Studies of genetic diversity and genome‐wide association for vitamin C content in lettuce (Lactuca sativa L.) using high‐throughput SNP arrays
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 associatio...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2024-12-01
|
| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20518 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850163756698435584 |
|---|---|
| author | Inés Medina‐Lozano Juan Ramón Bertolín Jörg Plieske Martin Ganal Heike Gnad Aurora Díaz |
| author_facet | Inés Medina‐Lozano Juan Ramón Bertolín Jörg Plieske Martin Ganal Heike Gnad Aurora Díaz |
| author_sort | Inés Medina‐Lozano |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-5dfc0a9fc0c94cfd882a80fe4d2bc3b0 |
| institution | OA Journals |
| issn | 1940-3372 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj-art-5dfc0a9fc0c94cfd882a80fe4d2bc3b02025-08-20T02:22:10ZengWileyThe Plant Genome1940-33722024-12-01174n/an/a10.1002/tpg2.20518Studies of genetic diversity and genome‐wide association for vitamin C content in lettuce (Lactuca sativa L.) using high‐throughput SNP arraysInés Medina‐Lozano0Juan Ramón Bertolín1Jörg Plieske2Martin Ganal3Heike Gnad4Aurora Díaz5Department of Plant Sciences Agrifood Research and Technology Centre of Aragon (CITA) Zaragoza SpainAgriFood Institute of Aragon–IA2 (CITA‐University of Zaragoza) Zaragoza SpainSGS Institut Fresenius GmbH TraitGenetics Section Seeland GermanySGS Institut Fresenius GmbH TraitGenetics Section Seeland GermanySGS Institut Fresenius GmbH TraitGenetics Section Seeland GermanyDepartment of Plant Sciences Agrifood Research and Technology Centre of Aragon (CITA) Zaragoza SpainAbstract 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.https://doi.org/10.1002/tpg2.20518 |
| spellingShingle | Inés Medina‐Lozano Juan Ramón Bertolín Jörg Plieske Martin Ganal Heike Gnad Aurora Díaz 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 |
| title | Studies of genetic diversity and genome‐wide association for vitamin C content in lettuce (Lactuca sativa L.) using high‐throughput SNP arrays |
| title_full | Studies of genetic diversity and genome‐wide association for vitamin C content in lettuce (Lactuca sativa L.) using high‐throughput SNP arrays |
| title_fullStr | Studies of genetic diversity and genome‐wide association for vitamin C content in lettuce (Lactuca sativa L.) using high‐throughput SNP arrays |
| title_full_unstemmed | Studies of genetic diversity and genome‐wide association for vitamin C content in lettuce (Lactuca sativa L.) using high‐throughput SNP arrays |
| title_short | Studies of genetic diversity and genome‐wide association for vitamin C content in lettuce (Lactuca sativa L.) using high‐throughput SNP arrays |
| title_sort | studies of genetic diversity and genome wide association for vitamin c content in lettuce lactuca sativa l using high throughput snp arrays |
| url | https://doi.org/10.1002/tpg2.20518 |
| work_keys_str_mv | AT inesmedinalozano studiesofgeneticdiversityandgenomewideassociationforvitaminccontentinlettucelactucasativalusinghighthroughputsnparrays AT juanramonbertolin studiesofgeneticdiversityandgenomewideassociationforvitaminccontentinlettucelactucasativalusinghighthroughputsnparrays AT jorgplieske studiesofgeneticdiversityandgenomewideassociationforvitaminccontentinlettucelactucasativalusinghighthroughputsnparrays AT martinganal studiesofgeneticdiversityandgenomewideassociationforvitaminccontentinlettucelactucasativalusinghighthroughputsnparrays AT heikegnad studiesofgeneticdiversityandgenomewideassociationforvitaminccontentinlettucelactucasativalusinghighthroughputsnparrays AT auroradiaz studiesofgeneticdiversityandgenomewideassociationforvitaminccontentinlettucelactucasativalusinghighthroughputsnparrays |