Identification of superior alleles for seedling stage salt tolerance in the USDA rice mini-core collection

Authors: Rohila, Jai; Edwards, Jeremy; TRAN, GIOI - Cuu Long Delta Rice Research Institute; Jackson, Aaron; McClung, Anna

Submitted to: Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/31/2019
Publication Date: 11/5/2019
Citation: Rohila, J.S., Edwards, J., Tran, G.D., Jackson, A.K., McClung, A.M. 2019. Identification of superior alleles for seedling stage salt tolerance in the USDA rice mini-core collection. Plants. https://doi.org/10.3390/plants8110472.
DOI: https://doi.org/10.3390/plants8110472

Interpretive Summary: The salt stress causes damage especially at the seedling stage in rice due to inundations near coastal areas during tidal surges from tropical storms or from pumping of saline water from depleted aquifers in areas away from the coast. Rice is very sensitive to the presence of salt in the root zone compared with other crops commonly grown in these areas. In a replicated hydroponics study, we were focused on identifying availability of salt tolerant germplasm in the USDA rice mini core collection and simultaneously finding genetic loci that may serve as molecular markers for salt tolerant traits in rice breeding programs. To accomplish these two objectives, we screened 162 rice accessions including 123 from the USDA rice mini core collection that included 4 subpopulations of rice, 26 entries from a Vietnam breeding program utilizing a major salt tolerant allele Saltol, 7 entries from US breeding germplasm, and 6 varieties that have been documented to display a range in susceptibility for salt exposure, and conducted genome wide association study(GWAS). We identified 14 potential accessions showing tolerance to salt stress conditions of an electrical conductivity (EC) of 6.0 dS m-1 at 5.8 pH. For comparison purpose – most freshwater used for irrigations has an EC value of 0-1.2 dS m-1, while sea water has a value of 50 dS m-1. Several accessions in the USDA rice mini core collection performed better than the advanced salt tolerant varieties from Vietnam indicating that there is the opportunity to pyramid diverse alleles to make for further gains in salt tolerance. Further, by utilizing over 3 million SNPs available on USDA rice mini core collection, we identified 9 loci that were highly associated with 8 desirable salt tolerant traits. Of these 9 loci, 5 were found as promising targets for marker-assisted selection (MAS) with tolerant alleles coming from the indica subspecies in four cases and the japonica subspecies in one case. The study provided previously untapped genetic variation and identification of rice germplasm for improving salt tolerance in modern US rice varieties that will mitigate salt affected soils and waters and increase profitability for rice production in the USA.

Technical Abstract: Salt stress is a major constraint to rice acreage and production worldwide. The purpose of this study was to evaluate natural genetic variation available in the 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, seedlings of 162 accessions were subjected to 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% moderately tolerant, and 16.7% highly tolerant. Pokkali was the most tolerant and Nerica-6 was the most sensitive variety. Adapting standard International Rice Research Institute (IRRI) protocols, 8 variables associated with salt tolerance component traits were phenotyped. GWAS of the URMC using over 3 million SNPs identified 9 genomic regions associated with salt tolerance that were mapped to 5 different chromosomes, none in the known Saltol region, suggesting different probable genes and mechanisms responsible for salt tolerance in URMC. The study uncovered genetic loci that explained a large portion of the variation in the salt tolerance phenotype at the seedling stage. Fourteen highly salt tolerant accessions, several novel loci and candidate genes were also 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.