Genome-Wide Association Studies of Salt Tolerance at Seed Germination and Seedling Stages in Brassica napus

Abstract

Most crops are sensitive to salt stress, but their degree of susceptibility varies among species and cultivars. In order to understand the salt stress adaptability of Brassica napus to salt stress, we collected the phenotypic data of 505 B. napus accessions at the germination stage under 150 or 215 mM sodium chloride (NaCl) and at the seedling stage under 215 mM NaCl. Genome-wide association studies (GWAS) of 16 salt tolerance coefficients (STCs) were applied to investigate the genetic basis of salt stress tolerance of B. napus. In this study, we mapped 31 salts stress-related QTLs and identified 177 and 228 candidate genes related to salt stress tolerance were detected at germination and seedling stages, respectively. Overexpression of two candidate genes, BnCKX5 and BnERF3 overexpression, were found to increase the sensitivity to salt and mannitol stresses at the germination stage. This study demonstrated that it is a feasible method to dissect the genetic basis of salt stress tolerance at germination and seedling stages in B. napus by GWAS, which provides valuable loci for improving the salt stress tolerance of B. napus. Moreover, these candidate genes are rich genetic resources for the following exploration of molecular mechanisms in adaptation to salt stress in B. napus.

Genome-Wide Association Studies of Salt-Alkali Tolerance at Seedling and Mature Stages in Brassica napus

“…GO analysis revealed that most genes were associated with the cellular process, the metabolic process, biological regulation, and response to stimulus ( Supplementary Figure 10 ). Moreover, we also found that the most of these candidate genes were significantly differentially expressed under salt stress according to the RNA-seq data (PRJCA008229, https://ngdc.cncb.ac.cn/omix/ ) (Zhang et al, 2022 ). The relative expression of some candidate genes under normal and salt conditions was taken as an example ( Figure 3D ; Supplementary Table 19 ), which was consistent with the previous study (Zhang et al, 2019 ), showing the accuracy of candidate gene prediction.…”

“…The broad sense heritability ( H 2 b ) of all traits is calculated as follows: H 2 b = /( + /n + /nr) where was the genotype variance, was the error variance, and was interaction between genetic and environmental effects. The estimates of H2b were analyzed by the AVOVA for ANOVA using the lmer function of the lme4 package by R environment ( https://www.r-project.org/ ) (Chen et al, 2014 ; Li et al, 2020 ; Zhang et al, 2022 ).…”

“…About 142 significant SNP markers and 117 possible candidate genes associated with salt tolerance of B. napus were also identified for SSI and STI values using 201,817 high-quality SNPs (Wassan et al, 2021 ). In addition, our previous study has revealed that a total of 177 and 228 candidate genes related to salt stress tolerance were identified at germination and seedling stages, respectively, and some important candidate genes, such as BnCKX5 and BnERF3 , which were found to play a positive role in salt and mannitol stress response at the germination stage (Zhang et al, 2022 ). Although a great number of QTLs and candidate genes related to salt stress have been identified, the molecular mechanism for salt-alkali tolerance of B. napus remains unclear (Chen et al, 2021 ).…”

Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits in Brassica napus L.

“…Additionally, 20 of 30 SNPs were detected simultaneously in two replicate experiments, indicating the reliability of these loci. Previous studies have explored the genetic basis of salt stress responses at the germination or seedling stage using traditional QTL mapping or GWAS analysis [13,[17][18][19][20][21][22][23]45]. Compared with the previous results, four SNPs (ChrA10: 15,189,187,15,189,200,15,189,284,15, 188, 859 bp) could be repeatedly detected at the seedling and mature stages [23], and controlled different traits, suggesting that the four SNPs are common loci that control the salt tolerance of rapeseed at different stages.…”

“…With the development of next-generation sequencing (NGS) technology, the genome-wide association study (GWAS) has become an effective approach to map QTLs related to complex traits of crops and has been applied in various crops, such as rice, soybean, and B. napus [14][15][16]. Some QTLs and candidate genes associated with salt-tolerance-related traits at the germination and seedling stages [17][18][19][20][21][22][23] and yield-related traits [24][25][26] have gradually been identified through GWAS in B. napus. Although a number of QTLs and candidate genes have been identified for salt tolerance, the molecular mechanisms underlying the regulation of salt tolerance and yield remain unclear in B. napus.…”