Identification of fusarium head blight resistance markers in a genome-wide association study of CIMMYT spring synthetic hexaploid derived wheat lines.

Fusarium head blight (FHB), caused by Fusarium graminearum, is one of the most destructive wheat diseases worldwide. FHB infection can dramatically reduce grain yield and quality due to mycotoxins contamination. Wheat resistance to FHB is quantitatively inherited and many low-effect quantitative trait loci (QTL) have been mapped in the wheat genome. Synthetic hexaploid wheat (SHW) represents a novel source of FHB resistance derived from Aegilops tauschii and Triticum turgidum that can be transferred into common wheat (T. aestivum). In this study, a panel of 194 spring Synthetic Hexaploid Derived Wheat (SHDW) lines from the International Maize and Wheat Improvement Center (CIMMYT) was evaluated for FHB response under field conditions over three years (2017-2019). A significant phenotypic variation was found for disease incidence, severity, index, number of Fusarium Damaged Kernels (FDKs), and deoxynivalenol (DON) content. Further, 11 accessions displayed < 10 ppm DON in 2017 and 2019. Genotyping of the SHDW panel using a 90 K Single Nucleotide Polymorphism (SNP) chip array revealed 31 K polymorphic SNPs with a minor allele frequency (MAF) > 5%, which were used for a Genome-Wide Association Study (GWAS) of FHB resistance. A total of 52 significant marker-trait associations for FHB resistance were identified. These included 5 for DON content, 13 for the percentage of FDKs, 11 for the FHB index, 3 for disease incidence, and 20 for disease severity. A survey of genes associated with the markers identified 395 candidate genes that may be involved in FHB resistance. Collectively, our results strongly support the view that utilization of synthetic hexaploid wheat in wheat breeding would enhance diversity and introduce new sources of resistance against FHB into the common wheat gene pool. Further, validated SNP markers associated with FHB resistance may facilitate the screening of wheat populations for FHB resistance.

Transcriptomic Analysis of Early Flowering Signals in 'Royal' Flax.

Canada is one of the world's leading producers and exporters of flax seed, with most production occurring in the Prairie Provinces. However, reduced season length and risk of frost restricts production in the northern grain belt of the Canadian Prairies. To expand the growing region of flax and increase production in Canada, flax breeders need to develop earlier-flowering varieties capable of avoiding the risk of abiotic stress. A thorough understanding of flowering control of flax is essential for the efficient breeding of such lines. We identified 722 putative flax flowering genes that span all major flowering-time pathways. Frequently, we found multiple flax homologues for a single Arabidopsis flowering gene. We used RNA sequencing to quantify the expression of genes in the shoot apical meristem (SAM) at 10, 15, 19, and 29 days after planting (dap) using the 'Royal' cultivar. We observed the expression of 80% of putative flax flowering genes and the differential expression of only 30%; these included homologues of major flowering regulators, such as SOC1, FUL, and AP1. We also found enrichment of differentially expressed genes (DEGs) in transcription factor (TF) families involved in flowering. Finally, we identified the candidates' novel flowering genes amongst the uncharacterized flax genes. Our transcriptomic dataset provides a useful resource for investigating the regulatory control of the transition to flowering in flax and for the breeding of northern-adapted varieties.

High-performance pipeline for MutMap and QTL-seq.

Summary: Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5-8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies. Availability: The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq).

Fine-mapping of a putative glutathione S-transferase (GST) gene responsible for yellow seed colour in flax (Linum usitatissimum).

