Nitrogen (N) is the most important macro-nutrient for plant growth and development, which not only results in the highest cost in crop production but may also lead to environmental pollution. Hence, there is a need to develop N and use efficient genotypes, a prerequisite for which is a better understanding of N stress adaptation. Here, responses of two contrasting linseed accessions at the seedling stage were assessed for N stress-induced changes in twelve phenotypic traits and for gene expression profiling in the roots. The results showed that nine out of twelve phenotypic traits were affected under N stress conditions, and include total root length (TRL), root tips (RT), shoot dry weight (SDW), root dry weight (RDW), root-to-shoot ratio (R/S), plant nitrogen content (PNC), shoot nitrogen content (SNC), root nitrogen content (RNC), and nitrogen use efficiency (NUE). For example, under N stress, the TRL, RDW, SDW, PNC, SNC, and RNC showed reductions of 7.1, 7.6, 16.0, 43.7, 43.3, and 38.7%, respectively. The N-efficient (NE) genotype outperformed the N-inefficient (NI) genotype for all root and shoot traits and NUE under N stress and N normal conditions. Transcriptome analysis identified 1034 differentially expressed genes (DEGs) under the contrasting N conditions and uncovered the opposite responses of the two linseed genotypes to N starvation at the gene expression level. DEGs included 153 transcription factors distributed in 27 families, among which ERF, MYB, NAC, and WRKY were the most represented. In addition, DEGs involved in N absorption and transport, root development, amino acid transport, and antioxidant activity were found to be differentially expressed. The candidate genes identified in the current study are purported for their roles in N metabolism in other crops and might also play a pivotal role in N stress adaptation in linseed, and therefore could be useful for further detailed research on N stress response in linseed, paving the way toward developing N-efficient linseed cultivars with improved root system architecture.

Boron (B) is an essential microelement for plants, and its deficiency can lead to impaired development and function. Around 50% of arable land in the world is acidic, and low pH in the soil solution decreases availability of several essential mineral elements, including B, magnesium (Mg), calcium (Ca), and potassium (K). Plants take up soil B in the form of boric acid (H3BO3) in acidic soil or tetrahydroxy borate [B(OH)4]- at neutral or alkaline pH. Boron can participate directly or indirectly in plant metabolism, including in the synthesis of the cell wall and plasma membrane, in carbohydrate and protein metabolism, and in the formation of ribonucleic acid (RNA). In addition, B interacts with other nutrients such as Ca, nitrogen (N), phosphorus (P), K, and zinc (Zn). In this review, we discuss the mechanisms of B uptake, absorption, and accumulation and its interactions with other elements, and how it contributes to the adaptation of plants to different environmental conditions. We also discuss potential B-mediated networks at the physiological and molecular levels involved in plant growth and development.

Studies on the northeastern American native hops (Humulus lupulus ssp. lupuloides) from the Canadian Maritimes are scarce. This study aimed to evaluate the genetic structure and diversity among 25 wild-collected hops from three Canadian Maritime provinces using microsatellite (simple sequence repeat (SSR)) markers. Based on 43 SSR markers, four distinct subgroups were found, with a low molecular variance (19%) between subgroups and a high variance (81%) within subgroups. The Nei's unbiased genetic distance between clusters ranged from 0.01 to 0.08, the genetic distance between clusters 2 and 3 being the farthest and that between clusters 1 and 2 the closest. Cluster 2 captured the highest overall diversity. A total of 18 SSR markers clearly discriminated hop clones by detecting putative subspecies-specific haplotypes, differentiating clones of native-wild H. lupulus ssp. lupuloides from the naturalized old and modern hop cultivars. Seven of the 18 SSR markers also differentiated two clones from the same site from one another. The study is the first, using molecular markers, to identify SSR markers with potential for intellectual property protection in Canadian Maritimes hops. The SSR markers herein used can be prime tools for hop breeders and growers in the region.

