| China is the largest flax fiber producing and processing country. However, due to the shortage of high-quality raw flax fiber, our flax industry was heavily dependent on imported raw flax fiber over the past decade. Increasing per unit yield of flax is therefore an immediate imperative of flax breeding. In this study, phenotypic traits variations and genetic diversity of535different flax varieties from38countries and regions were analyzed, a primary flax core germplasm collection consisting of182varieties was subsequently constructed, and multiple analysis of the agronomic traits were conducted to identify the primary indexes of flax fiber and seed yield. New SSR markers were developed from flax genome sequences and were used to analyze the phenotypic traits variations and genetic diversity. An association study was performed on the flax core germplasm collection to identify the SSR loci that were closely linked to yield related traits, with the aim at laying the foundation for the cloning of the flax yield related genes, and molecular marker-assisted breeding for high yield flax cultivars. The main results are as follows:A total of22665EST-SSRs were identified from the EST sequences and40435genomic-SSRs were identified from the genome sequencing data, and the distribution of SSR frequencies were1/7.48kb and1/6.94kb respectively. Trinucleotides, dinucleotide and mononucleotide were the most abundant type of all the repeat sequences both in genomic-SSRs and EST-SSRs. The repeating numbers of the SSR repeat units were higher in most genomic-SSRs tended than that in EST-SSRs. Through comparative analysis,25,142genomic SSR loci were obtained, and a database including19,939pairs of candidate flax SSR primers was established. Sixty one novel polymorphic SSR markers were developed from145pairs of candidate primers. According to the polymorphism analysis results of91pairs of EST-SSR and102pairs of genomic-SSR primers, genomic-SSR markers were better than EST-SSRs, the compound SSRs were prior to perfect type SSRs, and dinucleotides and hexanucleotide SSRs were better than others.The correlation, path analysis and multiple linear regression analysis of the agronomic traits535flax germplasm suggested that the major determining factors of flax seed yield were branch number, days of emergence to flowering and branching habit, and the major determining factors of flax fiber yield were total fiber ratio, plant height and retted stem ratio.The quantitative traits of flax showed higher level of genetic diversity than the qualitative traits. Among nine geographical populations, the population from China has the highest genetic diversity in phenotypic traits. PCA-based analysis of phenotypic traits divided all the germplasm into fiber flax and linseed subgroups, and a primary flax core germplasm bank of182collections was established.A total of735alleles were identified at222SSR loci in flax core collection from the bands amplified by193pairs of SSR primers. The average number of alleles per locus, PIC value and Shannon’s index were3.31,0.283and0.5856respectively. The population from China also has the highest genetic diversity among different geographical populations. And all the germplasm can also be divided into fiber flax and linseed based on SSR markers. A certain degree of LD was found from flax germplasm populations, and the LD was mainly caused by recombinant. Using the GLM and MLM models, a total of25and11marker loci were associated with two-year phenotypic traits respectively. Only three SSR loci are correlated to two-year phenotypic traits in both of the two models. Altogether57allelic variation were found through analysis of allelic variation effect, including31alleles with positive effect value and26alleles with negative effect. |
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