OBJECTIVE: The brown seed coat colour of flax (Linum ustiatissimum) results from proanthocyanidin synthesis and accumulation. Glutathione S-transferases (GSTs), such as the TT19 protein in Arabidopsis, have been implicated in the transport of anthocyanidins during the synthesis of the brown proanthocyanidins. This study fine mapped the g allele responsible for yellow seed colour in S95407 and identified it as a putative mutated GST. RESULTS: We developed a Recombinant Inbred Line population with 320 lines descended from a cross between CDC Bethune (brown seed coat) and S95407 (yellow seed) and used molecular markers to fine map the G gene on Chromosome 6 (Chr 6). We used Next Generation Sequencing (NGS) to identify a putative GST was identified in this region and Sanger sequenced the gene from CDC Bethune, S95407 and other yellow seeded genotypes. The putative GST from S95407 had 13 SNPs encoding, including four non-synonymous amino acid changes, compared to the CDC Bethune reference sequence and the other genotypes. The GST encoded by Lus10019895 is a lambda-GST in contrast to the Arabidopsis TT19 which is a phi-GST.

Fungicide Management of Pasmo Disease of Flax and Sensitivity of Septoria linicola to Pyraclostrobin and Fluxapyroxad.

Among the diseases that have the potential to cause damage to flax (Linum usitatissimum L.) every year, the fungal disease pasmo, caused by Septoria linicola, is the most important. Fungicide application and a diverse crop rotation are the most important strategies to control this disease because there is little variation in resistance among flax cultivars. However, few fungicide products are available to flax growers. Field studies were conducted at four locations in Western Canada in 2014, 2015, and 2016 to determine the effect of two fungicide active ingredients applied singly and in combination: pyraclostrobin, fluxapyroxad, and fluxapyroxad + pyraclostrobin; and two application timings (early-flower, mid-flower, and at both stages) on pasmo disease severity, seed yield, and quality of flaxseed. The results indicated that among the three fungicide treatments, both pyraclostrobin and fluxapyroxad + pyraclostrobin controlled pasmo effectively; however, fluxapyroxad + pyraclostrobin was the most beneficial to improve the quality and quantity of the seed for most of the site-years. Disease severity in the fungicide-free control was 70%, and application of fluxapyroxad + pyraclostrobin decreased disease severity to 18%, followed by pyraclostrobin (23%) and fluxapyroxad (48%). Application of fluxapyroxad + pyraclostrobin also improved seed yield to 2,562 kg ha-1 compared with 1,874 kg ha-1 for the fungicide-free control, followed by pyraclostrobin (2,391 kg ha-1) and fluxapyroxad (2,340 kg ha-1). Fungicide application at early and mid-flowering stage had the same effects on disease severity and seed yield; however, seed quality was improved more when fungicide was applied at mid-flowering stage. Continuous use of the same fungicide may result in the development of fungicide insensitivity in the pathogen population. Thus, sensitivity of S. linicola isolates to pyraclostrobin and fluxapyroxad fungicides was determined by the spore germination and microtiter assay methods. Fungicide insensitivity was not detected among the 73 isolates of S. linicola tested against either of these fungicides.

Comparative analysis of cadmium uptake and distribution in contrasting canadian flax cultivars.

OBJECTIVE: Humans consume low quantities of cadmium (Cd), a non-nutritive and potentially toxic heavy metal, primarily via the dietary intake of grains. A trial experiment was conducted to investigate physiological and developmental differences in Cd content in four flax cultivars ('AC Emerson', 'Flanders', 'CDC Bethune', and 'AC McDuff') as part of a study to provide information that will assist in the breeding of low Cd-accumulating flax cultivars. Our objective was to identify varietal differences in the uptake and distribution of Cd in various tissues among flax cultivars grown in naturally Cd-containing soil in a controlled environment. RESULTS: Cadmium concentration was dependent on genotype, developmental stage, and tissue type, as well as their interaction. Cadmium concentration was higher in roots and leaves, relative to all other tissues, with a general trend of decreasing Cd content over time within leaves and stems. Notably, the concentration of Cd was higher in 'AC Emerson' relative to 'AC McDuff' across tissues and ages, including the seeds, while the concentration of 'Flanders' was higher than in 'AC McDuff' in seeds and other reproductive organs but similar in roots and leaves. The results suggest varietal differences in the mechanisms that determine Cd content in seeds.

