Development and application of novel InDel markers in flax (Linum usitatissimum L.) through whole-genome re-sequencing

Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of flax molecular breeding and has improved yield and quality. Presently, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in the whole genome have been developed for flax. However, the development of flax insertion/deletion (InDel) markers have not been reported. A total of 17,110 InDel markers were identified by comparing whole-genome re-sequencing data of two accessions (87-3 and 84-3) with the flax reference genome. The length of InDels ranged from 1 to 277 bp, with 1-15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of a single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and Ch2 (1505) showed the highest number of InDels among flax chromosomes, while Ch10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the flax genome were selected. Thirty-two pairs of polymorphic primers were detected in two flax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analysis (PCA) divided 69 flax accessions into two categories, namely oilseed flax and fibre flax using thirty-two pairs of polymorphic primers. Additionally, correlation analysis showed that InDel-26 and InDel-81 were associated with oil content traits, and two candidate genes (lus10031535 and lus10025284) tightly linked to InDel-26 and InDel-81, might be involved in flax lipid biosynthesis and lipid metabolism. This study is the first to develop InDel markers based on re-sequencing in flax and clustered the accessions into two well-separated groups for oil and fibre. The results demonstrated that InDel markers developed herein could be used for flax germplasm identification, genetic diversity analysis, and molecular marker-assisted breeding.