Seed size and weight are key traits determining crop yield, which often undergo strongly artificial selection during crop domestication. Although seed sizes differ significantly between oil flax and fiber flax, the genetic basis of morphological differences and artificial selection characteristics in seed size remains largely unclear. Here we re-sequenced 200 flax cultivated accessions to generate a genome variation map based on chromosome assembly reference genomes. We provide evidence that oil flax group is the ancestor of cultivated flax, and the oil-fiber dual purpose group (OF) is the evolutionary intermediate transition state between oil and fiber flax. Genome-wide association studies (GWAS) were combined with LD Heatmap to identify candidate regions related to seed size and weight, then candidate genes were screened based on detailed functional annotations and estimation of nucleotide polymorphism effects. Using this strategy, we obtained 13 candidate genes related to seed size and weight. Selective sweeps analysis indicates human-involved selection of small seeds during the oil to fiber flax transition. Our study shows the existence of elite alleles for seed size and weight in flax germplasm and provides molecular insights into approaches for further improvement.

Soil salinization seriously affects the growth and distribution of flax. However, there is little information about the salt tolerance of flax. In this study, the salt tolerance of 200 diverse flax accessions during the germination stage was evaluated, and then the Genome-wide Association Study (GWAS) was carried out based on the relative germination rate (RGR), relative shoot length (RSL) and relative root length (RRL), whereby quantitative trait loci (QTLs) related to salt tolerance were identified. The results showed that oil flax had a better salt tolerance than fiber flax. A total of 902 single nucleotide polymorphisms (SNPs) were identified on 15 chromosomes. These SNPs were integrated into 64 QTLs, explaining 14.48 to 29.38% (R²) of the phenotypic variation. In addition, 268 candidate genes were screened by combining previous transcriptome data and homologous gene annotation. Among them, Lus10033213 is a single-point SNP repeat mapping gene, which encodes a Glutathione S-transferase (GST). This study is the first to use GWAS to excavate genes related to salt tolerance during the germination stage of flax. The results of this study provide important information for studying the genetic mechanism of salt tolerance of flax, and also provide the possibility to improve the salt tolerance of flax.

Soil salinity constrains agricultural development in arid regions. Flax is an economically important crop in many countries, and screening or breeding salinity-resistant flax cultivars is necessary. Based on the previous screening of flaxseed cultivars C71 (salt-sensitive) and C116 (salt-tolerant) as test materials, flax seedlings stressed with different concentrations of NaCl (0, 100, 150, 200, and 250 mmol/L) for 21 days were used to investigate the effects of salt stress on the growth characteristics, osmotic regulators, and antioxidant capacity of these flax seedlings and to reveal the adaptive responses of flax seedlings to salt stress. The results showed that plant height and root length of flax were inhibited, with C116 showing lower growth than C71. The concentrations of osmotic adjustment substances such as soluble sugars, soluble proteins, and proline were higher in the resistant material, C116, than in the sensitive material, C71, under different concentrations of salt stress. Consistently, C116 showed a better rapid scavenging ability for reactive oxygen species (ROS) and maintained higher activities of antioxidant enzymes to balance salt injury stress by inhibiting growth under salt stress. A transcriptome analysis of flax revealed that genes related to defense and senescence were significantly upregulated, and genes related to the growth and development processes were significantly downregulated under salt stress. Our results indicated that one of the important adaptations to tolerance to high salt stress is complex physiological remediation by rapidly promoting transcriptional regulation in flax.

Seed size is a key determinant of crop yields. Understanding the regulatory mechanisms of seed size is beneficial for improving flax seed yield. In this study, the development of large flax seeds lagged behind that of small seeds, and 1,751 protein-coding genes were differentially expressed in early seeds, torpedo-stage embryos, and endosperms of CIli2719 and Z11637 using RNA sequencing. Homologous alignment revealed that 129 differentially expressed genes (DEGs) in flax were homologous with 71 known seed size–related genes in Arabidopsis thaliana and rice (Oryza sativa L.). These DEGs controlled seed size through multiple processes and factors, among which phytohormone pathways and transcription factors were the most important. Moreover, 54 DEGs were found to be associated with seed size and weight in a DEG-based association study. Nucleotide diversity (π) analysis of seed size–related candidate DEGs by homologous alignment and association analysis showed that the π values decreased significantly during flax acclimation from oil to fiber flax, suggesting that some seed size–related candidate genes were selected in this acclimation process. These results provide important resources and genetic foundation for further research on seed size regulation and seed improvement in flax.