Genomic Prediction Accuracy of Seven Breeding Selection Traits Improved by QTL Identification in Flax.

Molecular markers are one of the major factors affecting genomic prediction accuracy and the cost of genomic selection (GS). Previous studies have indicated that the use of quantitative trait loci (QTL) as markers in GS significantly increases prediction accuracy compared with genome-wide random single nucleotide polymorphism (SNP) markers. To optimize the selection of QTL markers in GS, a set of 260 lines from bi-parental populations with 17,277 genome-wide SNPs were used to evaluate the prediction accuracy for seed yield (YLD), days to maturity (DTM), iodine value (IOD), protein (PRO), oil (OIL), linoleic acid (LIO), and linolenic acid (LIN) contents. These seven traits were phenotyped over four years at two locations. Identification of quantitative trait nucleotides (QTNs) for the seven traits was performed using three types of statistical models for genome-wide association study: two SNP-based single-locus (SS), seven SNP-based multi-locus (SM), and one haplotype-block-based multi-locus (BM) models. The identified QTNs were then grouped into QTL based on haplotype blocks. For all seven traits, 133, 355, and 1,208 unique QTL were identified by SS, SM, and BM, respectively. A total of 1420 unique QTL were obtained by SS+SM+BM, ranging from 254 (OIL, LIO) to 361 (YLD) for individual traits, whereas a total of 427 unique QTL were achieved by SS+SM, ranging from 56 (YLD) to 128 (LIO). SS models alone did not identify sufficient QTL for GS. The highest prediction accuracies were obtained using single-trait QTL identified by SS+SM+BM for OIL (0.929 ± 0.016), PRO (0.893 ± 0.023), YLD (0.892 ± 0.030), and DTM (0.730 ± 0.062), and by SS+SM for LIN (0.837 ± 0.053), LIO (0.835 ± 0.049), and IOD (0.835 ± 0.041). In terms of the number of QTL markers and prediction accuracy, SS+SM outperformed other models or combinations thereof. The use of all SNPs or QTL of all seven traits significantly reduced the prediction accuracy of traits. The results further validated that QTL outperformed high-density genome-wide random markers, and demonstrated that the combined use of single and multi-locus models can effectively identify a comprehensive set of QTL that improve prediction accuracy, but further studies on detection and removal of redundant or false-positive QTL to maximize prediction accuracy and minimize the number of QTL markers in GS are warranted.

Photoperiod sensitivity of Canadian flax cultivars and 5-azacytidine treated early flowering derivative lines.

BACKGROUND: Early flowering and maturing flax (Linum usitatissimum L.) cultivars are better adapted than lines with a longer reproductive phase for the short growing season of the northern Canadian Prairies. We examined the role of long days (LD) and short days (SD) on the time taken to flower in five established flax cultivars and three mutant-derived F10 lines. The photoperiod sensitivity of these eight different genotypes was determined using a reciprocal transfer experiment involving weekly transfers between LD and SD environments. RESULTS: The genotypes tested had varying degrees of photoperiod sensitivity and demonstrated reduced time to flowering if exposed to LD environments prior to a critical time point. The duration of each of the three phases of vegetative growth differed among the genotypes studied. Transfers from SD to LD shortened the vegetative stage, reduced time to flowering, and extended the reproductive phase in the genotypes studied. Mutant-derived lines RE1/2/3 flowered significantly earlier compared to CDC Sorrel, CDC Bethune, Flanders, Prairie Thunder, and Royal. Modelling of the flowering times indicated that transferring the cultivars from SD to LD increased the photoperiod sensitive time; however, different reproductive phases for mutant lines were not defined as parsimonious models were not identified. Expression of the putative flax homologs for CONSTANS (CO), FLOWERING LOCUS T (FT), and GIGANTEA (GI) was examined in the leaves of Royal and RE1/2/3 plants at 10, 15, 19 and 29 days after planting. Expression of putative FT homologs was detected in all three early-flowering lines but expression was negligible, or not detected, in Royal. CONCLUSIONS: Models defining the three phases of reproductive development were established for the five cultivars studied; however, it was not possible to identify these phases for the three early flowering and photoperiod insensitive epimutant-derived lines. A putative flax homolog of FT, a key regulator of flowering time, is more highly expressed in RE plants, which may condition the day-length insensitivity in the early flowering 'epimutant' lines.

Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax.

A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19× using the Illumina Hi-Seq platform. Phenotypic data for 11 seed yield and oil quality traits were collected in eight year/location environments. A total of 17,288 single nucleotide polymorphisms were identified, which explained more than 80% of the phenotypic variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO) and linolenic (LIN) acid contents. Twenty-three unique genomic regions associated with 33 quantitative trait loci (QTL) for the studied traits were detected, thereby validating four genomic regions previously identified. The 33 QTL explained 48⁻73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN but only 8⁻14% for plant height, DTM and seed yield. A genome-wide selective sweep scan for selection signatures detected 114 genomic regions that accounted for 7.82% of the flax pseudomolecule and overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for 11 traits. The results demonstrate the utility of GWAS combined with selection signatures for dissection of the genetic structure of traits and for pinpointing genomic regions for breeding improvement.

Genetic Variability of 27 Traits in a Core Collection of Flax (Linum usitatissimum L.).

Assessment of genetic variability of plant core germplasm is needed for efficient germplasm utilization in breeding improvement. A total of 391 accessions of a flax core collection, which preserves the variation present in the world collection of 3,378 accessions maintained by Plant Gene Resources of Canada (PGRC) and represents a broad range of geographical origins, different improvement statuses and two morphotypes, was evaluated in field trials in up to 8 year-location environments for 10 agronomic, eight seed quality, six fiber and three disease resistance traits. The large phenotypic variation in this subset was explained by morphotypes (22%), geographical origins (11%), and other variance components (67%). Both divergence and similarity between two basic morphotypes, namely oil or linseed and fiber types, were observed, whereby linseed accessions had greater thousand seed weight, seeds m-2, oil content, branching capability and resistance to powdery mildew while fiber accessions had greater straw weight, plant height, protein content and resistance to pasmo and fusarium wilt diseases, but they had similar performance in many traits and some of them shared common characteristics of fiber and linseed types. Weak geographical patterns within either fiber or linseed accessions were confirmed, but specific trait performance was identified in East Asia for fiber type, and South Asia and North America for linseed type. Relatively high broad-sense heritability was obtained for seed quality traits, followed by agronomic traits and resistance to powdery mildew and fusarium wilt. Diverse phenotypic and genetic variability in the flax core collection constitutes a useful resource for breeding.

Ex-post assessment of genetically modified, low level presence in Canadian flax.

Canada is the world's largest producer and exporter of flaxseed. In 2009, DNA from deregistered genetically modified (GM) CDC Triffid was detected in a shipment of Canadian flaxseed exported to Europe, causing a large decrease in the amount of flax planted in Canada and a major shift in export markets. The flax industry in Canada undertook major changes to ensure the removal of transgenic flax from the supply chain. To demonstrate compliance, Canada adopted a protocol involving testing grain samples (post-harvest) using an RT-PCR test for the construct found in CDC Triffid. Efforts to remove the presence of GM flax from the value chain included reconstituting major flax varieties from GM-free plants. The reconstituted varieties represented the majority of planting seed in 2014. This study re-evaluates GM flax presence in Canadian grain stocks for an updated dataset (2009-2015) using a previously described simulation model to estimate low-level GM presence. Additionally, losses to the Canadian economy resulting from the reduction in flax production and export opportunities, costs associated with reconstituting major flax varieties, and testing for the presence of GM flax along the flax value chain are estimated.

