Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology.

Liuxi Yi,Yu Zhou,Fengyun Gao,Xiaoqing Zhao,Xiaoyun Jia,Bateer Siqin,Hui Zhang,Qiang Li,Pawan L Kulwal

doi:10.1371/journal.pone.0189785

Liuxi Yi, Yu Zhou + Show 7 more

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https://doi.org/10.1371/journal.pone.0189785

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Abstract

Flax is an important crop for oil and fiber, however, no high-density genetic maps have been reported for this species. Specific length amplified fragment sequencing (SLAF-seq) is a high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. In this study, SLAF-seq was employed to develop SNP markers in an F2 population to construct a high-density genetic map for flax. In total, 196.29 million paired-end reads were obtained. The average sequencing depth was 25.08 in male parent, 32.17 in the female parent, and 9.64 in each F2 progeny. In total, 389,288 polymorphic SLAFs were detected, from which 260,380 polymorphic SNPs were developed. After filtering, 4,638 SNPs were found suitable for genetic map construction. The final genetic map included 4,145 SNP markers on 15 linkage groups and was 2,632.94 cM in length, with an average distance of 0.64 cM between adjacent markers. To our knowledge, this map is the densest SNP-based genetic map for flax. The SNP markers and genetic map reported in here will serve as a foundation for the fine mapping of quantitative trait loci (QTLs), map-based gene cloning and marker assisted selection (MAS) for flax.

Highlights

Flax (Linum usitatissimum L), which belongs to the Linaceae family, is an annual, self-pollinating, and diploid (2n = 2x = 30) crop with a genome size of ~ 370 Mb [1, 2]
After in silico double digestion of flax reference genome with HeaIII + RsaI, restriction fragments of 314–414 bp were defined as SLAF tags, and 118,778 of them were expected
Genetic maps are essential for fine mapping of quantitative trait locus (QTL), map-based gene cloning and marker-assisted selection (MAS), the quality of genetic maps depends on the types and number of markers used

Summary

Introduction

Flax (Linum usitatissimum L), which belongs to the Linaceae family, is an annual, self-pollinating, and diploid (2n = 2x = 30) crop with a genome size of ~ 370 Mb [1, 2]. Flax has been used by human beings for several thousands years as a source of high quality oil (linseed) and stem fiber (linen) [3]. Flaxseed oil is well known for its nutraceutical functions because it contains high percentage of unsaturated fatty acids and lignans. The unsaturated fatty acids in flaxseed oil, especially, the linolenic acid (LIN, ~55%), known as α- linolenic acid, is the precursor. Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using SLAF-seq nmkjt.gov.cn/; BS; and 2) the Fund for the China Agriculture Research System, CARS-17-GW-3; China’s Ministry of Agriculture; http://www.moa. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

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