Transcriptome combined with population level validation reveals genomic loci controlling plant height in flax (Linum usitatissimum L.)

•The variation of plant height among flax were mainly formed in the fast growth stage.•A total of 532 genes were identified as preliminary candidate genes for plant height.•Thirty genes associated with plant height were identified by population level validation.•These genomic loci provide targets for genetic improvements in flax breeding. Plant height is a key agronomic trait in bidirectional regulation of flax bast fiber and seeds yield. Although plant height is significantly distinct between oil flax and fiber flax, the genetic basis of plant height remains largely unknown. In this study, plant height related genes in model species Arabidopsis thaliana and rice (Oryza sativa L.) were homologous aligned to flax genome. And combined with the reported flax plant height candidate genes, 1593 genes were considered to have potential association with plant height in flax. Subsequently, a transcriptome analysis of tall and dwarf flax cultivars revealed that 532 candidates were differentially expression in young stem tissue above snap point, which were regarded as preliminary candidate genes for plant height. Next, the population level validation was performed using a core collection containing 200 flax accessions across four environments, and 30 genes repeatedly detected at least two environments were significantly associated with plant height. Taken together, our study provides a new strategy to rapid identify candidate genes associated with agronomic traits by combining transcriptome and population level validation. Meanwhile, our results provide valuable genomic resources and molecular insight into variation of plant height in flax subgroups, and may accelerate the improvement of high yield flax based on genomics-assisted breeding.