Genome-wide association study in a lettuce core collection from 811 accessions reveals genetic loci for anthocyanin accumulation and cultivar development

Abstract

Lettuce (Lactuca sativa) is a globally cultivated leafy vegetable with leafy morphology critically influencing consumer preference and market value. Despite the agronomic importance of leaf traits, the genetic basis underlying their diversity remains poorly characterized. To address this, we resequenced 811 accessions collected from major lettuce production areas as well as the relative wild species, and developed a publicly accessible core collection of 268 accessions that captures 99.4% of the total genetic variation. Phenotypic evaluation of 16 leaf morphological traits across two growing seasons identified significant correlations, including negative associations between plant width and anthocyanin content, and positive correlations between apical margin incision and multiple traits. Population structure analysis revealed frequent introgression events from looseleaf type into domesticated varieties (butterhead, crisphead, romaine, and stem lettuce), highlighting dynamic gene flow during breeding. Genome-wide association studies (GWAS) pinpointed 13 robust quantitative trait loci (QTLs) and candidate genes regulating leaf morphology, including a validated anthocyanin biosynthesis regulator (ANS). Notably, we pinpointed the causal gene genotypes responsible for leaf anthocyanin coloration. Leveraging these findings, we successfully aggregated favorable alleles through genomic design breeding to develop a novel high-anthocyanin variety binfen5 with desirable leaf morphology. This integrative approach demonstrates the value of core germplasms and genomic tools for accelerating lettuce improvement.

Acknowledgements

This work funded by the Shanghai Science and Technology Support Project (24010700800), Shared Platform of Crop Germplasm Resources in Shanghai (21DZ2290600), and National Crop Germplasm Resources Center (NCGRC-2024-21). We acknowledge the Germplasm Resources Information Network (USDA) for kindly providing the lettuce accessions used in this study.

Authors contributions

S.W. and L.L. conceived the study and designed the experiments. G.H., S.H., G.G., G.X., Y.H., and Y.Y.H. planted and collected the leaf tissue samples. Y.Z., X.Y., L.W., and Z.L. performed data analysis. H.W. and S.W. were mainly involved in preparation of the manuscript. L.L. and S.W. revised the article. All authors provided input during the writing of the manuscript. All authors reviewed and approved the final manuscript.

Data availability

Genome resequencing data from a diverse collection of 811 lettuce accessions and the core collection of 268 accessions have been deposited in the NCBI Sequence Read Archive (SRA) under accession numbers PRJNA1250783 and PRJNA1127331, respectively. The raw VCF file of the complete SNP dataset for all 811 lettuce accessions is available for download at the following doi: 10.6084/m9.figshare.30017797.

Conflicts of interest statement

The authors declare that they have no competing or financial interests.

Supplementary material

Supplementary material is available at Horticulture Research online.

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