Cultivated potato (Solanum tuberosum) is known to be highly susceptible to drought. With climate change and its frequent episodes of drought, potato growers will face increased challenges to achieving their yield goals. Currently, a high proportion of untapped potato germplasm remains within the diploid potato relatives, and the genetic architecture of the drought tolerance and maturity traits of diploid potatoes is still unknown. As such, a panel of 384 ethyl methanesulfonate-mutagenized diploid potato clones were evaluated for drought tolerance and plant maturity under field conditions. Genome-wide association studies (GWAS) were conducted to dissect the genetic architecture of the traits. The results obtained from the genetic structure analysis of the panel showed five main groups and seven subgroups. Using the Genome Association and Prediction Integrated Tool–mixed linear model GWAS statistical model, 34 and 17 significant quantitative trait nucleotides (QTNs) were found associated with maturity and drought traits, respectively. Chromosome 5 carried most of the QTNs, some of which were also detected by using the restricted two-stage multi-locus multi-allele-GWAS haploblock-based model, and two QTNs were found to be pleiotropic for both maturity and drought traits. Using the non-parametric U-test, one and three QTNs, with 5.13%–7.4% phenotypic variations explained, showed favorable allelic effects that increase the maturity and drought trait values. The quantitaive trait loci (QTLs)/QTNs associated with maturity and drought trait were found co-located in narrow (0.5–1 kb) genomic regions with 56 candidate genes playing roles in plant development and senescence and in abiotic stress responses. A total of 127 potato clones were found to be late maturing and tolerant to drought, while nine were early to moderate–late maturing and tolerant to drought. Taken together, the data show that the studied germplasm panel and the identified candidate genes are prime genetic resources for breeders and biologists in conventional breeding and targeted gene editing as climate adaptation tools.

Ascorbic acid (ASC) is an important antioxidant in plant cells, being the main biosynthesis pathway is L-galactose or Smirnoff-Wheeler. ASC is involved in plant growth and development processes, being a cofactor and regulator of multiple signaling pathways in response to abiotic stresses. Aluminum toxicity is an important stressor under acidic conditions, affecting plant root elongation, triggering ROS induction and accumulation of hydrogen peroxide (H2O2). To mitigate damage from Al-toxicity, plants have evolved mechanisms to resist stress conditions, such as Al-tolerance and Al-exclusion or avoidance, both strategies related to the forming of non-phytotoxic complexes or bind-chelates among Al and organic molecules like oxalate. Dehydroascorbate (DHA) degradation generates oxalate when ASC is recycled, and dehydroascorbate reductase (DHAR) expression is inhibited. An alternative strategy is ASC regeneration, mainly due to a higher level of DHAR gene expression and low monodehydroascorbate reductase (MDHAR) gene expression. Therefore, studies performed on Fagopyrum esculentum, Nicotiana tabacum, Poncirus trifoliate, and V. corymbosum suggest that ASC is associated with the Al-resistant mechanism, given the observed enhancements in defense mechanisms, including elevated antioxidant capacity and oxalate production. This review examines the potential involvement of ASC metabolism in Al-resistant mechanisms.

Drought stress causes a decrease in agricultural yields. Recently, it has been reported that the phytohormone melatonin (MT), participates in different plant growth and developmental processes. Highbush blueberry (Vaccinium corymbosum L.) is quickly affected by drought, decreasing plant growth, yield, and quality. Thus, the aim of this study was to evaluate the role of melatonin on physiological performance, water status, chlorophyll concentration, and antioxidant metabolism in V. corymbosum plants exposed to drought stress. One-year-old V. corymbosum plants were subjected to four treatments: 1) 100% field capacity (FC) without melatonin; 2) 100% FC with 0.1 mM MT; 3) 50% FC without MT; and 4) 50% FC with MT. Plant water content, leaf area, photosynthetic performance, antioxidants compounds, and chlorophyll concentration were determined at different times post MT application (0, 3, 7, and 10 days). In our study, leaf area, plant water status, the photosynthetic performance and photosynthetic pigments decreased in the treatments with irrigation at 50% FC compared to the treatment whit irrigation at 100% FC. Interestingly, MT application improved plant water potential, CO2 assimilation, chlorophyll a, and total phenols by 35, 65, 22, and 27% respectively, at 50% FC treated with MT compared to plants without MT at 10 days of the experiment. Our results demonstrate that MT enhanced physiological and biochemical responses of V. corymbosum plants to cope with drought stress.

