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