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Int. J. Mol. Sci. 2018, 19(10), 3145;

A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage

9,* and 1,9,*
Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea
State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
School of Biotechnology, Jiangsu University of Science and Technology, Sibaidu, Zhenjiang, Jiangsu 212018, China
National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Leader of Eco. Energy & Bio (LEEBCOR), 190-26 Hwangyeonggongwon-ro, Asan-si, Chungcheongnam-do 31529, Korea
Suzhou GENEWIZ Biotechnology Co. LTD, C3 218 Xinghu Road Suzhou Industrial Park, Suzhou 215123, China
Chemical Safety Division, National Institute of Agricultural Sciences (NIAS), Wanju 55365, Korea
Breeding & Research Institute, Koregon Co. LTD, Anseong Center 60-34, Gokcheon-gil, Bogae-Myeon, Anseong-Si, Gyeonggi-Do 17509, Korea
Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Korea
These authors contributed equally to this work.
Authors to whom correspondence should be addressed.
Received: 21 September 2018 / Revised: 9 October 2018 / Accepted: 9 October 2018 / Published: 12 October 2018
(This article belongs to the Special Issue Salinity Tolerance in Plants)
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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. View Full-Text
Keywords: rice; genome-wide association study; salt stress; germination; natural variation rice; genome-wide association study; salt stress; germination; natural variation

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Yu, J.; Zhao, W.; Tong, W.; He, Q.; Yoon, M.-Y.; Li, F.-P.; Choi, B.; Heo, E.-B.; Kim, K.-W.; Park, Y.-J. A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage. Int. J. Mol. Sci. 2018, 19, 3145.

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