Nanoparticles (NPs) of titanium dioxide (TiO 2 ) alter photosynthetic and biochemical parameters in Solanum lycopersicum L., possibly due to their photocatalytic properties given by energy absorption in the UV-A range; however, the joint effects TiO 2 NPs and UV-A radiation are not well understood. This work evaluates the combined responses of TiO 2 NPs and UV-A radiation at the physiological and molecular levels in S. lycopersicum . In a split growth chamber, the presence (UV-A +) and absence (UV-A −) of UV-A were combined with 0 (water as a control), and 1000 and 2000 mg L −1 of TiO 2 NPs applied at sowing. At the end of exposure (day 30 after sowing), the photosynthetic performance was determined, and biochemical and molecular parameters were evaluated in leaf tissues. Better photochemical performance in UV-A + than UV-A − in control plants was observed, but these effects decreased in 1000 and 2000 mg TiO 2 L −1 , similar to net CO 2 assimilation. A clear increase in photosynthetic pigment levels was recorded under UV-A + compared to UV-A − that was positively correlated with photosynthetic parameters. A concomitant increase in total phenols was observed on adding TiO 2 in UV-A − conditions, while a decreasing trend in lipid peroxidation was observed for the same treatments. There was an increase in psb B gene expression under TiO 2 /UV-A + treatments, and a reduced expression of rbc S and rbc L under UV-A − . These results suggest that the reduction in photosynthetic performance on applying high doses of TiO 2 NPs is probably due to biochemical limitation, while UV-A achieves the same result via the photochemical component.

Nitrogen (N), the most important macro-nutrient for plant growth and development, is a key factor that determines crop yield. Yet its excessive applications pollute the environment and are expensive. Hence, studying nitrogen use efficiency (NUE) in crops is fundamental for sustainable agriculture. Here, an association panel consisting of 123 flax accessions was evaluated for 21 NUE-related traits at the seedling stage under optimum N (N+) and N deficiency (N−) treatments to dissect the genetic architecture of NUE-related traits using a multi-omics approach integrating genome-wide association studies (GWAS), transcriptome analysis and genomic selection (GS). Root traits exhibited significant and positive correlations with NUE under N− conditions (r = 0.33 to 0.43, p < 0.05). A total of 359 QTLs were identified, accounting for 0.11% to 23.1% of the phenotypic variation in NUE-related traits. Transcriptomic analysis identified 1034 differentially expressed genes (DEGs) under contrasting N conditions. DEGs involved in N metabolism, root development, amino acid transport and catabolism and others, were found near the QTLs. GS models to predict NUE stress tolerance index (NUE_STI) trait were tested using a random genome-wide SNP dataset and a GWAS-derived QTLs dataset. The latter produced superior prediction accuracy (r = 0.62 to 0.79) compared to the genome-wide SNP marker dataset (r = 0.11) for NUE_STI. Our results provide insights into the QTL architecture of NUE-related traits, identify candidate genes for further studies, and propose genomic breeding tools to achieve superior NUE in flax under low N input.

Water stress is a major constraint on crop production and, root systems are one of the key features of plants determining drought tolerance and yield. In this study, five root morphological traits and their stability indices were evaluated at the reproductive stage on an association panel consisting of 120 diverse Linum usitatissimum accessions grown under well-watered and water-limiting conditions. To identify quantitative trait loci (QTL) and candidate genes positively influencing root traits under drought, combined multi-locus genome-wide association studies (ML-GWAS) and transcriptomic data analysis were carried out. A total of 112 QTL were identified accounting for 0.45-24.28 % of the phenotypic variation for root-related traits. Fifty QTL were detected by at least two ML-GWAS models, and 26 were co-located with previously reported QTL associated with yield-related traits under drought and early root and shoot development. Phenotypic differences between two contrasting subsets of accessions for the traits assessed were attributable to the accumulation of positive QTL alleles (PQTL), where the subset with the largest number of PQTL registered 154 % and 69 % greater total root length and yield under drought stress, respectively, than the subset with the fewest PQTL. Transcriptomic data analysis identified 766 differentially expressed genes (DEGs) responsive to drought stress in 108 QTL. Annotation of the 766 DEGs yielded functional genes involved in root development, stomatal closure, ROS (reactive oxygen species) scavenging, and hormone responses, among others. Taken together, the combined use of GWAS and transcriptomic data analyses provide the foundation for our enhanced understanding of root trait morphological changes in response to drought stress, and to achieve superior yield resilience/stability under water shortages in flax through enhanced molecular breeding. Data availability: All data supporting the findings of this study are available within the paper and within its Supplementary data