Genetics, structure, and prevalence of FP967 (CDC Triffid) T-DNA in flax.

The detection of T-DNA from a genetically modified flaxseed line (FP967, formally CDC Triffid) in a shipment of Canadian flaxseed exported to Europe resulted in a large decrease in the amount of flax planted in Canada. The Canadian flaxseed industry undertook major changes to ensure the removal of FP967 from the supply chain. This study aimed to resolve the genetics and structure of the FP967 transfer DNA (T-DNA). The FP967 T-DNA is thought to be inserted in at single genomic locus. The junction between the T-DNA and genomic DNA consisted of two inverted Right Borders with no Left Border (LB) flanking genomic DNA sequences recovered. This information was used to develop an event-specific quantitative PCR (qPCR) assay. This assay and an existing assay specific to the T-DNA construct were used to determine the genetics and prevalence of the FP967 T-DNA. These data supported the hypothesis that the T-DNA is present at a single location in the genome. The FP967 T-DNA is present at a low level (between 0.01 and 0.1%) in breeder seed lots from 2009 and 2010. None of the 11,000 and 16,000 lines selected for advancement through the Flax Breeding Program in 2010 and 2011, respectively, tested positive for the FP967 T-DNA, however. Most of the FP967 T-DNA sequence was resolved via PCR cloning and next generation sequencing. A 3,720 bp duplication of an internal portion of the T-DNA (including a Right Border) was discovered between the flanking genomic DNA and the LB. An event-specific assay, SAT2-LB, was developed for the junction between this repeat and the LB.

QTL for fatty acid composition and yield in linseed (Linum usitatissimum L.).

KEY MESSAGE: The combined SSR-SNP map and 20 QTL for agronomic and quality traits will assist in marker assisted breeding as well as map-based cloning of key genes in linseed. Flax is an important nutraceutical crop mostly because it is a rich source of omega-3 fatty acids and antioxidant compounds. Canada is the largest producer and exporter of oilseed flax (or linseed), creating a growing need to improve crop productivity and quality. In this study, a genetic map was constructed based on selected 329 single nucleotide polymorphic markers and 362 simple sequence repeat markers using a recombinant inbred line population of 243 individuals from a cross between the Canadian varieties CDC Bethune and Macbeth. The genetic map consisted of 15 linkage groups comprising 691 markers with an average marker density of one marker every 1.9 cM. A total of 20 quantitative trait loci (QTL) were identified corresponding to 14 traits. Three QTL each for oleic acid and stearic acid, two QTL each for linoleic acid and iodine value and one each for palmitic acid, linolenic acid, oil content, seed protein, cell wall, straw weight, thousand seed weight, seeds per boll, yield and days to maturity were identified. The QTL for cell wall, straw weight, seeds per boll, yield and days to maturity all co-located on linkage group 4. Analysis of the candidate gene regions underlying the QTL identified proteins involved in cell wall and fibre synthesis, fatty acid biosynthesis as well as their metabolism and yield component traits. This study provides the foundation for assisting in map-based cloning of the QTL and marker assisted selection of a wide range of quality and agronomic traits in linseed and potentially fibre flax.

Effect of Heating Method on Alteration of Protein Molecular Structure in Flaxseed: Relationship with Changes in Protein Subfraction Profile and Digestion in Dairy Cows.

