Genome-wide association of 10 horticultural traits with expressed sequence tag-derived SNP markers in a collection of lettuce lines

Genetic diversity, population structure, and genome-wide marker-trait association analyses were conducted on a special collection of 298 homozygous lettuce(Lactuca sativa L.) lines. Each of these lines was derived from a single plant that had been genotyped with 384 SNP markers using LSGermOPA. They included 122 butterhead, 53 romaine, 63 crisphead, 53 leaf and 7 stem types. Genetic diversity among these plants was assessed by pairwise comparison based on 322 high-quality SNP markers selected from 384 SNPs. Only 258 unique genotypes were identified among the 298 lines because 26 pairs or small groups(a total of 66 lines) shared identical genotypes. The average genetic similarity coefficient(GS) among these unique genotypes was 63.9% with a range of 40.6% to 99.8%. A phylogenetic tree was constructed based on the genotypic data. The most likely number of populations was estimated to be two or six. Association analysis between the 322 SNP markers and 10 phenotypic traits using the 258 homozygous lines was performed by three different methods: single factor analysis, general linear model analysis, and mixed linear model analysis. Nine significant marker-trait associations(SMTAs) were detected at P < 0.0001 with all three methods and also when considering kinship and/or population structure for this collection, with five SMTAs for seed coat color, one for leaf undulation, two for leaf anthocyanin, and one for stem anthocyanin. These markers will be useful in marker-assisted selection after further validation with segregating populations.

Molecular markers reliably predict post-harvest deterioration of fresh-cut lettuce in modified atmosphere packaging

Fresh-cut lettuce is popular,but highly perishable product.Genetic studies of two bi-parental populations derived from crossing parents with rapid and slow rates of deterioration showed that the deterioration rate is a heritable trait(broad spectrum heritability,H2 of 0.56–0.87).The major genetic determinant of the deterioration rate in both populations was the quantitative trait locus(QTL),qSL4,located on linkage group 4.This QTL explained 40–74%of the total phenotypic variation of the trait in the two populations.Saturating the qSL4 region with single-nucleotide(SNP)markers allowed detection of six haplotypes in a set of 16 lettuce accessions with different rates of deterioration.Three of the haplotypes were always associated with very rapid rates of deterioration,while the other three haplotypes were associated with slow rates of deterioration.Two SNPs located 53 bp apart were sufficient to separate the 16 accessions into two groups with different rates of deterioration.The accuracy of markers-trait association was subsequently tested on 350 plants from seven F2 families that originated from crossing parents with different rates of deterioration.The H2 of deterioration rate in these seven families ranged from 0.64 to 0.90.The SNP-based analysis accurately identified individuals with rapid,intermediate,and slow rates of deterioration in each family.Intermediate rate of deterioration was found in individuals having heterozygous alleles at qSL4,indicating an additive effect of the alleles.The assay can be used for fast,accurate,and reliable identification of deterioration rate after processing for salad.