Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel

Abstract

Salinity is a major abiotic stress which inhibits rice production in coastal, arid and semiaid areas in many countries, such as India and Bangladesh. Identification of salt tolerant cultivars, quantitative trait loci (QTLs) and genes is essential for breeding salt tolerant rice. The aus subpopulation of rice is considered to have originated predominantly from Bangladesh and India and have rich genetic diversity with wide variation in abiotic stress resistance. The objective of this study was to identify QTLs, and subsequently candidate genes using cultivars from the aus subpopulation and compare the results of two different seedling stage screening methods. Salt tolerance at the rice seedling stage was evaluated on 204 rice accessions from the Bengal and Assam Aus Panel (BAAP) grown in both hydroponics and soil under control and salt stress conditions. Ten salt related traits of stress symptoms, plant growth and the content of sodium and potassium were measured. Three cultivars, BRRI dhan 47, Goria, and T 1 showed more salt tolerance than the tolerant check Pokkali in both systems. Genome-wide association mapping was conducted on salt indices traits with 2 million SNPs using an efficient mixed model (EMMA) controlling population structure and kinship, and a significance threshold of P < 0.0001 was used to determine significant SNPs. A total of 97 and 74 QTLs associated with traits in hydroponic and soil systems were identified, respectively, including 11 QTLs identified in both systems. A total of 65 candidate genes were found including a well-known major gene OsHKT1;5. The most significant QTL was detected at around 40 Mb on chromosome 1 coinciding with two post-translational modifications SUMOylation genes (OsSUMO1 and OsSUMO2), this QTL was investigated. The salt tolerance rice cultivars and QTLs/genes identified here will provide useful information for future studies on genetics and breeding salt tolerant rice.

Genome-wide association mapping of sodium and potassium concentration in rice grains and shoots under alternate wetting and drying and continuously flooded irrigation

“…3), were previously identified as having high shoot Na + concentration and high salt sensitivity in both soil and hydroponic salt tolerance screens of seedlings. Similarly, cultivars in groups 1, 4 and 5, which have low Na + concentration and Na + /K + ratio in this study, had low shoot Na + and were tolerant to Na + in the seedling screen (Chen et al 2020). These results highlight the reliability of the tolerance tests and the value of measuring Na + concentration in field grown plants in the absence of salt stress.…”

“…The BAAP has been screened for salt tolerance at the seedling stage under both a hydroponic (EC: 7 dS m −1 ) and a soil (EC: gradually increased from 2 to 9 dS m −1 ) system, and Na + and K + concentrations in shoots were measured (Chen et al 2020…”

“…The salt tolerance of these five groups in hydroponics and soil (under controlled environmental conditions) has previously been estimated (Chen et al 2020). Group 3 cultivars, which have high shoot and grain Na + when grown in the field (Fig.…”

“…This study utilizes a population of rice derived from the aus subpopulation of rice that has been genotyped and can be used for GWA mapping. This population has previously been tested for seedling-stage salt tolerance using both a hydroponic and a soil-based system (Chen et al 2020).…”

Genome-wide association analysis for rice salt tolerance at seedling and reproductive stages

“…Through marker assisted selection (MAS), the SKC1 had been incorporated into some rice varieties with apparently enhanced ST in the seedling stage. It has been well recognized that ST at seedling and reproductive stages are different (Moradi et al, 2003;Liu et al, 2019;Lei et al, 2020;Chen et al, 2020); while, only few studies have reported ST QTLs/genes at the reproductive phase so far (Hossain et al, 2015;Liu et al, 2019;Lekklar et al, 2019;Ganie et al, 2019;Theerawitaya et al, 2020). Through the linkage mapping method, Hossain et al (2015) reported 16 QTLs affecting 6 agronomic traits plus Na + content and the K + /Na + ratio in the ag leaf under stress conditions at the reproductive stage.…”