This study evaluated the effect of heating methods on alteration of protein molecular structure in flaxseed (Linum usitatissimum L.) in relation to changes in protein subfraction profile and digestion in dairy cows. Seeds from two flaxseed varieties, sampled from two replicate plots at two locations, were evaluated. The seeds were either maintained in their raw state or heated in an air-draft oven (dry heating) or autoclave (moist heating) for 60 min at 120 °C or by microwave irradiation (MIR) for 5 min. Compared to raw seeds, moist heating decreased (P < 0.05) soluble protein (SP) content [56.5 ± 5.55 to 25.9 ± 6.16% crude protein (CP)] and increased (P < 0.05) rumen undegraded protein (RUP) content (36.0 ± 5.19 to 46.9 ± 2.72% CP) and intestinal digestibility of RUP (61.0 ± 2.28 to 63.8 ± 2.67% RUP). Dry heating did not alter (P > 0.05) the protein subfraction profile and rumen degradation kinetics, whereas MIR increased (P < 0.05) the RUP content from 36.0 ± 5.19 to 40.4 ± 4.67% CP. The MIR and dry heating did not alter (P > 0.05) the amide I to amide II ratio, but moist heating decreased (P < 0.05) both the amide I to amide II ratio and α-helix-to-ß-sheet ratio. Regression equations based on protein molecular spectral intensities provided high prediction power for estimation of heat-induced changes in SP (R2 = 0.62), RUP (R2 = 0.71), and intestinal digestibility of RUP (R2 = 0.72). Overall, heat-induced changes in protein nutritive value and digestion were strongly associated with heat-induced alteration in protein molecular structures.

Molecular structures and metabolic characteristics of protein in brown and yellow flaxseed with altered nutrient traits.

The objectives of this study were to investigate the chemical profiles; crude protein (CP) subfractions; ruminal CP degradation characteristics and intestinal digestibility of rumen undegraded protein (RUP); and protein molecular structures using molecular spectroscopy of newly developed yellow-seeded flax (Linum usitatissimum L.). Seeds from two yellow flaxseed breeding lines and two brown flaxseed varieties were evaluated. The yellow-seeded lines had higher (P < 0.001) contents of oil (44.54 vs 41.42% dry matter (DM)) and CP (24.94 vs 20.91% DM) compared to those of the brown-seeded varieties. The CP in yellow seeds contained lower (P < 0.01) contents of true protein subfraction (81.31 vs 92.71% CP) and more (P < 0.001) extensively degraded (70.8 vs 64.9% CP) in rumen resulting in lower (P < 0.001) content of RUP (29.2 vs 35.1% CP) than that in the brown-seeded varieties. However, the total supply of digestible RUP was not significantly different between the two seed types. Regression equations based on protein molecular structural features gave relatively good estimation for the contents of CP (R(2) = 0.87), soluble CP (R(2) = 0.92), RUP (R(2) = 0.97), and intestinal digestibility of RUP (R(2) = 0.71). In conclusion, molecular spectroscopy can be used to rapidly characterize feed protein molecular structures and predict their nutritive value.

Association mapping of seed quality traits using the Canadian flax (Linum usitatissimum L.) core collection.

KEY MESSAGE: The identification of stable QTL for seed quality traits by association mapping of a diverse panel of linseed accessions establishes the foundation for assisted breeding and future fine mapping in linseed. Linseed oil is valued for its food and non-food applications. Modifying its oil content and fatty acid (FA) profiles to meet market needs in a timely manner requires clear understanding of their quantitative trait loci (QTL) architectures, which have received little attention to date. Association mapping is an efficient approach to identify QTL in germplasm collections. In this study, we explored the quantitative nature of seed quality traits including oil content (OIL), palmitic acid, stearic acid, oleic acid, linoleic acid (LIO) linolenic acid (LIN) and iodine value in a flax core collection of 390 accessions assayed with 460 microsatellite markers. The core collection was grown in a modified augmented design at two locations over 3 years and phenotypic data for all seven traits were obtained from all six environments. Significant phenotypic diversity and moderate to high heritability for each trait (0.73-0.99) were observed. Most of the candidate QTL were stable as revealed by multivariate analyses. Nine candidate QTL were identified, varying from one for OIL to three for LIO and LIN. Candidate QTL for LIO and LIN co-localized with QTL previously identified in bi-parental populations and some mapped nearby genes known to be involved in the FA biosynthesis pathway. Fifty-eight percent of the QTL alleles were absent (private) in the Canadian cultivars suggesting that the core collection possesses QTL alleles potentially useful to improve seed quality traits. The candidate QTL identified herein will establish the foundation for future marker-assisted breeding in linseed.

