QTL mapping and molecular characterization of the classical D locus controlling seed and flower color in Linum usitatissimum (flax)

Abstract

The flowers of flax (linseed) are blue-hued, ephemeral and self-pollinating, and the seeds are typically brown. A century-old interest in natural yellow seed variants and a historical model point to recessive alleles in B1, D and G loci being responsible, but the functional aspects had remained unknown. Here, we characterized the “D” locus by quantitative trait loci (QTL) mapping and identified a FLAVONOID 3′5′ HYDROXYLASE (F3′5′H) gene therein. It does not belong to the F3′5′H clade, but resembles biochemically characterized F3′Hs (flavonoid 3′ hydroxylase) but without F3′H activity. The genome lacks other F3′H or F3′H-like genes. The apparent neo-functionalization from F3′H is associated with a Thr498 → Ser498 substitution in a substrate recognition site (SRS). The yellow seed and white flower phenotypes of the classical d mutation was found to be due to one nucleotide deletion that would truncate the deduced product and remove three of the six potential SRS, negatively impacting delphinidin synthesis. Delphinidin is sporadic in angiosperms, and flax has no known pollination syndrome(s) with functional pollinator group(s) that are attracted to blue flowers, raising questions on the acquisition of F3′5′H. The appearance of d allele is suggestive of the beginning of the loss of F3′5′H in this species.

Genome-Wide Association Analysis of Mucilage and Hull Content in Flax (Linum usitatissimum L.) Seeds

“…QTL for seed coat color to indirectly increase oil content and minimize HC have been identified in B. napus and soybean [ 37 , 59 , 60 ]. In flax, a pleiotropic QTL controlling yellow seed and white flower color was recently dissected at the molecular level, but its effect on HC has not been addressed [ 23 ]. Here, we identified four QTL whose effects reduced HC by 2.6%, on average.…”

“…Genetic variation for MC and HC in flaxseed has been assessed [ 4 , 7 , 16 , 17 , 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 ].…”

Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.)

“…For example, Cloutier et al construct a consensus linkage map by combined three individual linkage maps incorporating 770 markers based on 371 shared markers including 114 that were shared by all three populations and 257 shared between any two populations [ 14 ]. Most of the QTL mapping analysis focused on fatty acid related traits, such as fatty acid composition, yield [ 15 , 16 ], seed and flower color [ 17 ]. For example, Sudarshan et al,(2017) identified a seed and flower color QTL “D” by QTL mapping analysis and identified a candidate gene [ 17 ].Today, SNP markers are the most efficient and abundant markers for mapping [ 18 ] and other applications, such as GWASs [ 19 , 20 ], diversity analyses [ 21 ] and bulked segregate analysis [ 22 ].…”

Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security

“…The identified 183 seed oil QTLs in soybean, which was annotated as part of Soybase database (Grant et al 2009), providing key information related to seed development and associated molecular mechanism to set up soybean as a model legume crop (Gupta et al 2017). In a very interesting study Sudarshan et al (2017) characterized "D" locus Linum usitatissimum (flax) by QTL mapping and identified an underlying FLAVONOID 3′5′ HYDROXYLASE (F3′5′H) gene which determine the seed and flower color. A single nucleotide deletion in this gene truncates the deduced product thus leading to yellow seed and white flower phenotypes in flax (Sudarshan et al 2017).…”