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.
Highlights
Rice is a staple food for billions of people, and it is the only food crop that provides more than50% of daily calories by direct consumption to more than half of the world’s population [1]
The USDA rice mini-core collection (URMC) and breeding lines from Vietnam were intermediate to the checks in plant height (PHT), and there were no significant differences among the four subpopulations at either d10 or d16
A similar trend was observed for the change in number of green leaves following 14 d of salt stress, with the URMC and breeding lines from Vietnam being intermediate to the checks
Summary
Rice is a staple food for billions of people, and it is the only food crop that provides more than50% of daily calories by direct consumption to more than half of the world’s population [1]. A rice crop can be exposed to salt stress due to natural soil salinity or by salt-water intrusion in irrigation resources and fields in low-lying coastal areas. Salt stress is one of the most important yield-limiting abiotic stresses in flooded lowland rice production areas and because there are limited opportunities for the mitigation of salt-water intrusion, efforts toward crop adaptation through breeding are needed. Salinity conditions in the field during early plant growth stages affect stand establishment, and later in the growth cycle can influence many morphological (e.g., root length and diameter, photosynthetically active canopy area, plant height), physiological (e.g., net photosynthesis, stomatal conductance), and biochemical processes (e.g., accumulation of reactive oxygen species, osmolytes, ion homeostasis), which eventually contribute to grain yield reduction [9,11]
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