Leaf morphology and pigmentation are central to lettuce quality, influencing consumer preference, market value, and nutritional properties. However, these traits are genetically complex, shaped by domestication history, gene flow, and environmental interactions. Although global germplasm collections preserve extensive genetic diversity, their size and redundancy often limit efficient utilization in breeding programs. At the same time, advances in genome sequencing and association mapping have created new opportunities to link phenotypic traits with underlying genetic variation. Despite these tools, lettuce breeding has lagged behind other crops in translating genomic insights into practical cultivar development. Based on these challenges, there is a clear need to systematically integrate genetic diversity, trait dissection, and breeding strategies through in-depth research.
Researchers from the Shanghai Agrobiological Gene Center and collaborating institutions report a comprehensive genomic study that bridges lettuce genetic diversity and practical breeding outcomes. Published (DOI: 10.1093/hr/uhaf258) in Horticulture Research in 2025, the work presents a globally representative lettuce core collection and applies genome-wide association analyses to dissect key leaf traits, including anthocyanin coloration. By combining genetic discovery with genomic design breeding, the team successfully developed a new anthocyanin-enriched lettuce variety with optimized leaf morphology, demonstrating how genomic tools can directly accelerate cultivar innovation in horticultural crops.
The study began with whole-genome resequencing of 811 lettuce accessions collected worldwide, capturing extensive genetic and phenotypic diversity. From this resource, the researchers constructed a core collection of 268 accessions that retained more than 99% of the total genetic variation while remaining manageable for detailed analysis. Sixteen leaf traits—including shape, size, surface texture, and pigmentation—were evaluated across multiple growing seasons, revealing strong correlations among architectural traits and anthocyanin accumulation.
Genome-wide association studies identified 13 robust quantitative trait loci linked to leaf morphology and pigmentation. Notably, two major loci controlling anthocyanin coloration were traced to functional variants in key flavonoid biosynthesis genes, providing direct genetic explanations for red leaf coloration. Importantly, leaf pigmentation and morphology were shown to be genetically separable, allowing targeted improvement without compromising structural quality.
Building on these insights, the team implemented a genomic design breeding strategy by crossing complementary parental lines carrying favorable alleles. Through successive selection, they developed a stable lettuce variety combining high anthocyanin content with commercially desirable leaf shape. This approach demonstrates how genetic mapping and allele selection can be integrated into a streamlined breeding pipeline, transforming genomic data into tangible agricultural products.
“This work shows that genetic diversity is not just something to conserve—it is something we can actively design with,” said one of the study’s senior authors. “By constructing a representative core collection and linking precise genetic variants to visible traits, we were able to move beyond discovery and directly guide breeding decisions. The success of genomic design breeding in lettuce illustrates a powerful framework that can be applied to many horticultural crops, especially those where quality traits and nutritional value must be improved together.”
The findings provide a practical blueprint for accelerating crop improvement in leafy vegetables and beyond. Anthocyanin-rich lettuce varieties offer enhanced antioxidant properties alongside strong visual appeal, meeting growing consumer demand for healthier and more attractive foods. More broadly, the core collection and genomic design breeding strategy reduce breeding time and uncertainty, enabling precision selection of favorable trait combinations. This framework can be extended to other crops to improve nutrition, stress resilience, and market quality while preserving genetic diversity. By closing the gap between genomic research and field-ready cultivars, the study highlights how modern breeding can support sustainable agriculture and future food security.
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References
DOI
10.1093/hr/uhaf258
Original Source URL
https://doi.org/10.1093/hr/uhaf258
Funding information
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).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.