Rohila JS, Edwards JD, Tran GD, Jackson AK, McClung AM.

Plants (Basel). 2019 Nov 5;8(11). pii: E472. doi: 10.3390/plants8110472.

Abstract

Salt stress is a major constraint to rice acreage and production worldwide. The purpose of this study was to evaluate the natural genetic variation available in the United States Department of Agriculture (USDA) rice mini-core collection (URMC) for early vigor traits under salt stress and identify quantitative trait loci (QTLs) for seedling-stage salt tolerance via a genome-wide association study (GWAS). Using a hydroponic system, the seedlings of 162 accessions were subjected to electrical conductivity (EC) 6.0 dS m^-1 salt stress at the three-to-four leaf stage. After completion of the study, 59.4% of the accessions were identified as sensitive, 23.9% were identified as moderately tolerant, and 16.7% were identified as highly tolerant. Pokkali was the most tolerant variety, while Nerica-6 was the most sensitive. Adapting standard International Rice Research Institute (IRRI) protocols, eight variables associated with salt tolerance were determined. The GWAS of the URMC, using over three million single-nucleotide polymorphisms (SNPs), identified nine genomic regions associated with salt tolerance that were mapped to five different chromosomes. Of these, none were in the known Saltol QTL region, suggesting different probable genes and mechanisms responsible for salt tolerance in the URMC. The study uncovered genetic loci that explained a large portion of the variation in salt tolerance at the seedling stage. Fourteen highly salt-tolerant accessions, six novel loci, and 16 candidate genes in their vicinity were identified that may be useful in breeding for salt stress tolerance. Identified QTLs can be targeted for fine mapping, candidate gene verification, and marker-assisted breeding in future studies.

See https://www.mdpi.com/2223-7747/8/11/472

Figure 1: Two-way phenotypic dendrogram showing three clusters for variation in salt tolerance among 162 rice accessions including 123 URMC accessions. Four early vigor traits associated with salt stress tolerance at the seedling stage were used for constructing the dendrogram and are denoted by numbers: 1: SSI score d16; 2: Δ PHT d16; 3: Δ green leaf#; and 4: Total biomass plant⁻¹ on the x-axis of the heatmap. The blue color illustrates low values, while the red color illustrates high values for the measured trait.