Natural variation in LuGnTL modulates the trade-off between plant height and seed size in flax (Linum usitatissimum L.)

Abstract

Flax is an ancient crop cultivated for both fiber and oil, and it has undergone divergent selection into two distinct morphotypes: semi-dwarf oil flax with large seeds and tall fiber flax with small seeds. However, the genetic architecture underlying the trade-off between plant height and seed size in flax remains unclear. In this study, a genome-wide association study was performed using a diverse panel of 200 flax accessions. A major pleiotropic locus on chromosome 7 ( PS7 ) that controls the trade-off between plant height and seed size was identified. Integrative analysis combining a local Manhattan plot, a linkage disequilibrium heat map, haplotype analysis, and differential expression analysis revealed that LuGnTL , encoding a β-1,6-N-acetylglucosaminyl transferase, is the causal gene underlying this trade-off. Functional studies demonstrated that overexpression of LuGnTL reduces plant height but increases seed size. Natural variation analysis demonstrates that oil flax predominantly harbors semi-dwarf and large-seed haplotypes, whereas fiber flax preferentially retain tall and small-seed haplotypes. Population genomic evidence suggests strong divergent selection at LuGnTL during flax improvement. This study reveals that LuGnTL is a key regulator governing the trade-off between plant height and seed size in flax, and highlights its historically selected haplotypes that have contributed to the divergent improvement of oil flax and fiber flax cultivars.