Studies of genetic diversity and genome‐wide association for vitamin C content in lettuce (Lactuca sativa L.) using high‐throughput SNP arrays

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. Core Ideas Lettuce is ideal to be biofortified as it is nutritionally poor (i.e., vitamin C) but highly demanded by consumers. Traditional varieties harbor a great genetic diversity, essential for the breeding of this autogamous species. These are the first genetic associations with dehydroascorbic acid content found in lettuce: a 5.1Mb region in chromosome 2. High linkage disequilibrium values were only found between the lead single nucleotide polymorphism (SNP) and other significantly associated SNPs. Some of the candidate genes in the region of interest are involved in vitamin C metabolism in other crops. Plain Language Summary Domestication and breeding have impoverished many crops, like lettuce, in terms of nutritional value. We have explored the genetic and nutritional diversity in cultivated lettuces,