Flax (Linum usitatissimum. L) is an ancient oilseed and natural fiber crop. It could be divided into three categories by use, namely oil flax, fiber flax and oil-fiber dual purpose (OF). Cultivated flax is widely used in the food and textile industry. It is of great significance to elucidate the genetic characteristics of flax collections for accelerating the process of breeding improvement in this dual purpose crop. With the development of next-generation sequencing, we can use new methods, such as SLAF-seq (specific-locus amplified fragment sequencing), to decode unknown genomes of species. In this study, a high-through sequencing of flax collections using SLAF-seq was conducted. The evolutionary tendency was defined and candidate genes associated with agronomic traits of flax species were identified by Genome-Wide Association Studying (GWAS). A flax collection consisting of 224 varieties were sequenced by SLAF-seq. In total, 346,639 SLAF tags were developed from all accessions, with an average sequencing depth of 7.19 for each accession. A total of 584,987 SNPs (single nucleotide polymorphism) with an MAF > 0.05 were identified from these SLAFs. The population structure division and phylogenetic analysis indicated a strong divergence among three kinds of flax groups. The genome-wide variation uncovered that oil flax had the highest genetic diversity and was considered to be the ancestor of fiber flax and oil-fiber flax. Sixteen associated peak SNPs for six traits were obtained by GWAS of oil-related traits using EMMAX (efficient mixed-model association eXpedited). Candidate genes and their related pathway were evaluated. A new GWAS was developed for fiber properties using the GLM (General linear model) model and a number of loci were identified. To our knowledge, this is the first study on discovery multiple loci for important agronomic traits of flax species using GWAS strategy. These results will provide the highest possibility of incorporating both high fiber and good oil traits in a single variety.

Processing quality is an important economic wheat trait. The marker-assisted selection (MAS) method plays a vital role in accelerating genetic improvement of processing quality. In the present study, processing quality in a panel of 165 cultivars grown in four environments was evaluated by mixograph. An association mapping analysis using 90 K and 660 K single nucleotide polymorphism (SNP) arrays identified 24 loci in chromosomes 1A, 1B (4), 1D, 2A, 2B (2), 3A, 3B, 3D (2), 4A (3), 4B, 5D (2), 6A, 7B (2) and 7D (2), explaining 10.2–42.5% of the phenotypic variances. Totally, 15 loci were stably detected in two or more environments. Nine loci coincided with known genes or QTL, whereas the other fifteen were novel loci. Seven candidate genes encoded 3-ketoacyl-CoA synthase, lipoxygenase, pyridoxal phosphate-dependent decarboxylase, sucrose synthase 3 and a plant lipid transfer protein/Par allergen. SNPs significantly associated with processing quality and accessions with more favorable alleles can be used for marker-assisted selection.

Common vetch (Vicia sativa L.) is a globally green manure and forage crop, cultivated extensively worldwide. Its seeds serve as an important concentrated feed. Due to the late release of the reference genome, few studies were conducted to analyze the genetic mechanisms of grain yield, which hindered the progress of common vetch breeding. Marker-assisted selection (MAS) is the best and most effective way to accelerate the genetic improvement of grain yield-related traits in common vetch. In this study, we performed a genome-wide association study (GWAS) using the high-density single nucleotide polymorphism (SNP) data obtained through re-sequencing to better understand the genetic basis of grain yield-related traits. In total, six grain yield-related traits were evaluated in 172 accessions mainly sourced from China and Russia, across four environments, including branches per plant (NB), pod length (PL), number of pods per plant (NP), number of grains per pod (NG), hundred-grain weight (HGW), and grain yield (GY). Population structure analysis of the 172 accessions revealed four distinct subpopulations, exhibiting strong geographical correlation. In total, 38 loci have been identified as significantly associated with six grain yield-related traits, accounting for 13.3–31.7% of the phenotypic variances. Among them, qGY1.1 and qNG1.1, qNG2.2 and qPL2.1, qNG3.2 and qGY3.2, qNG4.1 and qPL4.1, qGY4.1 and qHGW4.1, qNG6.1 and qPL6.1, and qNB6.2 and qGY6.2 exhibit overlapping regions, suggesting that these regions are pleiotropic and should be prioritized for further research and breeding. In total, 12 candidate genes encoding auxin response factor, F-box repeat protein, gibberellin receptor, serine/threonine-protein kinase-like protein, and cellulose synthase-like protein were identified. Furthermore, we successfully developed and verified a kompetitive allele-specific PCR (KASP) marker (Kasp-NB6.2) for the number of branches. These findings provide molecular insights into grain yield-related traits in common vetch and offer valuable loci and molecular tools for MAS breeding.

Background/Objectives: Common vetch (Vicia sativa L.) is a globally cultivated leguminous crop, valued for its high nutritional content and role in sustainable agriculture. Methods: To identify loci or genes significantly associated with salt tolerance, we conducted a genome-wide association study (GWAS) using 172 common vetch accessions primarily from diverse geographic regions. Single-nucleotide polymorphisms (SNPs) were obtained through re-sequencing, and five salt tolerance-related traits, including the germination rate (GR), germination potential (GP), germination index (GI), shoot length (SL), and root length (RL), were evaluated under salt stress conditions. We have identified 20 loci significantly associated with salt tolerance-related traits, and explaining 9.7–21.8% of the phenotypic variation. Notably, 13 loci exhibited pleiotropic effects on multiple traits; include qST1.1 (associated with SL, GR, GI), qST1.3 (RL, SL, GP), qST2.5 (SL, GR, GI, GP), and qST2.7 (SL, RL, GP, GI), and should be prioritized in future breeding programs. All 20 loci are novel compared to previous reports. Furthermore, we identified 7 candidate genes encoding key regulatory proteins, including a zinc finger MYM-type protein, ubiquitin-like domain-containing protein, transcription factor bHLH, ethylene-responsive transcription factor, auxin-responsive protein, and serine/threonine-protein kinase, as potential regulators of salt tolerance. Conclusions: This study advances our understanding of the genetic basis of salt tolerance in common vetch and provides valuable loci, molecular tools, and elite accessions. HZMC1352, GLF303, GLF301, HZMC1387, GLF306, GLF368, GLF342, HZMC1384, HZMC1355, GLF307, HZMC1366 are used for improving salt tolerance in breeding programs.

WRKY transcription factors play key roles in plant immune responses, including resistance to fungal pathogens. In the present study, we identified a flax resistance-related gene Lus10021999, named LuWRKY39. Here, to identify the role of WRKY transcription factor in resistance of flax against Septoria linicola, we cloned and analyzed the gene LuWRKY39 via homologous cloning using bioinformatics methods and localized the encoded protein. Quantitative real-time PCR (qRT-PCR) was used to explore the response of this gene to S. linicola. The results showed that the gene that is 948 bp long exhibited the closest genetic relationship to WRKY in castor (Ricinus communis), as revealed by phylogenetic analysis, and the encoded protein was localized in the nucleus. The LuWRKY39 gene showed higher expression levels in resistant flax materials than in susceptible ones, and higher in roots and stems than in leaves. Furthermore, gene expression showed an upward trend following treatment with salicylic acid (SA) and methyl jasmonate (MeJA), indicating that LuWRKY39 is involved in the regulation of SA and JA signals. By silencing LuWRKY39 in flax using virus-induced gene silencing (VIGS), the processed plants were more sensitive to S. linicola than untreated plants. Gene expression analysis and disease index statistics confirmed that the silenced plants were more susceptible, highlighting the crucial role of LuWRKY39 in flax disease resistance. This study provides a foundation for functional investigations of WRKY genes in flax and the identification of disease resistance genes.