Genetic determinants of lettuce resistance to drop caused by Sclerotinia minor identified through genome-wide association mapping frequently co-locate with loci regulating anthocyanin content

Genetic Diversity and Evaluation of Agro-Morphological Traits in Lettuce Core Collection

Lettuce (Lactuca sativa) is a globally significant leafy vegetable, valued for both its economic and nutritional contributions. The efficient conservation and use of the lettuce germplasm are crucial for breeding and genetic improvement. This study examined the genetic diversity and population structure of a core collection of the lettuce germplasm using genotyping by sequencing (GBS). A total of 7136 high-quality single-nucleotide polymorphisms (SNPs) were identified across nine chromosomes. Population analysis through Bayesian clustering and discriminant analysis of principal components (DAPC) revealed three distinct genetic clusters. Cluster 2 exhibited the greatest genetic diversity (He = 0.29, I = 0.44), while Cluster 3 had high levels of inbreeding (F = 0.79). Agro-morphological trait evaluation further identified significant differences in leaf length, plant weight, and head height across clusters. These findings provide valuable insights into the genetic and phenotypic diversity of lettuce, facilitating the development of more robust breeding programs. Additionally, the core collection established in this study offers a representative subset of the lettuce germplasm for future genomic research and conservation efforts.

Spatio-Temporal Dynamics of Lettuce Metabolome: A Framework for Targeted Nutritional Quality Improvement

Lettuce (Lactuca sativa L.) is a popular leafy vegetable valued for its dietary fiber, antioxidants, and beneficial vitamins. This study presents a comprehensive spatio-temporal analysis of the lettuce metabolome, revealing complex dynamics in metabolite accumulation influenced by plant age, leaf position, proximodistal distribution within a leaf, and head closure. Samples were collected from plants at five maturity stages (ranging from baby leaf to full commercial maturity and eventually to bolting) and from five leaf positions (from the apex to the base of each plant). A widely targeted metabolomics approach identified 1905 compounds, with flavonoids, phenolic acids, and lipids as the largest classes. Younger plants exhibited higher levels of flavonoids, while older plants accumulated more saccharides and amino acids. Metabolites showed distinct proximodistal distributions, with flavonoids and vitamins concentrated at leaf tips and terpenoids declining from base to tip. Head closure significantly reduced levels of flavonoids, retinol (vitamin A1), and riboflavin (vitamin B2), while it was associated with increased content of other beneficial vitamins, such as thiamine (B1), pantothenate (B5), and pyridoxine (B6). Broad-sense heritability (H2) estimates for metabolites yielded mean H2 values of 0.648 and 0.743 for plants at baby-leaf and commercial maturity stages, respectively. The overall highest heritability was observed in tannins (H2 = 0.909) in younger plants and chalcones (H2 = 0.894) in older plants, suggesting strong genetic control over specific metabolite classes and subclasses. These findings offer a robust framework for optimizing lettuce's nutritional profile by linking metabolite distributions to developmental processes, plant architecture, and genetic regulation. By leveraging these insights, breeders and producers can develop targeted strategies to enhance metabolite content through optimized breeding and harvesting strategies.

Genome-wide association study of salt tolerance at the seed germination stage in lettuce

Developing lettuce varieties with salt tolerance at the seed germination stage is essential since lettuce seeds are planted half an inch deep in soil where salt levels are often highest in the salinity-affected growing regions. Greater knowledge of genetics and genomics of salt tolerance in lettuce will facilitate breeding of improved lettuce varieties with salt tolerance. Accordingly, we conducted a genome-wide association study (GWAS) in lettuce to identify marker-trait association for salt tolerance at the seed germination stage. The study involved 445 diverse lettuce accessions and 56,820 single nucleotide polymorphism (SNP) markers obtained through genotype-by-sequencing technology using lettuce reference genome version v8. GWAS using two single-locus and three multi-locus models for germination rate (GR) under salinity stress, 5 days post seeding (GR5d_S) and a salinity susceptibility index (SSI) based on GR under salinity stress and control conditions, 5 days post seeding (SSI_GR5d) revealed 10 significant SNPs on lettuce chromosomes 2, 4, and 7. The 10 SNPs were associated with five novel QTLs for salt tolerance in lettuce, explaining phenotyping variations of 5.85%, 4.38%, 4.26%, 3.77%, and 1.80%, indicating the quantitative nature of these two salt tolerance-related traits. Using the basic local alignment search tool (BLAST) within 100 Kb upstream and downstream of each of the 10 SNPs, we identified 25 salt tolerance-related putative candidate genes including four genes encoding for major transcription factors. The 10 significant salt tolerance-related SNPs and the 25 candidate genes identified in the current study will be a valuable resource for molecular marker development and marker-assisted selection for breeding lettuce varieties with improved salt tolerance at the seed germination stage.

