Dataset Information

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

ABSTRACT: Salt stress severely affects crop growth and development and reduces the yield of Brassica napus. Exploring natural genetic variations for high salt tolerance in B. napus seedlings is an effective approach to improve productivity under salt stress. Using 10,658 high-quality single nucleotide polymorphic (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, genome-wide association studies (GWAS) were performed to investigate the genetic basis of salt tolerance and yield-related traits of B. napus. The results revealed that 77 and 497 SNPs were significantly associated with salt tolerance and yield-related traits, of which 40 and 58 SNPs were located in previously reported QTLs/SNPs, respectively. We identified nineteen candidate genes orthologous with Arabidopsis genes known to be associated with salt tolerance and seven potential candidates controlling both salt tolerance and yield. Our study provides a novel genetic resource for the breeding of high-yield cultivars resistant to salt stress.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC9785822 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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

Zhang Yan Y Li Ping P Zhang Jie J Li Yaqi Y Xu Aixia A Huang Zhen Z

International journal of molecular sciences 20221214 24

Salt stress severely affects crop growth and development and reduces the yield of Brassica napus. Exploring natural genetic variations for high salt tolerance in B. napus seedlings is an effective approach to improve productivity under salt stress. Using 10,658 high-quality single nucleotide polymorphic (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, genome-wide association studies (GWAS) were performed to investigate the genetic basis ...[more]

PMID: 36555533

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Project description:BackgroundImproving the salt tolerance of direct-seeding rice at the seed germination stage is a major breeding goal in many Asian rice-growing countries, where seedlings must often establish in soils with a high salt content. Thus, it is important to understand the genetic mechanisms of salt tolerance in rice and to screen for germplasm with salt tolerance at the seed germination stage. Here, we investigated seven seed germination-related traits under control and salt-stress conditions and conducted a genome-wide association study based on the re-sequencing of 478 diverse rice accessions.ResultsThe analysis used a mixed linear model and was based on 6,361,920 single nucleotide polymorphisms in 478 rice accessions grouped into whole, indica, and non-indica panels. Eleven loci containing 22 significant salt tolerance-associated single nucleotide polymorphisms were identified based on the stress-susceptibility indices (SSIs) of vigor index (VI) and mean germination time (MGT). From the SSI of VI, six major loci were identified, explaining 20.2% of the phenotypic variation. From the SSI of MGT, five major loci were detected, explaining 26.4% of the phenotypic variation. Of these, seven loci on chromosomes 1, 5, 6, 11, and 12 were close to six previously identified quantitative gene loci/genes related to tolerance to salinity or other abiotic stresses. The strongest association region for the SSI of MGT was identified in a ~ 13.3 kb interval (15450039-15,463,330) on chromosome 1, near salt-tolerance quantitative trait loci controlling the Na+: K+ ratio, total Na+ uptake, and total K+ concentration. The strongest association region for the SSI of VI was detected in a ~ 164.2 kb interval (526662-690,854) on chromosome 2 harboring two nitrate transporter family genes (OsNRT2.1 and OsNRT2.2), which affect gene expression under salt stress. The haplotype analysis indicated that OsNRT2.2 was associated with subpopulation differentiation and its minor/rare tolerant haplotype was detected.ConclusionsThese results provide valuable information for salt tolerance-related gene cloning and for understanding the genetic mechanisms of salt tolerance at the seed germination stage. This information will be useful to improve the salt tolerance of direct-seeding rice varieties by genomic selection or marker-assisted selection.

Project description:Cotton is an important cash crop with a certain salt tolerance, but its germination stage is very susceptible to the damage of salt stress, causing significant yield loss. However, few studies have evaluated the cotton salt tolerance and selected salt tolerance traits at germination stage. Therefore, in this study, 16 cotton samples with geographical representation were randomly selected from 308 cotton germplasms to determine the optimal 200 mmol·L-1 NaCl in cotton germination experiments. On this basis, the salt tolerance of 308 upland cotton varieties and the growth, ion distribution and transport of highly salt-tolerant and non salt-tolerant cotton germplasms were analyzed. The results showed that the 308 germplasms were classified into five classes through cluster analysis, i.e, (1) highly salt-tolerant germplasms (HST, 49), (2) salt-tolerant germplasms (ST, 169), (3) moderately salt-tolerant class (MST,43), (4) lowly salt-tolerant germplasms (LST, 16), and (5) non-salt-tolerant germplasms (NST, 31). By calculating the salt tolerance index (STI) of various cotton germination and growth parameters and principal component analysis, combined with the correlation analysis and linear regression between mean membership function value (MFV) and STI, the key indexes of cotton germination and growth under salt stress, including total fresh weight, shoot fresh weight, and shoot length, were determined. In addition, three salt tolerance evaluation models constructed with different variables (6 variables in Model 1; 3 variables in Model 2; 1 variable in Model 3) found that the total fresh weight was the most reliable trait for the salt tolerance evaluation. In practical application, the variable selection for modelling could be adjusted based on the experimental workload. The comparison of the K+, Na+, and Ca2+ contents between HST and NST found that the higher the salt tolerance of cotton germplasms, the lower the Na+ content in the root system. Besides, the ion ratios and ion selective transport coefficients (ST) was found to be significantly positively correlated with the salt tolerance of cotton. This study will provide a basis for evaluating and breeding salt-tolerant cotton germplasms.

Project description:Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic, and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination-associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA, and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulator are conserved in B. napus, suggesting a shared regulatory network with other plant species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable not only to evaluate germination performance of B. napus accessions but also to identify key targets for crop improvement in this important process.

Dataset Information

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

Publications

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

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