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

Yingyao Shi,Mingming Wang,Yongli Zhou,Congshun Zhang,Zhichao Wu,Zhikang Li,Xiaojing Zhang,Lingling Gao,Fan Zhang

doi:10.1186/s12870-017-1044-0

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.

Highlights

Improving 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
Seed germination of rice accessions under salt stress The germination index (GI), vigor index (VI), germination rate (GR), mean germination time (MGT), and imbibition rate (IR) were determined for 35 rice accessions randomly selected from the whole panel under three salt treatments (60, 80 and 100 mM NaCl) (Additional file 1: Table S1)
The GI, VI, and GR at 5 d (GR-5d) and GR at 10 d (GR-10d) significantly decreased as the NaCl concentration increased, and MGT was significantly higher in the 100 mM NaCl treatment than in the 60 and 80 mM NaCl treatments

Summary

Introduction

Improving 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. 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. Salinity affects rice growth during all developmental stages from seed germination to reproduction [3]. With the development and spread of direct-seeding technology, which requires high levels of seedling establishment in rice paddy fields that are salinized to some degree, salt tolerance at the seed germination stage has become a major rice breeding goal in many Asian countries. It is necessary to understand the genetic mechanisms of salt tolerance at the seed germination stage in rice

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