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.

株高是双向调节亚麻韧皮纤维和种子产量的关键农艺性状。尽管油麻和纤维亚麻的株高有显着差异，但植株高度的遗传基础在很大程度上仍是未知的。本研究对模式种拟南芥和水稻（Oryza sativaL.) 与亚麻基因组同源对齐。并结合报道的亚麻株高候选基因，认为有1593个基因与亚麻株高有潜在关联。随后，对高大和矮小亚麻品种的转录组分析显示，532 个候选基因在断裂点以上的年轻茎组织中差异表达，被视为植物高度的初步候选基因。接下来，使用包含四个环境中的 200 个亚麻种质的核心集合进行种群水平验证，并且重复检测到至少两个环境与植物高度显着相关的 30 个基因。总之，我们的研究提供了一种新策略，通过结合转录组和种群水平验证来快速识别与农艺性状相关的候选基因。