Dataset Information

Genome-Wide Association Study of Salt Tolerance-Related Traits during Germination and Seedling Development in an Intermedium-Spike Barley Collection.

ABSTRACT: Increased salinity is one of the major consequences of climatic change affecting global crop production. The early stages in the barley (Hordeum vulgare L.) life cycle are considered the most critical phases due to their contributions to final crop yield. Particularly, the germination and seedling development are sensitive to numerous environmental stresses, especially soil salinity. In this study, we aimed to identify SNP markers linked with germination and seedling development at 150 mM NaCl as a salinity treatment. We performed a genome-wide association study (GWAS) using a panel of 208 intermedium-spike barley (H. vulgare convar. intermedium (Körn.) Mansf.) accessions and their genotype data (i.e., 10,323 SNPs) using the genome reference sequence of "Morex". The phenotypic results showed that the 150 mM NaCl salinity treatment significantly reduced all recorded germination and seedling-related traits compared to the control treatment. Furthermore, six accessions (HOR 11747, HOR 11718, HOR 11640, HOR 11256, HOR 11275 and HOR 11291) were identified as the most salinity tolerant from the intermedium-spike barley collection. GWAS analysis indicated that a total of 38 highly significantly associated SNP markers under control and/or salinity traits were identified. Of these, two SNP markers on chromosome (chr) 1H, two on chr 3H, and one on chr 4H were significantly linked to seedling fresh and dry weight under salinity stress treatment. In addition, two SNP markers on chr 7H were also significantly associated with seedling fresh and dry weight but under control condition. Under salinity stress, one SNP marker on chr 1H, 5H and 7H were detected for more than one phenotypic trait. We found that in most of the accessions exhibiting the highest salinity tolerance, most of the salinity-related QTLs were presented. These results form the basis for detailed studies, leading to improved salt tolerance breeding programs in barley.

SUBMITTER: Sayed MA

PROVIDER: S-EPMC9569600 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Genome-Wide Association Study of Salt Tolerance-Related Traits during Germination and Seedling Development in an <i>Intermedium-Spike</i> Barley Collection.

Sayed Mohammed A MA Maurer Andreas A Schmutzer Thomas T Schnurbusch Thorsten T Börner Andreas A Hansson Mats M Pillen Klaus K Youssef Helmy M HM

International journal of molecular sciences 20220921 19

Increased salinity is one of the major consequences of climatic change affecting global crop production. The early stages in the barley (<i>Hordeum vulgare</i> L.) life cycle are considered the most critical phases due to their contributions to final crop yield. Particularly, the germination and seedling development are sensitive to numerous environmental stresses, especially soil salinity. In this study, we aimed to identify SNP markers linked with germination and seedling development at 150 mM ...[more]

PMID: 36232362

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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:BackgroundGenome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS.ResultsPopulation structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions.ConclusionsOur results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity.

Dataset Information

Genome-Wide Association Study of Salt Tolerance-Related Traits during Germination and Seedling Development in an Intermedium-Spike Barley Collection.

Publications

Genome-Wide Association Study of Salt Tolerance-Related Traits during Germination and Seedling Development in an <i>Intermedium-Spike</i> Barley Collection.

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