A comprehensive lettuce variation map reveals the impact of structural variations in agronomic traits

Zhaowu Zhang, Rob van Treuren, Ting Yang, Yulan Hu, Wenhui Zhou, Huan Liu*, Tong Wei*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Background: As an important vegetable crop, cultivated lettuce is grown worldwide and a great variety of agronomic traits have been preserved within germplasm collections. The mechanisms underlying these phenotypic variations remain to be elucidated in association with sequence variations. Compared with single nucleotide polymorphisms, structural variations (SVs) that have more impacts on gene functions remain largely uncharacterized in the lettuce genome. Results: Here, we produced a comprehensive SV set for 333 wild and cultivated lettuce accessions. Comparison of SV frequencies showed that the SVs prevalent in L. sativa affected the genes enriched in carbohydrate derivative catabolic and secondary metabolic processes. Genome-wide association analysis of seven agronomic traits uncovered potentially causal SVs associated with seed coat color and leaf anthocyanin content. Conclusion: Our work characterized a great abundance of SVs in the lettuce genome, and provides a valuable genomic resource for future lettuce breeding.

Original languageEnglish
Article number659
JournalBMC Genomics
Volume24
Issue number1
DOIs
Publication statusPublished - Dec 2023

Keywords

  • Cultivated lettuce
  • Genome-wide association analysis
  • Structural variations

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