Genome-wide association analysis for rice salt tolerance at seedling and reproductive stages

Abstract Background Salinity is one of the main adverse environmental factors severely inhibiting rice growth and decreasing grain productivity. Developing rice varieties with salt tolerance (ST) is one of the most economical approaches to cope with salinity stress. However, the valuable resources for rice breeding towards ST remain to be identified. In this study, the salt tolerance of 220 rice accessions from RDP1, representing five subpopulations, were evaluated at both seedling and reproductive stages. Results An apparent inconsistency was found for ST between the two stages. Through a gene-based / tightly linked genome-wide association study, a total of 214 single nucleotide polymorphisms (SNPs) related to 251 genes, significantly associated with 16 ST-related indices, were detected at both stages. Eighty-two SNPs with low frequency favorable (LFF) alleles in the population were proposed to hold high breeding potential in improving rice ST. Fifty-four rice accessions collectively containing all these LFF alleles were identified as donors of these alleles. Through the integration of meta-QTL for ST and the response patterns of differential expression genes to salt stress, thirty-one candidate genes were suggested to be involved in the regulation of rice ST. Conclusions In total, the present study provides valuable information for further characterizing ST-related genes and for breeding ST varieties across whole developmental stages through marker-assisted selection (MAS).