveyed and in > 30% of the 140 component individuals that were genotyped. Heteroplasmy ranged from a very small proportion of the total genotype (e.g., 0.995:0.005) to near even mixtures (e.g., 0.590:0.410) in some individuals. These results have important implications for the role of intra-genomic recombination in the generation of plant mitochondrial genome genotypic novelty. The consequences of such recombination are evident in the results of this study through analysis of the degree of linkage disequilibrium (LD) between the SNP sites at the two genes studied.

SUBMITTER: Mandel JR

PROVIDER: S-EPMC4546501 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Pervasive Mitochondrial Sequence Heteroplasmy in Natural Populations of Wild Carrot, Daucus carota spp. carota L.

Mandel Jennifer R JR McCauley David E DE

PloS one 20150821 8

Exceptions to the generally accepted rules that plant mitochondrial genomes are strictly maternally inherited and that within-individual sequence diversity in those genomes, i.e., heteroplasmy, should be minimal are becoming increasingly apparent especially with regard to sequence-level heteroplasmy. These findings raise questions about the potential significance of such heteroplasmy for plant mitochondrial genome evolution. Still studies quantifying the amount and consequences of sequence heter ...[more]

PMID: 26295342

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Project description:BackgroundDairy products like ice cream, yogurt and buttermilk are consumed widely due to their rich taste but these products lack anthocyanins, which are polyphenol and exhibit great antioxidant activity in both in vivo and in vitro studies. Therefore, adding a natural source of these antioxidants to the commonly consumed dairy product will be beneficial to the masses. Among all the sources, black carrots are the extraordinary and cheapest source of anthocyanins, which are commonly consumed as a natural fermented drink. In this study, an attempt has been made to examine the feasibility of black carrot concentrate as an ingredient into dairy products.MethodologyIce cream, yogurt and buttermilk were prepared by incorporating black carrot concentrate at 2.5, 5.0, 7.5 and 10% level and were subjected to sensory analysis. The most acceptable products with 7.5% black carrot concentrate were analyzed for minerals, polyphenols and antioxidant activity. Effects of storage on physicochemical, microbial and sensory attributes of black carrot concentrate incorporated dairy products were further analyzed.ResultsSensory analysis revealed that black carrot concentrate could be used up to 7.5% as an ingredient into dairy product with high acceptability. Significant improvement in mineral content (Mg and Fe), polyphenols and antioxidant activity were reported in black carrot concentrate added dairy products. Developed dairy products exhibited an excellent amount of 24.52-113.27 mg/100g anthocyanins. Flavonoids increased by 14.52-34.62 times and Folin-Ciocalteu reducing capacity increased by 26.39-35.87 times in experimental dairy products. The storage study revealed that ice cream could be stored for more than 60 days, yogurt up to 5 days and buttermilk up to 10 days with excellent stability attributes.ConclusionIncorporation of black carrot concentrate at the level of 7.5% resulted in high acceptability and exceptional nutraceutical property of dairy products. Incorporation of black carrot concentrate into dairy products would enhance the nutraceutical properties and mineral content of food, which could be highly significant in preventing hidden hunger and oxidative stress-induced disorders in developing countries.

Project description:Purple carrots can accumulate large quantities of anthocyanins in their roots and -in some genetic backgrounds- petioles, and therefore they represent an excellent dietary source of antioxidant phytonutrients. In a previous study, using linkage analysis in a carrot F2 mapping population segregating for root and petiole anthocyanin pigmentation, we identified a region in chromosome 3 with co-localized QTL for all anthocyanin pigments of the carrot root, whereas petiole pigmentation segregated as a single dominant gene and mapped to one of these "root pigmentation" regions conditioning anthocyanin biosynthesis. In the present study, we performed fine mapping combined with gene expression analyses (RNA-Seq and RT-qPCR) to identify candidate genes controlling anthocyanin pigmentation in the carrot root and petiole. Fine mapping was performed in four carrot populations with different genetic backgrounds and patterns of pigmentation. The regions controlling root and petiole pigmentation in chromosome 3 were delimited to 541 and 535 kb, respectively. Genome wide prediction of transcription factor families known to regulate the anthocyanin biosynthetic pathway coupled with orthologous and phylogenetic analyses enabled the identification of a cluster of six MYB transcription factors, denominated DcMYB6 to DcMYB11, associated with the regulation of anthocyanin biosynthesis. No anthocyanin biosynthetic genes were present in this region. Comparative transcriptome analysis indicated that upregulation of DcMYB7 was always associated with anthocyanin pigmentation in both root and petiole tissues, whereas DcMYB11 was only upregulated with pigmentation in petioles. In the petiole, the level of expression of DcMYB11 was higher than DcMYB7. DcMYB6, a gene previously suggested as a key regulator of carrot anthocyanin biosynthesis, was not consistently associated with pigmentation in either tissue. These results strongly suggest that DcMYB7 is a candidate gene for root anthocyanin pigmentation in all the genetic backgrounds included in this study. DcMYB11 is a candidate gene for petiole pigmentation in all the purple carrot sources in this study. Since DcMYB7 is co-expressed with DcMYB11 in purple petioles, the latter gene may act also as a co-regulator of anthocyanin pigmentation in the petioles. This study provides linkage-mapping and functional evidence for the candidacy of these genes for the regulation of carrot anthocyanin biosynthesis.

Dataset Information

Pervasive Mitochondrial Sequence Heteroplasmy in Natural Populations of Wild Carrot, Daucus carota spp. carota L.

Publications

Pervasive Mitochondrial Sequence Heteroplasmy in Natural Populations of Wild Carrot, Daucus carota spp. carota L.

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