Abstract
Anthocyanin biosynthesis is one of the most studied pathways in plants due to the important ecological role played by these compounds and the potential health benefits of anthocyanin consumption. Given the interest in identifying new genetic factors underlying anthocyanin content we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses. By using an expanded SNP dataset, we identified candidate genes that had not been associated with anthocyanin variation in potatoes, namely a Myb transcription factor, a Leucoanthocyanidin dioxygenase gene and a vacuolar membrane protein. Importantly, a genomic region in chromosome 10 harbored the SNPs with strongest associations with anthocyanin content in GWAS. Some of these SNPs were associated with multiple anthocyanin compounds and therefore could underline the existence of pleiotropic genes or anthocyanin biosynthetic clusters. We identified multiple anthocyanin homologs in this genomic region, including four transcription factors and five enzymes that could be governing anthocyanin variation. For instance, a SNP linked to the phenylalanine ammonia-lyase gene, encoding the first enzyme in the phenylpropanoid biosynthetic pathway, was associated with all of the five anthocyanins measured. Finally, we combined a pathway analysis and GWAS of other agronomic traits to identify pathways related to anthocyanin biosynthesis in potatoes. We found that methionine metabolism and the production of sugars and hydroxycinnamic acids are genetically correlated to anthocyanin biosynthesis. The results contribute to the understanding of anthocyanins regulation in potatoes and can be used in future breeding programs focused on nutraceutical food.
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Claims 5
Claim · model-written summary
Candidate genes not previously associated with anthocyanin variation in potatoes were identified: a Myb transcription factor, a leucoanthocyanidin dioxygenase gene and a vacuolar membrane protein.
- Taxon
- diploid potatoese0
- Material
- diverse collection of diploid potatoese0
- Gene
- Myb transcription factor, a Leucoanthocyanidin dioxygenase gene and a vacuolar membrane proteine1
- Outcome
- anthocyanin variatione1
Not reportedDirection
Verbatim
e0“we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses”
e1“we identified candidate genes that had not been associated with anthocyanin variation in potatoes, namely a Myb transcription factor, a Leucoanthocyanidin dioxygenase gene and a vacuolar membrane protein”
Claim · model-written summary
SNPs in a genomic region of chromosome 10 showed the strongest associations with anthocyanin content in GWAS.
Not reportedDirection
Verbatim
e0“we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses”
e2“a genomic region in chromosome 10 harbored the SNPs with strongest associations with anthocyanin content in GWAS”
Claim · model-written summary
Some SNPs were associated with multiple anthocyanin compounds, which may reflect pleiotropic genes or anthocyanin biosynthetic clusters.
- Taxon
- diploid potatoese0
- Material
- diverse collection of diploid potatoese0
- Outcome
- multiple anthocyanin compoundse3
- Qualifier
- could underline the existence of pleiotropic genes or anthocyanin biosynthetic clusterse3
Not reportedDirection
Verbatim
e0“we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses”
e3“Some of these SNPs were associated with multiple anthocyanin compounds and therefore could underline the existence of pleiotropic genes or anthocyanin biosynthetic clusters”
Claim · model-written summary
A SNP linked to the phenylalanine ammonia-lyase gene was associated with all five anthocyanins measured.
- Taxon
- diploid potatoese0
- Gene
- phenylalanine ammonia-lyase genee4
- Outcome
- all of the five anthocyanins measurede4
Not reportedDirection
Verbatim
e0“we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses”
e4“a SNP linked to the phenylalanine ammonia-lyase gene, encoding the first enzyme in the phenylpropanoid biosynthetic pathway, was associated with all of the five anthocyanins measured”
Claim · model-written summary
Methionine metabolism, sugar production and hydroxycinnamic acid production are genetically correlated with anthocyanin biosynthesis.
Not reportedDirection
Verbatim
e0“we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses”
e5“We found that methionine metabolism and the production of sugars and hydroxycinnamic acids are genetically correlated to anthocyanin biosynthesis”