In a rapidly changing climate, flowering time (FL) adaptation is important to maximize seed yield in flax (Linum usitatissimum L.). However, our understanding of the genetic mechanism underlying FL in this multipurpose crop remains limited. With the aim of dissecting the genetic architecture of FL in flax, a genome-wide association study (GWAS) was performed on 200 accessions of the flax core collection evaluated in four environments. Two single-locus and six multi-locus models were applied using 70,935 curated single nucleotide polymorphism (SNP) markers. A total of 40 quantitative trait nucleotides (QTNs) associated with 27 quantitative trait loci (QTL) were identified in at least two environments. The number of QTL with positive-effect alleles in accessions was significantly correlated with FL (r = 0.77 to 0.82), indicating principally additive gene actions. Nine QTL were significant in at least three of the four environments accounting for 3.06–14.71% of FL variation. These stable QTL spanned regions that harbored 27 Arabidopsis thaliana and Oryza sativa FL-related orthologous genes including FLOWERING LOCUS T (Lus10013532), FLOWERING LOCUS D (Lus10028817), transcriptional regulator SUPERMAN (Lus10021215), and gibberellin 2-beta-dioxygenase 2 (Lus10037816). In silico gene expression analysis of the 27 FL candidate gene orthologous suggested that they might play roles in the transition from vegetative to reproductive phase, flower development and fertilization. Our results provide new insights into the QTL architecture of flowering time in flax, identify potential candidate genes for further studies, and demonstrate the effectiveness of combining different GWAS models for the genetic dissection of complex traits.

The advent of high-throughput next-generation sequencing technologies in the last decade, coupled with its substantial decrease in cost in the recent years and development of complementary array-based genotyping platforms, has revolutionized the generation of genome-wide markers and propelled several statistical methods for unearthing marker-phenotype association. This chapter provides an outline of the conceptual principles and steps of methods widely used for genome-wide association studies (GWAS) in cereals. Specifically, we focussed on presenting practical steps, starting from assembling populations suitable for phenotyping, genotyping platforms, estimation of population structure from genome-wide markers, estimation of linkage disequilibrium (LD), and methods of GWAS. We also highlighted the available sources of cereal genome assemblies and major software packages used for GWAS, namely, TASSEL-5.0, PLINK, and GAPIT-3.0.

Flaxʼs fiber yield and quality can be severely impaired due to water deprivation. Herein, 41 diverse flax accessions were evaluated for four agronomic and four root traits under drought stress (DS) and irrigated (IR) conditions. In order to identify quantitative trait nucleotides (QTNs) positively influencing the stability of these traits under DS, the stress tolerance index (STI) and trait stability index were calculated, which were analyzed using two single-locus and three multi-locus genome-wide association (GWA) methods with 170,534 single-nucleotide polymorphisms (SNPs). Significant genotype and treatment effects (p < 0.001) were observed for the traits assessed. A total of 118 QTNs were identified by multiple GWA methods. Fifteen QTNs were commonly detected by two or more methods. One QTN for STI was consistently identified by four methods and explained between 45 and 65% of the phenotypic variation (R2). A maximum of 12 out of 15 favorable QTNs were observed in flax accessions. Genotypes F_UNK_C_CN33393 and F_NLD_C_CN18987 showed superior plant height and root trait stability under DS, each one harboring 12 and 10 favorable QTNs, respectively. QTNs were further validated in an independent set of accessions under DS and IR conditions. Most of accessions performed as expected based on their corresponding haplotypes, confirming the robustness of the QTNs indentified by multiple GWA methods. Candidate genes involved in drought-responsive pathways and root and vascular tissue development were identified nearby QTNs. Collectively, our results should facilitate marker-assisted breeding toward the goal of improving flax production under water scarcity.

