Abstract
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.
Highlights
Flax (Linum usitatissimum L., 2n = 30) is an important economic crop that is mainly cultivated in Canada, China, America, and India
In this study, based on the two materials with different oil contents developed in our laboratory in the early stage, our aims were to: 1) re-sequence the two materials (87 − 3 and 84 − 3) and compare them with the reference genome sequence to develop the InDel marker; 2) design the InDel primers and evaluate the quality of InDel markers use the two accessions (87 − 3 and 84 − 3); 3) use polymorphic primers to analyse the genetic diversity of 69 flax accessions; and 4) conduct correlation analysis between InDel markers and oil content traits, as well as perform the screening of candidate genes related to oil content traits
In this study, using 84 − 3 and 87 − 3 with different oil contents constructed in the early stage of experiments, the InDel marker was developed for the first time in flax by re-sequencing, which was helpful for conducting flax molecular marker-assisted breeding
Summary
Cultivation of high-yield and high-quality flax varieties has emerged as one of the current breeding goals. Molecular marker-assisted breeding (MAS) is a new type of breeding technology that can help achieve the breeding goal of increasing crop yield and quality in a more direct, rapid, and efficient manner. With the development of sequencing technology, development of high-quality molecular markers in the whole genome has been realised. There no research has been conducted on flax InDel molecular markers. The development of InDel for the expansion of molecular markers can accelerate the process of flax molecular breeding, thereby aiding the cultivation of high-quality flax varieties
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