Articles
Genome-wide association studies reveal a key region in chromosome 2 to explain variation in dehydroascorbic acid content in lettuce (Lactuca sativa L.)
Article number
1454_58
Pages
421 – 428
Language
English
Abstract
Lettuce (Lactuca sativa L.) is a widely consumed leafy vegetable that contains a great variety of health-promoting compounds, although usually in low quantities.
Total ascorbic acid (TAA, vitamin C), one of the main indicators of the nutritional quality of plant-based food, is the predominant vitamin in lettuce.
A genome-wide association study (GWAS) of vitamin C content was conducted in 21 commercial and traditional lettuce cultivars and a population of 205 plants from ‘Lechuga del Pirineo’, which was the cultivar with the highest TAA content among the 21 assayed.
All samples were genotyped using 9,242 SNP (single nucleotide polymorphism) markers.
Three different methods were used to assess the population structure, cluster membership coefficients, multidimensional scaling and principal component analysis (PCA). The three approaches detected significant genetic associations with dehydroascorbic acid (DHAA) content, a form of vitamin C, in a 5.1 Mb region of chromosome 2. Both the largest number of significantly associated SNPs (17) and the highest significance values were found using PCA. Strong linkage disequilibrium (LD) with the lead SNP was only observed for markers that were also significantly associated with DHAA content (12 SNPs in 7 different genes). The highest LD values were not always obtained among the physically closest or the most significantly associated SNPs, suggesting that multiple loci could be contributing to the variation in DHAA content.
Among the 84 genes within the region, some are putatively related to vitamin C, as they have been reported to be involved in vitamin C content in other crops, like those encoding F-box proteins, a pectinesterase/pectinesterase inhibitor and a long noncoding RNA. Although further studies are needed to elucidate their role in vitamin C content, this work contributes to a better understanding of the genetic basis of this quality trait, which might be helpful in breeding programmes for lettuce biofortification.
Total ascorbic acid (TAA, vitamin C), one of the main indicators of the nutritional quality of plant-based food, is the predominant vitamin in lettuce.
A genome-wide association study (GWAS) of vitamin C content was conducted in 21 commercial and traditional lettuce cultivars and a population of 205 plants from ‘Lechuga del Pirineo’, which was the cultivar with the highest TAA content among the 21 assayed.
All samples were genotyped using 9,242 SNP (single nucleotide polymorphism) markers.
Three different methods were used to assess the population structure, cluster membership coefficients, multidimensional scaling and principal component analysis (PCA). The three approaches detected significant genetic associations with dehydroascorbic acid (DHAA) content, a form of vitamin C, in a 5.1 Mb region of chromosome 2. Both the largest number of significantly associated SNPs (17) and the highest significance values were found using PCA. Strong linkage disequilibrium (LD) with the lead SNP was only observed for markers that were also significantly associated with DHAA content (12 SNPs in 7 different genes). The highest LD values were not always obtained among the physically closest or the most significantly associated SNPs, suggesting that multiple loci could be contributing to the variation in DHAA content.
Among the 84 genes within the region, some are putatively related to vitamin C, as they have been reported to be involved in vitamin C content in other crops, like those encoding F-box proteins, a pectinesterase/pectinesterase inhibitor and a long noncoding RNA. Although further studies are needed to elucidate their role in vitamin C content, this work contributes to a better understanding of the genetic basis of this quality trait, which might be helpful in breeding programmes for lettuce biofortification.
Authors
I. Medina-Lozano, J.R. Bertolín, J. Plieske, M. Ganal, H. Gnad, A. Díaz
Keywords
candidate genes, linkage disequilibrium, nutritional value, population structure, single nucleotide polymorphism, vitamin C
Groups involved
- Division Plant Genetic Resources, Breeding and Biotechnology
- Working Group Genetic Transformation and Gene Editing
- Working Group Horticultural Biotechnology and Breeding
- Division Ornamental Plants
- Division Vegetables, Roots and Tubers
- Division Temperate Tree Fruits
- Division Vine and Berry Fruits
- Division Horticulture for Development
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