Genome-wide association study of salt tolerance at the seed germination stage in rice

Abstract

BackgroundImproving the salt tolerance of direct-seeding rice at the seed germination stage is a major breeding goal in many Asian rice-growing countries, where seedlings must often establish in soils with a high salt content. Thus, it is important to understand the genetic mechanisms of salt tolerance in rice and to screen for germplasm with salt tolerance at the seed germination stage. Here, we investigated seven seed germination-related traits under control and salt-stress conditions and conducted a genome-wide association study based on the re-sequencing of 478 diverse rice accessions.ResultsThe analysis used a mixed linear model and was based on 6,361,920 single nucleotide polymorphisms in 478 rice accessions grouped into whole, indica, and non-indica panels. Eleven loci containing 22 significant salt tolerance-associated single nucleotide polymorphisms were identified based on the stress-susceptibility indices (SSIs) of vigor index (VI) and mean germination time (MGT). From the SSI of VI, six major loci were identified, explaining 20.2% of the phenotypic variation. From the SSI of MGT, five major loci were detected, explaining 26.4% of the phenotypic variation. Of these, seven loci on chromosomes 1, 5, 6, 11, and 12 were close to six previously identified quantitative gene loci/genes related to tolerance to salinity or other abiotic stresses. The strongest association region for the SSI of MGT was identified in a ~ 13.3 kb interval (15450039–15,463,330) on chromosome 1, near salt-tolerance quantitative trait loci controlling the Na+: K+ ratio, total Na+ uptake, and total K+ concentration. The strongest association region for the SSI of VI was detected in a ~ 164.2 kb interval (526662–690,854) on chromosome 2 harboring two nitrate transporter family genes (OsNRT2.1 and OsNRT2.2), which affect gene expression under salt stress. The haplotype analysis indicated that OsNRT2.2 was associated with subpopulation differentiation and its minor/rare tolerant haplotype was detected.ConclusionsThese results provide valuable information for salt tolerance-related gene cloning and for understanding the genetic mechanisms of salt tolerance at the seed germination stage. This information will be useful to improve the salt tolerance of direct-seeding rice varieties by genomic selection or marker-assisted selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-1044-0) contains supplementary material, which is available to authorized users.

Identification and fine mapping of a novel qGR6.2 locus controlling rice salt tolerance during seed germination

“…Salinity seriously affects rice seed germination and seedling establishment, especially in the directseeding area, leading to a reduction of rice yields (Wang et al 2012b;Shi et al 2017). In this study, the indica landrace WJZ from Yunnan province in China showed a strong capability of seed germination and seedling establishment under high salinity stress.…”

“…The co-located putative QTLs and associated physical locus in this study compared with previously mapped QTLs of salt tolerance in rice. The main associated QTLs from this study are shown on the left (orange frame and pentagram) and previously identified QTLs for salt tolerance are shown on the right (blue frame) (Dubouzet et al 2003;Wang et al 2011;Wang et al 2012;Wang et al 2012;Vinod et al 2015;Sushma et al 2016;Shi et al 2017;Yu et al 2018). Expression pattern of candidate genes in various developmental stages (a) and response to seed germination and salt stress (b) based on Affymetrix microarray datasets and mRNASeq data from the GENEVESTIGATOR (http://www.genevestigator.com).…”

“…Up to now, more than hundreds of salt-response QTLs have been reported at different developmental growth stages in rice (Ganie et al 2019). Salt tolerance during seed germination is not consistently related to other stages, such as vegetative growth or fruit development (Johnson et al 1992, Shi et al 2017). So far, few studies aimed at salt tolerance during seed germination in rice.…”

“…Wang et al (2011) detected 16 QTLs of rice seed germination ability from the salt tolerance variety Jiucaiqing at 100 mM NaCl. Recently, around 50 salt tolerance loci have been identified using GWAS at the seed germination stage (Cheng et al 2015;Shi et al 2017;Yu et al 2018). Fujino et al (2008) reported that qLTG3-1 responded to seed germination under salt stress because of tissue vacuolation and weakening.…”

Identification and fine mapping of a novel qGR6.2 locus controlling rice salt tolerance during seed germination

“…Salt tolerance during seed germination is not consistently related to other stages (Johnson et al 1992, Shi et al 2017. To date, few studies aimed at genetically dissect salt tolerance during seed germination in rice.…”