QTNs associated with drought tolerance traits and indices were identified in a flax mini-core collection through multiple GWAS models and phenotyping at multiple locations under irrigated and non-irrigated field conditions. Drought is a critical phenomenon challenging today’s agricultural sector. Crop varieties adapted to moisture deficit are becoming vital. Flax can be greatly affected by limiting moisture conditions, especially during the early development and reproductive stages. Here, a mini-core collection comprising genotypes from more than 20 major growing countries was evaluated for 11 drought-related traits in irrigated and non-irrigated fields for 3 years. Heritability of the traits ranged from 44.7 to 86%. Six of the 11 traits showed significant phenotypic difference between irrigated and non-irrigated conditions. A genome-wide association study (GWAS) was performed for these six traits and their corresponding stress indices based on 106 genotypes and 12,316 single nucleotide polymorphisms (SNPs) using six multi-locus and one single-locus models. The SNPs were then assigned to 8050 linkage disequilibrium (LD) blocks to which a restricted two-stage multi-locus multi-allele GWAS was applied. A total of 144 quantitative trait nucleotides (QTNs) and 13 LD blocks were associated with at least one trait or stress index. Of these, 16 explained more than 15% of the genetic variance. Most large-effect QTN loci harbored gene(s) previously predicted to play role(s) in the associated traits. Genes mediating responses to abiotic stresses resided at loci associated with stress indices. Flax genes Lus10009480 and Lus10030150 that are predicted to encode WAX INDUCER1 and STRESS-ASSOCIATED PROTEIN (SAP), respectively, are among the important candidates detected. Accessions with multiple favorable alleles outperformed others for grain yield, thousand seed weight and fiber/biomass in non-irrigated conditions, suggesting their potential usefulness in breeding and genomic selection.

Linum usitatissimum (flax) is an ancient crop that has now a rapidly expanding set of genomic resources. The development of molecular markers from restriction fragment length polymorphisms to simple sequence repeats and single nucleotide polymorphisms has followed the evolution of these technologies and then expanded through the advent of high-throughput sequencing technologies. The combination of markers, next-generation sequencing, and optical mapping techniques has supported the development of genetic maps with an increasing density of markers resulting in the assembly of chromosome-based pseudomolecules. These marker resources have been used to identify quantitative trait loci for numerous agronomically important traits within the cultivated flax and its wild progenitor core collections.

Drought hampers flax yield and oil quality particularly at the reproductive stage. Here, 105 flax accessions were assessed for drought tolerance under irrigated and drought-stressed conditions across three environments using eight stress indices. Total root length (TRL), total root volume (TRV) and diameter class length (DCL) were analyzed in two selected groups of accessions contrasting for drought tolerance. These genotypes were further submitted to selective sweep analysis using 394 genome-wide microsatellite (SSR) loci to identify markers potentially associated with drought tolerance and drought-responsive candidate genes. The results obtained for yield under stress (Ys) and yield under irrigated condition (Yp) indicated significant genotypic response to water treatments (P<0.001). Hierarchical clustering and heatmap analyses of stress indices identified the oil type flax cultivars O_CAN_C_CN19004 (AC Emerson) and O_CAN_C_CN19003 (AC McDuff) as the most drought tolerant. Some fiber type flax accessions were also clustered in the tolerant group. The drought tolerant group showed 29, 42, and 22% superior TRL, TRV and DCL, respectively, than its sensitive counterpart under drought. The SSR loci under selective sweep, Lu254 and Lu709 were significantly associated with Ys, and accessions carrying the favorable haplotype exhibited 21.7% higher Ys. Various candidate genes involved in absicic acid pathway, auxin signaling, Ca2+ signaling, photosynthesis regulation, and drought-responsive transcription factors were identified at the selective sweep loci. The identified tolerant accessions can be used for conferring drought tolerance to elite cultivars, while the selective sweep SSR loci linked to drought-responsive candidate genes could be useful in MAS.

New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC and HC in 200 diverse flaxseed accessions genotyped with 1.7 million single nucleotide polymorphism (SNP) markers. The data obtained for MC and HC indicated a broad phenotypic variation and high (~70%) and a moderate (~49%) narrow sense heritability, respectively. MC and HC did not differ statistically between fiber and oil morphotypes, but yellow-seeded accessions had 2.7% less HC than brown-seeded ones. The genome-wide linkage disequilibrium (LD) decayed to r2 = 0.1 at a physical distance of ~100 kb. Seven and four quantitative trait loci (QTL) were identified for MC and HC, respectively. Promising candidate genes identified include Linum usitatissimum orthologs of the Arabidopsis thaliana genes TRANSPARENT TESTA 8, SUBTILISIN-LIKE SERINE PROTEASE, GALACTUROSYL TRANSFERASE-LIKE 5, MUCILAGE-MODIFIED 4, AGAMOUS-LIKE MADS-BOX PROTEIN AGL62, GLYCOSYL HYDROLASE FAMILY 17, and UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE. These genes have been shown to play a role in mucilage synthesis and release, seed coat development and anthocyanin biosynthesis in A. thaliana. The favorable alleles will be useful in flaxseed breeding towards the goal of achieving the ideal MC and HC composition for food and feed by genomic-based breeding.

