Abstract
Flax (Linum usitatissimum L.) is an important cash crop, and its agronomic traits directly affect yield and quality. Molecular studies on flax remain inadequate because relatively few flax genes have been associated with agronomic traits or have been identified as having potential applications. To identify markers and candidate genes that can potentially be used for genetic improvement of crucial agronomic traits, we examined 224 specimens of core flax germplasm; specifically, phenotypic data for key traits, including plant height, technical length, number of branches, number of fruits, and 1000-grain weight were investigated under three environmental conditions before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome-wide association study (GWAS) for these five agronomic traits. Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the important agronomic traits. Our analyses identified a total of 42 SNP loci that showed significant correlations with the five important agronomic flax traits. Next, candidate genes were screened in the 10 kb zone of each of the 42 SNP loci. These SNP loci were then analyzed by a more stringent screening via co-identification using both a general linear model (GLM) and a mixed linear model (MLM) as well as co-occurrences in at least two of the three environments, whereby 15 final candidate genes were obtained. Based on these results, we determined that UGT and PL are candidate genes for plant height, GRAS and XTH are candidate genes for the number of branches, Contig1437 and LU0019C12 are candidate genes for the number of fruits, and PHO1 is a candidate gene for the 1000-seed weight. We propose that the identified SNP loci and corresponding candidate genes might serve as a biological basis for improving crucial agronomic flax traits.
Highlights
Flax (Linum usitatissimum L.) is one of the oldest plants cultivated for fiber and edible oil and remains an important cash crop worldwide
Under three different environmental conditions, plant height had a minimum value of 42.20 cm, a maximum value of 125.40 cm, and a maximum coefficient of variation of 18.09%; technical length had a minimum value of 27.60 cm, a maximum value of 103.20 cm, and a maximum coefficient of variation of 22.76%; number of branches had a minimum value of 2, a maximum value of 12, and a maximum coefficient of variation of 55.57%; number of fruits had a minimum value of 2, a maximum value of 39, and a maximum coefficient of variation of 53.47%; and 1,000grain weight had a minimum value of 3.18 g, a maximum value of 9.21 g, and a maximum coefficient of variation of 16.27%
single nucleotide polymorphism (SNP) detection was performed in the collection of 224 germplasm resources of flax based on the predefined 346,639 SLAF tags, which generated a total of 584,987 SNP loci (MAF ≥ 0.05)
Summary
Flax (Linum usitatissimum L.) is one of the oldest plants cultivated for fiber and edible oil and remains an important cash crop worldwide. Deng et al (2014) used 61 pairs of SSR primers, 91 pairs of expressed sequence tag (EST)SSR primers, and 102 pairs of genomic-SSR primers to perform association analysis for yield-related traits in 182 core germplasm resources of flax; the authors identified 57 high-quality allelic variations, including 31 showing yield-enhancing effects and 26 showing the opposite. These association studies were all based on common molecular markers (e.g., SSR, ESTSSR) that might not be sufficient in light of the rapid development of new sequencing technologies. The investigations cited above were not enough to elucidate the genes related to the complicated agronomic traits of flax
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