The potential of pale flax as a source of useful genetic variation for cultivated flax revealed through molecular diversity and association analyses.

Pale flax (Linum bienne Mill.) is the wild progenitor of cultivated flax (Linum usitatissimum L.) and represents the primary gene pool to broaden its genetic base. Here, a collection of 125 pale flax accessions and the Canadian flax core collection of 407 accessions were genotyped using 112 genome-wide simple sequence repeat markers and phenotyped for nine traits with the aim of conducting population structure, molecular diversity and association mapping analyses. The combined population structure analysis identified two well-supported major groups corresponding to pale and cultivated flax. The L. usitatissimum convar. crepitans accessions most closely resembled its wild progenitor, both having dehiscent capsules. The unbiased Nei's genetic distance (0.65) confirmed the strong genetic differentiation between cultivated and pale flax. Similar levels of genetic diversity were observed in both species, albeit 430 (48 %) of pale flax alleles were unique, in agreement with their high genetic differentiation. Significant associations were identified for seven and four traits in pale and cultivated flax, respectively. Favorable alleles with potentially positive effect to improve yield through yield components were identified in pale flax. The allelic frequencies of markers associated with domestication-related traits such as capsular dehiscence indicated directional selection with the most common alleles in pale flax being absent or rare in cultivated flax and vice versa. Our results demonstrated that pale flax is a potential source of novel variation to improve multiple traits in cultivated flax and that association mapping is a suitable approach to screening pale flax germplasm to identify favorable quantitative trait locus alleles.

Genomic regions underlying agronomic traits in linseed (Linum usitatissimum L.) as revealed by association mapping.

The extreme climate of the Canadian Prairies poses a major challenge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core collection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bolls per area, 1,000 seed weight, seeds per boll, start of flowering, end of flowering, plant height, plant branching, and lodging collected from up to eight environments was used for association mapping. Based on a mixed model (principal component analysis (PCA) + kinship matrix (K)), 12 significant marker-trait associations for six agronomic traits were identified. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable alleles have additive effects. None of the modern cultivars carried the five favorable alleles and the maximum number of four observed in any accessions was mostly in breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while illustrating the potential for improvement through marker-assisted selection.

Genetic variation of six desaturase genes in flax and their impact on fatty acid composition.

Flax (Linum usitatissimum L.) is one of the richest plant sources of omega-3 fatty acids praised for their health benefits. In this study, the extent of the genetic variability of genes encoding stearoyl-ACP desaturase (SAD), and fatty acid desaturase 2 (FAD2) and 3 (FAD3) was determined by sequencing the six paralogous genes from 120 flax accessions representing a broad range of germplasm including some EMS mutant lines. A total of 6 alleles for sad1 and sad2, 21 for fad2a, 5 for fad2b, 15 for fad3a and 18 for fad3b were identified. Deduced amino acid sequences of the alleles predicted 4, 2, 3, 4, 6 and 7 isoforms, respectively. Allele frequencies varied greatly across genes. Fad3a, with 110 SNPs and 19 indels, and fad3b, with 50 SNPs and 5 indels, showed the highest levels of genetic variations. While most of the SNPs and all the indels were silent mutations, both genes carried nonsense SNP mutations resulting in premature stop codons, a feature not observed in sad and fad2 genes. Some alleles and isoforms discovered in induced mutant lines were absent in the natural germplasm. Correlation of these genotypic data with fatty acid composition data of 120 flax accessions phenotyped in six field experiments revealed statistically significant effects of some of the SAD and FAD isoforms on fatty acid composition, oil content and iodine value. The novel allelic variants and isoforms identified for the six desaturases will be a resource for the development of oilseed flax with unique and useful fatty acid profiles.