Identification of a Negative Regulator for Salt Tolerance at Seedling Stage via a Genome-Wide Association Study of Thai Rice Populations.

Thammaporn Kojonna,Supachitra Chadchawan,Duangjai Suriya-arunroj,Luca Comai,Nopphakhun Khunpolwattana,Monnat Pongpanich,Thiti Suttiyut,Teerapong Buaboocha

doi:10.3390/ijms23031842

Abstract

Salt stress is a major limiting factor in crop production and yield in many regions of the world. The objective of this study was to identify the genes responsible for salt tolerance in Thai rice populations. We performed a genome-wide association study with growth traits, relative water content, and cell membrane stability at the seedling stage, and predicted 25 putative genes. Eleven of them were located within previously reported salt-tolerant QTLs (ST-QTLs). OsCRN, located outside the ST-QTLs, was selected for gene characterization using the Arabidopsis mutant line with T-DNA insertion in the orthologous gene. Mutations in the AtCRN gene led to the enhancement of salt tolerance by increasing the ability to maintain photosynthetic pigment content and relative water content, while the complemented lines with ectopic expression of OsCRN showed more susceptibility to salt stress detected by photosynthesis performance. Moreover, the salt-tolerant rice varieties showed lower expression of this gene than the susceptible rice varieties under salt stress conditions. The study concludes that by acting as a negative regulator, OsCRN plays an important role in salt tolerance in rice.

Highlights

IntroductionRice is a staple food for more than half of the world’s population
Since the crn Arabidopsis mutant line was able to maintain chlorophyll and carotenoid pigments under salt stress, and previous reports suggested the importance of carbohydrate metabolism balance under abiotic stresses [42,43], we investigated the photosynthesis responses of the mutant, complemented lines, and the ectopically expressed lines to validate the function of CRN
With the negative effect of OsCRN gene expression in Arabidopsis during salt stress, we propose that OsCRN is a negative regulator of salt tolerance

Summary

Introduction

Rice is a staple food for more than half of the world’s population It is grown in more than a hundred countries; rice production has been lower than the consumption demand due to the rapidly growing population and the limited water availability [1]. Salinity tolerance is a complex trait whose expression depends on the action and interaction of different morphological, physiological, and biochemical characteristics of plants, including growth, photosynthesis, and grain yield [3,4]. Huang et al [6] successfully performed GWAS in a rice landrace collection in China for 14 agronomic traits and identified a substantial number of loci with high resolution. A total of 950 rice varieties were used to apply GWAS to discover the associate loci underlying flowering time and grain yield traits, and 32 novel loci were identified [7]. Kong et al (2021) [8] identified

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