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RSS FeedsIJMS, Vol. 19, Pages 3145: A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage (International Journal of Molecular Sciences)

 
 

13 october 2018 16:00:27

 
IJMS, Vol. 19, Pages 3145: A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage (International Journal of Molecular Sciences)
 




Salt toxicity is the major factor limiting crop productivity in saline soils. In this paper, 295 accessions including a heuristic core set (137 accessions) and 158 bred varieties were re-sequenced and ~1.65 million SNPs/indels were used to perform a genome-wide association study (GWAS) of salt-tolerance-related phenotypes in rice during the germination stage. A total of 12 associated peaks distributed on seven chromosomes using a compressed mixed linear model were detected. Determined by linkage disequilibrium (LD) blocks analysis, we finally obtained a total of 79 candidate genes. By detecting the highly associated variations located inside the genic region that overlapped with the results of LD block analysis, we characterized 17 genes that may contribute to salt tolerance during the seed germination stage. At the same time, we conducted a haplotype analysis of the genes with functional variations together with phenotypic correlation and orthologous sequence analyses. Among these genes, OsMADS31, which is a MADS-box family transcription factor, had a down-regulated expression under the salt condition and it was predicted to be involved in the salt tolerance at the rice germination stage. Our study revealed some novel candidate genes and their substantial natural variations in the rice genome at the germination stage. The GWAS in rice at the germination stage would provide important resources for molecular breeding and functional analysis of the salt tolerance during rice germination.


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32 viewsCategory: Biochemistry, Biophysics, Molecular Biology
 
IJMS, Vol. 19, Pages 3146: Phytohormones Regulate the Development of Arbuscular Mycorrhizal Symbiosis (International Journal of Molecular Sciences)
IJMS, Vol. 19, Pages 3144: Effects of Panax Notoginseng Saponins on Esterases Responsible for Aspirin Hydrolysis In Vitro (International Journal of Molecular Sciences)
 
 
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