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

Abstract

Flax is an important oil and bre crop grown in Northern Europe, Canada, India, and China. The development of molecular markers has accelerated the process of ax 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 ax. However, the development of ax insertion/deletion (InDel) markers has not been reported. A total of 17,110 InDel markers were identi ed by comparing whole-genome re-sequencing data of two accessions (87 − 3 and 84 − 3) with the ax reference genome. The length of InDels ranged from 1-277 bp, with 1-15 bp accounting for the highest rate (95.55%). The most common InDels were in the form of single nucleotide (8840), dinucleotide (3700), and trinucleotide (1349), and chromosome 2 (1505) showed the highest number of InDels among ax chromosomes, while chromosome 10 (913) presented with the lowest number. From 17,110 InDel markers, 90 primers that were evenly distributed in the ax genome were selected. Thirty-two pairs of polymorphic primers were detected in two ax accessions, and the polymorphism rate was 40.70%. Furthermore, genetic diversity analysis, population structure and principal component analyse (PCA) divided 69 ax accessions into two categories, namely oilseed ax and bre ax using 32 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 or InDel-81, might be involved in ax lipid biosynthesis and lipid metabolism. This study is the rst to develop InDel markers based on re-sequencing in ax and clustered the markers into two well-separated groups for oil and bre. The results demonstrated that InDel markers developed herein could be used for ax germplasm identi cation, genetic diversity analysis, and molecular marker-assisted breeding.

Molecular genetic diversity of flax cultivars (<i>Linum usitatissimum</i> l.) represented in the State Register for Selection Achievements of the Russian Federation

“…га., масличного льна -более 1 млн га. Благодаря тому, что из растения можно получать и волокнистую, и семенную продукцию, лен нашел применение в самых разных сферах народного хозяйства (Ponazhev et al, 2014;Saha et al, 2019;Nag et al, 2020;Jiang et al, 2022). Так, для получения льноволокна, необходимого для текстильной, медицинской, химической промышленности, используется до 40-50% тресты льна-долгунца.…”

“…Одним из эффективных индикаторов полиморфизма являются генетические маркеры (Jiang et al, 2022). Идентификация сортов с помощью ДНК-маркеров также является важным шагом на пути к повышению урожайности и качества (Pan et al, 2020).…”