Host cell wall composition and localized microenvironment implicated in resistance to basal stem degradation by lettuce drop (Sclerotinia minor)

BACKGROUND

Sclerotinia spp. are generalist fungal pathogens, infecting over 700 plant hosts worldwide, including major crops. While host resistance is the most sustainable and cost-effective method for disease management, complete resistance to Sclerotinia diseases is rare. We recently identified soft basal stem as a potential susceptibility factor to Sclerotinia minor infection in lettuce (Lactuca sativa) under greenhouse conditions.

RESULTS

Analysis of stem and root cell wall composition in five L. sativa and one L. serriola accessions with varying growth habits and S. minor resistance levels revealed strong association between hemicellulose constituents, lignin polymers, disease phenotypes, and basal stem mechanical strength. Accessions resistant to basal stem degradation consistently exhibited higher levels of syringyl, guaiacyl, and xylose, but lower levels of fucose in stems. These findings suggest that stem cell wall polymers recalcitrant to breakdown by lignocellulolytic enzymes may contribute to stem strength-mediated resistance against S. minor.

CONCLUSIONS

The lignin content, particularly guaiacyl and syringyl, along with xylose could potentially serve as biomarkers for identifying more resistant lettuce accessions and breeding lines. Basal stem degradation by S. minor was influenced by localized microenvironment conditions around the stem base of the plants.

Phenotypic characterization, plant growth and development, genome methylation, and mineral elements composition of neotetraploid lettuce (Lactuca sativa L.)

Stable neotetraploid lines of lettuce (Lactuca sativa L.) were produced from three phenotypically distinct cultivars (Annapolis, Eruption, Merlot) and an advanced breeding line (SM13-L2) using colchicine treatment of seeds or young seedlings. When tested under the greenhouse and field conditions, neotetraploids initially grew more rapidly than their diploid progenitors, however they reached their reproductive stage (bolting, flower bud formation, and flowering) substantially later. Seeds production on neotetraploids was delayed by more than 30 days compared to diploids. Tetraploid plants had fewer, but larger stomata and leaves, less chlorophyll per area, higher photosystem II photochemical efficiency, generally lighter root system, and produced less than 1% of seeds in comparison with diploids. Field-grown neotetraploids of all lines displayed a significant reduction in tipburn (1.8% vs. 22.2%, respectively), a highly undesirable physiological disorder. Changes in leaf and root mineral composition were detected in neotetraploids. Several elements were found in lower abundance than in diploids, most notably iron, calcium, and silicon. Whole genome bisulfite sequencing (WGBS) revealed 498 differentially methylated regions (DMR), with 106 of these regions having at least 50% difference in the level of methylation between neotetraploids and their diploid progenitors. At least 18 of the most prominent DMR were detected in proximity to genes predicted to be involved in plant development or reaction to biotic and abiotic stressors. Because neotetraploid lines have low seed production, they are not suitable for commercial cultivation. They can be used, however, in research to study the factors contributing to tipburn, traits affected by stomata size or density, and the effect of ploidy on resistance to environmental stressors.

Phytochemical and Agronomic Characterization of High-Flavonoid Lettuce Lines Grown under Field Conditions

Flavonoids are antioxidant phytochemicals that confer a beneficial effect on human health. We have previously developed and characterized eight lettuce (Latuca sativa L.) lines that accumulated high levels of diverse flavonoids and their precursors in controlled environment conditions. Three Rutgers Scarlet lettuce (RSL) lines selected in tissue culture for deep-red color (RSL-NAR, RSL-NBR, RSL-NFR) accumulate anthocyanins and quercetin, three lines identified in a chemically mutagenized red lettuce population accumulate kaempferol (KfoA and KfoB) or naringenin chalcone (Nco), and two lines that were spontaneous green mutants derived from the red line RSL-NAR (GSL, GSL-DG) accumulate quercetin. These eight lines were field-grown in the Salinas Valley of California for four years together with seven control accessions of varying colors (light green, dark green, red, and dark red). At market maturity, a substantial variation in plant composition was observed, but the three RSL lines consistently accumulated high levels of cyanidin, GSL and GSL-DG accumulated the highest levels of quercetin, KfoA and KfoB accumulated kaempferol, and Nco amassed naringenin chalcone, confirming that these mutant lines produce high levels of beneficial phytochemicals under field conditions. Mutant lines and control accessions were also assessed for their biomass production (plant weight, height, and width), overall content of pigments (leaf chlorophyll and anthocyanins), resistance to diseases (downy mildew, lettuce drop, and Impatiens necrotic spot virus), postharvest quality of processed tissue (deterioration and enzymatic discoloration), and composition of 23 mineral elements. All but one mutant line had a fresh plant weight at harvest comparable to commercial leaf cultivars; only Nco plants were significantly (p < 0.05) smaller. Therefore, except for Nco, the new, flavonoid hyperaccumulating lines can be considered for field cultivation.