Genetic analysis of seed and flower colour in flax (Linum usitatissimum L.) and identification of a candidate gene in the D locus

Flax (Linum usitatissimum L.) is a commercial oilseed crop in Canada. Globally flax is known for industrial oil and fiber. Flaxseed contains Omega 3 fatty acid, lignans like secoisolariciresinol diglucoside (SDG), flavonoids and polysaccharides which offer potential health benefits. Conventional flax cultivars are brown seeded and few mutant lines are yellow seeded. The darkness of seed colour depends on the presence of polymerized proanthocyanidins (PA; condensed tannins) in the seed coat. PAs are the product of the phenylpropanoid pathway. Previous genetic studies by Mittapalli and Rowland (2003) on G1186/94 showed the seed colour trait was governed by the homozygous recessive alleles at D locus and the same locus is closely linked to white or pink flower petals. To start with, single seeds of already developed stable recombinant inbred lines (RILs) (of F8:9 generation) from a cross of yellow seeded European recessive line (G1186/94) and brown seeded CDC Bethune (popular variety) were grown. In this study, seed colour phenotyping was done by measuring seed colour of each RIL in Red-Green-Blue (RGB) values. To understand the genetic basis of flax seed and flower colour, mapping with single sequence repeats (SSRs) and CAPS (Cleaved Amplified Polymorphic Sequences) markers were used. For the first time, a framework genetic linkage map was constructed from populations of CDC Bethune/ G1186/94 containing 19 linkage groups (LGs). LG 1 with four SSR markers was found to be linked with the seed colour locus D. During the fine-mapping, two SSR markers (LuM566 and Lu2351) were found to be linked with the seed colour trait. The D locus has been confined in a 2.8 cM region and the closest marker was LuM566 at a distance of 0.6 cM. This was observed to be a stable locus in two growth trials and in different environments with logarithm of odds (LOD) above 39 and more than 84 % of the trait expressed by the major locus in both trials. As there were no recombinants (off types) for flower colour in F8:9 plants i.e brown-seeded lines produced blue flowers and yellow-seeded lines produced white flowers, the same locus holds well for the flower colour trait. The marker associated with seed and flower colour in G1186/94 (European recessive yellow line) was identified and can be used in flax breeding. Additionally, an interesting putative candidate gene of potential significance was identified through genomics assisted gene search from the flax whole genome sequence database. The gene expression analyses showed lower expression of putative flavonoid 3’ hydroxylase (F3’H) (a gene involved in flavonoid biosynthesis pathway) in both seed coat and flower petal tissues of G1186/94 as compared to CDC Bethune. Therefore, this study represents the first report on genetic mapping based putative candidate gene finding for recessive yellow seed colour mutation in the D locus in flax