New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC and HC in 200 diverse flaxseed accessions genotyped with 1.7 million SNP markers. The data obtained for MC and HC indicated a broad phenotypic variation and high (~70%) and a moderate (~49%) narrow sense heritability, respectively. MC and HC did not differ statistically between fiber and oil morphotypes, but yellow-seeded accessions had 2.7% less HC than brown-seeded ones. The genome wide linkage disequilibrium (LD) decayed to r2&thinsp;=&thinsp;0.1 at a physical distance of ~100 Kb. Seven and four QTL were identified for MC and HC, respectively. Promising candidate genes included Linum usitatissimum orthologs of the Arabidopsis thaliana genes TRANSPARENT TESTA 8, SUBTILISIN-LIKE SERINE PROTEASE, GALACTUROSYL TRANSFERASE-LIKE 5, MUCILAGE-MODIFIED 4, AGAMOUS-LIKE MADS-BOX PROTEIN AGL62, GLYCOSYL HYDROLASE FAMILY 17 and UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE that have been shown to play a role in mucilage synthesis and release, seed coat development and anthocyanin biosynthesis in A. thaliana were identified. The favorable alleles will be useful in flaxseed breeding towards the goal of achieving the ideal flaxseed cultivars for food and feed by genomic-based breeding.

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 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.

New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC and HC in 200 diverse flaxseed accessions genotyped with 1.7 million SNP markers. The data obtained for MC and HC indicated a broad phenotypic variation and high (~70%) and a moderate (~49%) narrow sense heritability, respectively. MC and HC did not differ statistically between fiber and oil morphotypes, but yellow-seeded accessions had 2.7% less HC than brown-seeded ones. The genome wide linkage disequilibrium (LD) decayed to r2 = 0.1 at a physical distance of ~100 Kb. Seven and four QTL were identified for MC and HC, respectively. Promising candidate genes included Linum usitatissimum orthologs of the Arabidopsis thaliana genes TRANSPARENT TESTA 8, SUBTILISIN-LIKE SERINE PROTEASE, GALACTUROSYL TRANSFERASE-LIKE 5, MUCILAGE-MODIFIED 4, AGAMOUS-LIKE MADS-BOX PROTEIN AGL62, GLYCOSYL HYDROLASE FAMILY 17 and UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE that have been shown to play a role in mucilage synthesis and release, seed coat development and anthocyanin biosynthesis in A. thaliana were identified. The favorable alleles will be useful in flaxseed breeding towards the goal of achieving the ideal flaxseed cultivars for food and feed by genomic-based breeding.

Linseed (Linum usitatissimum L.) is well known for containing functional compounds with health‐related benefits. Assessed were the agronomic and seed‐quality traits of 13 linseed advanced breeding lines (ABLs) varying in seed mucilage content (SMC) that could be better suited to Chilean environments and food and feed market needs. Analysis of variance revealed highly significant genotype and environment effects for most of the traits assessed. Seed mucilage content ranged from 0.89 to 5.45%, and various ABLs exhibited similar yield and yield‐related traits to the controls, but some outperformed them for harvest index, plant height, and days to 5% flowering. The yellow‐seeded ABLs showed the highest and lowest oil and hull content, respectively, as compared with the brown‐seeded lines. The majority of the ABLs exhibited high linolenic acid content, ∼60%. The four most promising ABLs were further characterized for the content of the cyanogenic glycosides (CGs) linustatin and neolinustatin, where LuCGNA11 and LuCGNA67 had the lowest values for both CGs. We evaluated the effects of two ABLs contrasting in SMC on laying hen weight (control = 1794 g), egg production (control = 117 eggs), and egg weight (control = 62.9 g) over a 4‐wk period. Hens fed the low SMC diet had an increase of 78.6 g, 13 eggs, and 3.86 g, while the high SMC diet had a reduction of 36.8 g, 25 eggs, and 2.8 g for body weight, egg production, and egg weight, respectively. These new high and low SMC ABLs offer opportunities to the food and feed industry for the generation of new value‐added products.