Genome-Wide Association Study of Salt Tolerance at the Seed Germination Stage in Flax (Linum usitatissimum L.).

Xiao Li,Huiqing Liu,Dongliang Guo,Qingcheng Yan,Haixia Jiang,Jiaxun Chen,Yanfang Gao,Gongze Li,Liqiong Xie,Min Xue,Lepeng Duan

doi:10.3390/genes13030486

Abstract

Soil salinization seriously affects the growth and distribution of flax. However, there is little information about the salt tolerance of flax. In this study, the salt tolerance of 200 diverse flax accessions during the germination stage was evaluated, and then the Genome-wide Association Study (GWAS) was carried out based on the relative germination rate (RGR), relative shoot length (RSL) and relative root length (RRL), whereby quantitative trait loci (QTLs) related to salt tolerance were identified. The results showed that oil flax had a better salt tolerance than fiber flax. A total of 902 single nucleotide polymorphisms (SNPs) were identified on 15 chromosomes. These SNPs were integrated into 64 QTLs, explaining 14.48 to 29.38% (R2) of the phenotypic variation. In addition, 268 candidate genes were screened by combining previous transcriptome data and homologous gene annotation. Among them, Lus10033213 is a single-point SNP repeat mapping gene, which encodes a Glutathione S-transferase (GST). This study is the first to use GWAS to excavate genes related to salt tolerance during the germination stage of flax. The results of this study provide important information for studying the genetic mechanism of salt tolerance of flax, and also provide the possibility to improve the salt tolerance of flax.

Highlights

Soil salinization is one of the main abiotic stress factors during crop growth and development, which causes poor crop growth, and leads to yield reduction or even death [1,2]
The results showed that the salt tolerance indices (RGR, relative shoot length (RSL), relative root length (RRL) and D values) of the oil flax subpopulation were significantly higher than those of the oil-fiber dual purpose flax (OF) flax and fiber flax
Using general linear model (GLM) and mixed linear model (MLM) models, we identified 1075 single nucleotide polymorphisms (SNPs) significantly related to salt-related relative germination rate (RGR), RSL and RRL (Supplementary Figures S4–S6; Supplementary Table S5)

Summary

Introduction

Soil salinization is one of the main abiotic stress factors during crop growth and development, which causes poor crop growth, and leads to yield reduction or even death [1,2]. Under exposure to high concentrations of salt, ion toxicity destroyed the structure of the plasma membrane and ion imbalance promoted protein aggregation, the physiological and metabolic activities of the plant were severely inhibited [3]. 300 million hectares of land in the world are affected by salt stress, and salinization or secondary salinization caused by water and soil pollution increases significantly every year [4]. One of the most economical and effective ways to deal with soil salinization is to screen and cultivate salt tolerant crops [5]. The well-known sea (salt-tolerant) rice cultivation has been confirmed as improving the potential of saline-alkali land and ensuring food security [6]. Screening good salt-tolerant varieties and mining salt-tolerant genes are the effective approaches to dealing with environmental stress in recent years [7]

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Discussion

Conclusion