Unraveling the complex genetic bases and mechanisms underlying salt tolerance is of great importance for developing salt-tolerant varieties. In this study, we evaluated 42 chromosome segment substitution lines (CSSLs) carrying chromosome segments from IR64 on the genetic background of Koshihikari under salt stress. Two CSSLs, SL2007 and SL2038, produced higher plant dry weight and grain yield than did Koshihikari under the stress condition. These CSSLs also showed lower Na⁺ and Cl⁻ accumulation in the leaf and whole plant at the full heading stage, which might be related to the higher grain yield and yield components. To understand the genetic control of its grain yield and yield components, a SL2007/Koshihikari F₂ population was generated for quantitative trait locus (QTL) analysis. Six QTLs for grain yield and yield-related traits were detected on chromosome 2. Using near-isogenic lines (NILs) from a SL2007/Koshihikari F₅ population, qSTGY2.2 was delimited to a 2.5 Mb region and novel qSTPN2 was delimited to a 0.6 Mb region. We also detected a novel QTL, qSTGF2, for grain filling, which was considered an important contributor to grain yield under salt stress in this CSSL. Our results provide insights into mechanisms conferring grain yield under salinity stress and new genetic resources for cloning and breeding.

Rice, the major crop sustaining approximately half the world population, has been extensively reported to be sensitive to saline conditions. However, the genetic and physiological understanding related to long-term salinity stress remains unclear so far. The aim of this study was to evaluate the mechanisms of salinity tolerance in a salinity-tolerant variety of rice, Nona Bokra, and to detect the chromosomal regions responsible for it. We utilized chromosome segment substitution lines (CSSLs) carrying segments from Nona Bokra in the genetic background of a salt-sensitive variety Koshihikari by investigating the plant growth, grain productivity, and ion contents in plants subjected to long-term salinity stress. Comparison of plant growth and grain yield of CSSLs grown under long-term saline conditions suggests that the salinity tolerance of Nona Bokra involves the improvement of plant dry matter, panicle number, and percentage of ripened grains. Nona Bokra has the chromosomal regions for the improvement of the panicle number on chromosome 2 and the percentage of ripened grains on chromosome 6 or 10 under salinity conditions. It was suggested that these chromosomal regions were related to Na+ and Cl- exclusion. Low Na+ and Cl- contents in whole plant at full heading stage would be vital for improving the yield under long-term saline conditions.

Salinity is a major abiotic stress limiting rice production worldwide. This study aims to elucidate the effects of heading date on salt tolerance in rice. Five near-isogenic lines (NILs) developed from the SL2038/Koshihikari backcross population were grown with or without salt stress. SL2038 is a salt-tolerant line with delayed heading (~18 days) compared to the salt-sensitive background Koshihikari. The results showed that late-heading NILs produced significantly higher plant dry weight, panicle weight, percentage of filled grains, and grain weight (p < 0.05) under long-term salt stress. In Koshihikari, which exhibited delayed heading due to long-day treatment, the percentage of white heads was low, and panicle and grain weights were significantly higher under salt stress. Experiments with different sowing times indicated that late heading, such as sowing in June, resulted in higher grain weights. This is the first report to assess the impact of heading date on agronomic and yield-related traits under salt stress. In conclusion, even with a prolonged salt treatment period, heading during periods of low temperature and solar radiation results in higher grain weight under salt stress. This is proposed as one of the strategies for salt escape. These findings can be used to improve rice yield and implement crop management in salt-affected regions.

Soil salinity is a major constraint limiting rice productivity, particularly at the reproductive stage. To elucidate the genetic basis of reproductive stage salinity tolerance, this study validated and fine-mapped quantitative trait loci (QTL) for yield-related traits using a salinity-tolerant line SL506, identified through screening of Nona Bokra–CSSLs in a Koshihikari background. In 2016, the F₂ population derived from SL506/Koshihikari was evaluated under long-term salt stress; three QTLs associated with plant dry weight, panicle number, and grain weight were detected on chromosome 2. In 2023, validation analysis using F₃ individuals confirmed the presence of these QTLs. Subsequent fine-mapping using F₄ near-isogenic lines (NILs) delimited the QTL to a 1.7 Mb interval and high-resolution mapping using an F₅ recombinant population progressively refined it to a 473 kb genomic region containing 69 annotated genes. Variant Effect Predictor analysis identified 15 deleterious nonsynonymous variants (SIFT < 0.05) in six candidate genes. Based on annotated gene functions, predicted variant effects, and their membership in stress-related gene families, OsPP2C24, OsFbox102, and OsWAK14 were suggested as the most promising candidate genes underlying qPDW2. These findings provide insights into the genetic basis of reproductive-stage salinity tolerance from valuable resources for the future improvement of salt tolerance and yield stability in rice.

Soil salinity is a major abiotic stress affecting rice production globally. Previously, one promising salinity‐tolerant line (SL535) was identified through screening of Nona Bokra‐CSSLs with a Koshihikari background. In 2016, 102 F ₂ individuals derived from SL535/Koshihikari were evaluated under long‐term salt stress, with salt treatment imposed from the active tillering stage to maturity to investigate salt tolerance at the reproductive stage. Three QTLs for plant dry weight, panicle number, and panicle weight were detected on chromosome 6. This genomic region was further validated in 2019 and 2020 for plant dry weight, tiller number, and Na ⁺ and Cl ⁻ contents using homozygous lines with or without the Nona Bokra allele in a Koshihikari background. As expected, significantly higher tiller number and lower Na ⁺ and Cl ⁻ contents were maintained in plants carrying the Nona Bokra allele (NIL) at the full‐heading stage. In 2023, seven newly developed NILs were evaluated for agronomic traits under control and salt stress conditions. Based on their performance, the QTL for plant dry weight, qPDW6.1, was narrowed down to a 390 kb region ranging from 4.78 to 5.17 Mb on chromosome 6. Within this region, several stress‐related candidate genes were predicted based on annotation information and variant effect prediction analysis. Among them, two genes, Os06g0196700 (Auxin response factor 1) and Os06g0199100 (P‐type pentatricopeptide repeat protein), were considered the most likely candidate genes associated with salt tolerance. These findings provide a foundation for future gene cloning and functional validation studies, which may help elucidate the genetic and molecular mechanisms underlying salt tolerance at the reproductive stage.