Studies of genetic diversity and genome‐wide association for vitamin C content in lettuce (Lactuca sativa L.) using high‐throughput SNP arrays
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Date
2024
Authors
Medina Lozano, InésBertolín Pardos, Juan Ramón
Plieske, Jörg
Ganal, Martin
Gnad, Heike
Díaz Bermúdez, Aurora
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Abstract
Lettuce (Lactuca sativa L.) is a source of beneficial compounds though they are generally present in low quantities. We used 40K Axiom and 9K Infinium SNP (single nucleotide polymorphism) arrays to (i) explore the genetic variability in 21 varieties and (ii) carry out genome-wide association studies (GWAS) of vitamin C content in21 varieties and a population of 205 plants from the richest variety in vitamin C (‘Lechuga del Pirineo’). Structure and phylogenetic analyses showed that the group formed mainly by traditional varieties was the most diverse, whereas the red commercial varieties clustered together and very distinguishably apart from the rest. GWAS consistently detected, in a region of chromosome 2, several SNPs related to dehydroascorbic acid (a form of vitamin C) content using three different methods to assess population structure, subpopulation membership coefficients, multidimensional scaling, and principal component analysis. The latter detected the highest number of SNPs (17) and the most significantly associated, 12 of them showing a high linkage disequilibrium with the lead SNP. Among the 84 genes in the region, some have been reported to be related to vitamin C content or antioxidant status in other crops either directly, like those encoding long non-coding RNA, several F-box proteins, and a pectinesterase/pectinesterase inhibitor, or indirectly, like extensin-1-like protein and endoglucanase 2 genes. The involvement of other genes identified within the region in vitamin C levels needs to be further studied. Understanding the genetic control of such an important quality trait in lettuce becomes very relevant from a breeding perspective.
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Bibliographic citation
Medina-Lozano, I., Bertolín, J. R., Plieske, J., Ganal, M., Gnad, H., & Díaz, A. (2024). Studies of genetic diversity and genome-wide association for vitamin C content in lettuce (Lactuca sativa L.) using high-throughput SNP arrays. The Plant Genome, e20518. https://doi.org/10.1002/tpg2.20518
AGROVOC subjects
Lactuca sativaPolimorfismo de un solo nucleótido
Ácido ascórbico
Estudios de asociación del genoma completo
Diversidad genética (como recurso)
Other field subjects
Ácido AscórbicoDiversidad Genética (Como Recurso)
Estudios de asociación del genoma completo
Lactuca Sativa
Polimorfismo De Un Solo Nucleótido
Sponsorship
This work was funded by the projects PID2022-138484OR-I00 from the Spanish Ministry of Science and Innovation (MCIN) and State Research Agency (AEI) and AGROALNEXT BIODIVERSA from the MCIN with funding from European Union (EU) NextGenerationEU: PRTR-C17.I1, and by the European Social Fund from the EU through the Government of Aragon (A12_23R: “Grupo de investigación en fruticultura: caracterización, adaptación y mejora genética”). Inés Medina-Lozano was supported by a predoctoral contract for training doctors from the Spanish Ministry of Science, Innovation and Universities (MCIU) and the AEI.