**1. Introduction**

Flaxseed (*Linum usitatissimum* L.), one of the oldest crops, has been used as human food and animal feed since ancient times [1]. The two main morphotypes of cultivated *L. usitatissimum* are oil morphotype (flaxseed) and fiber morphotype (fiber flax). Flaxseed plants are shorter, more branched, and larger seeded, and branches cover a greater proportion of the main stem compared to fiber flax. Flaxseed currently enjoys new prospects in the functional food market because of growing consumer interest in food with health benefits [1]. Flaxseed is rich in bioactive compounds, such as α-linolenic acid (omega-3) that have cardiovascular benefits, lignans with anticancer properties, and insoluble and soluble fiber (mucilage) that is capable of lowering cholesterol and insulin [2].

Flaxseed mucilage is a heterogeneous polysaccharide composed of xylose, arabinose, glucose, galactose, rhamnose, and fructose [3] that can be purified into neutral and acidic polymers. Mucilage

abounds in the seed coat, where it makes up to 8–10% of the seed weight [4]. Mucilage synthesis is tightly linked to seed coat development [5] and both tissues form the seed hull, a structure representing 37–48% of the seed weight [6,7]. These two fractions, rich in polysaccharides, are components of the flaxseed meal, primarily used as a protein rich livestock and poultry feed [6,8]. Absorption of flaxseed meal0 s advantageous 31–45% protein content [9] may be hindered by mucilage and cell wall polysaccharides. This is due to the swelling capacity of polysaccharides in the digestive tract of monogastric animals that causes concomitant growth depression and reduced feed efficiency [7,10]. In that context, reduction of mucilage (MC) and hull (HC) contents in flaxseed meal is desirable to achieve improved feeding value for livestock and poultry. Studies of flaxseed mucilage degradation are focused on chemical retting, enzyme retting, and steam explosion [11]. Reduction of the hull content in flaxseed and rapeseed meal has been achieved through dehulling methods [12] and the use of yellow-seeded genotypes [7,13]. Food and feed markets demand flaxseed cultivars differing in mucilage and hull content. It is, therefore, crucial to decipher the genetic factors underlying these complex traits in order to accelerate the development of market-specific flaxseed cultivars.

In the model plant *Arabidopsis thaliana*, the genes necessary for the synthesis, modification, and release of mucilage, as well as seed coat development, are well understood [5,14]. Putative flax orthologs of the *RHAMNOSE SYNTHASE* (*AtRHM1*), *GALACTURONOSYLTRANSFERASE-LIKE 3* (*GATL3*), *GALACTURONOSYLTRANSFERASE 11* (*GAUT11*), *XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 3*(*XTH3*), and *ALPHA-XYLOSIDASE-1* (*AtBXL1*), involved in mucilage production, have been identified using gene expression analysis during seed development [15]. Similarly, putative flax orthologs of the *TRANSPARENT TESTA 3*, *4*, *5*, and *7* (*TT3*, *TT4*, *TT5*, and *TT7*), *FLAVONOL SYNTHASE* (*FLS*) and *BANYULS* (*BAN*), involved in flavonoids synthesis during seed coat development, have also been identified [15].

Genetic variation for MC and HC in flaxseed has been assessed [4,7,16–18] but no quantitative trait loci (QTL) have been reported so far. QTL for *Fusarium* wilt resistance [19], powdery mildew [20], iodine value, palmitic, linoleic, and linolenic acids [21,22], and seed and flower color [23], were reported. QTL for seed protein, cell wall, straw weight, yield-related traits, and phenological traits, have also been reported using bi-parental mapping and association mapping [22,24,25]. Recently, genome-wide association studies (GWAS) have been conducted for agronomic and seed quality traits using thousands of single nucleotide polymorphism (SNP) loci [26,27]. GWAS mines the natural sequence diversity within a species and captures historical recombination events. It is therefore a suitable approach to discover loci that control complex traits, leading to a higher mapping resolution to facilitate the identification of candidate genes [28]. Thus, the suite of genomic tools available for flaxseed genetic studies [21,22,26,27,29–32] make genomic evaluation of MC and HC feasible.

The objective of this research was to identify QTL and candidate genes contributing to mucilage content and hull content that could be capitalized upon to assist in breeding flaxseed cultivars with different mucilage content and with reduced hull content. Improving these traits will increase seed value of this important cash crop.
