Dataset Information

Epistatic association mapping for alkaline and salinity tolerance traits in the soybean germination stage.

ABSTRACT: Soil salinity and alkalinity are important abiotic components that frequently have critical effects on crop growth, productivity and quality. Developing soybean cultivars with high salt tolerance is recognized as an efficient way to maintain sustainable soybean production in a salt stress environment. However, the genetic mechanism of the tolerance must first be elucidated. In this study, 257 soybean cultivars with 135 SSR markers were used to perform epistatic association mapping for salt tolerance. Tolerance was evaluated by assessing the main root length (RL), the fresh and dry weights of roots (FWR and DWR), the biomass of seedlings (BS) and the length of hypocotyls (LH) of healthy seedlings after treatments with control, 100 mM NaCl or 10 mM Na2CO3 solutions for approximately one week under greenhouse conditions. A total of 83 QTL-by-environment (QE) interactions for salt tolerance index were detected: 24 for LR, 12 for FWR, 11 for DWR, 15 for LH and 21 for BS, as well as one epistatic QTL for FWR. Furthermore, 86 QE interactions for alkaline tolerance index were found: 17 for LR, 16 for FWR, 17 for DWR, 18 for LH and 18 for BS. A total of 77 QE interactions for the original trait indicator were detected: 17 for LR, 14 for FWR, 4 for DWR, 21 for LH and 21 for BS, as well as 3 epistatic QTL for BS. Small-effect QTL were frequently observed. Several soybean genes with homology to Arabidopsis thaliana and soybean salt tolerance genes were found in close proximity to the above QTL. Using the novel alleles of the QTL detected above, some elite parental combinations were designed, although these QTL need to be further confirmed. The above results provide a valuable foundation for fine mapping, cloning and molecular breeding by design for soybean alkaline and salt tolerance.

SUBMITTER: Zhang WJ

PROVIDER: S-EPMC3885605 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Epistatic association mapping for alkaline and salinity tolerance traits in the soybean germination stage.

Zhang Wen-Jie WJ Niu Yuan Y Bu Su-Hong SH Li Meng M Feng Jian-Ying JY Zhang Jin J Yang Sheng-Xian SX Odinga Medrine Mmayi MM Wei Shi-Ping SP Liu Xiao-Feng XF Zhang Yuan-Ming YM

PloS one 20140108 1

Soil salinity and alkalinity are important abiotic components that frequently have critical effects on crop growth, productivity and quality. Developing soybean cultivars with high salt tolerance is recognized as an efficient way to maintain sustainable soybean production in a salt stress environment. However, the genetic mechanism of the tolerance must first be elucidated. In this study, 257 soybean cultivars with 135 SSR markers were used to perform epistatic association mapping for salt toler ...[more]

PMID: 24416275

Similar Datasets

Project description:Simple Summary Drought stress inhibits seed germination, making it one of the primary environmental factors adversely affecting food security. Soybean is more sensitive to drought than other food crops, especially in germination stage. The purpose of our research is to identify the loci related to drought tolerance in soybean during germination. We used 410 soybean accessions to induce drought at germination stage by PEG, and conducted genome-wide association study. A total of 26 SNPs were found to be related to drought tolerance, and there were nine SNP markers located in or adjacent to (within 500 kb) previously reported drought tolerance QTLs. These SNP led to our identification of 41 candidate genes related to drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance. Abstract Drought stress influences the vigor of plant seeds and inhibits seed germination, making it one of the primary environmental factors adversely affecting food security. The seed germination stage is critical to ensuring the growth and productivity of soybeans in soils prone to drought conditions. We here examined the genetic diversity and drought-tolerance phenotypes of 410 accessions of a germplasm diversity panel for soybean and conducted quantitative genetics analyses to identify loci associated with drought tolerance of seed germination. We uncovered significant differences among the diverse genotypes for four growth indices and five drought-tolerance indices, which revealed abundant variation among genotypes, upon drought stress, and for genotype × treatment effects. We also used 158,327 SNP markers and performed GWAS for the drought-related traits. Our data met the conditions (PCA + K) for using a mixed linear model in TASSEL, and we thus identified 26 SNPs associated with drought tolerance indices for germination stage distributed across 10 chromosomes. Nine SNP sites, including, for example, Gm20_34956219 and Gm20_36902659, were associated with two or more phenotypic indices, and there were nine SNP markers located in or adjacent to (within 500 kb) previously reported drought tolerance QTLs. These SNPs led to our identification of 41 candidate genes related to drought tolerance in the germination stage. The results of our study contribute to a deeper understanding of the genetic mechanisms underlying drought tolerance in soybeans at the germination stage, thereby providing a molecular basis for identifying useful soybean germplasm for breeding new drought-tolerant varieties.

Project description:Rice tolerance to salinity stress involves diverse and complementary mechanisms, such as the regulation of genome expression, activation of specific ion-transport systems to manage excess sodium at the cell or plant level, and anatomical changes that avoid sodium penetration into the inner tissues of the plant. These complementary mechanisms can act synergistically to improve salinity tolerance in the plant, which is then interesting in breeding programs to pyramidize complementary QTLs (quantitative trait loci), to improve salinity stress tolerance of the plant at different developmental stages and in different environments. This approach presupposes the identification of salinity tolerance QTLs associated with different mechanisms involved in salinity tolerance, which requires the greatest possible genetic diversity to be explored. To contribute to this goal, we screened an original panel of 179 Vietnamese rice landraces genotyped with 21,623 SNP markers for salinity stress tolerance under 100 mM NaCl treatment, at the seedling stage, with the aim of identifying new QTLs involved in the salinity stress tolerance via a genome-wide association study (GWAS). Nine salinity tolerance-related traits, including the salt injury score, chlorophyll and water content, and K+ and Na+ contents were measured in leaves. GWAS analysis allowed the identification of 26 QTLs. Interestingly, ten of them were associated with several different traits, which indicates that these QTLs act pleiotropically to control the different levels of plant responses to salinity stress. Twenty-one identified QTLs colocalized with known QTLs. Several genes within these QTLs have functions related to salinity stress tolerance and are mainly involved in gene regulation, signal transduction or hormone signaling. Our study provides promising QTLs for breeding programs to enhance salinity tolerance and identifies candidate genes that should be further functionally studied to better understand salinity tolerance mechanisms in rice.

Dataset Information

Epistatic association mapping for alkaline and salinity tolerance traits in the soybean germination stage.

Publications

Epistatic association mapping for alkaline and salinity tolerance traits in the soybean germination stage.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets