Salt-alkaline stress is one of the most stressful occurrences, causing negative effects on plant development and agricultural yield. Identifying and utilizing genes that affect alkaline tolerance is an excellent approach to accelerate breeding processes and meet the needs for remediating saline-alkaline soil. Here, we employed a mapping population of 176 recombinant inbred lines (RILs) produced from a cross between alkali-tolerant Longdao5 and alkali-sensitive Zhongyouzao8 to identify the quantitative trait loci (QTLs) determining alkali tolerance at the seedling stage. For the evaluation of alkali tolerance, the recovered seedling's average alkali tolerance index (ATI), root number (RN), root length (RL), seedling dry weight (SW), root dry weight (RW), and seedling height (SH) were assessed, together with their relative alkaline damage rate. Under alkaline stress, the ATI was substantially negative connected with the root number, seedling height, seedling dry weight, and root dry weight; however, it was considerably positive correlated with the relative alkaline damage rate of the root number and root dry weight. A total of 13 QTLs for the root number, root length, seedling height, seedling dry weight, root dry weight, and alkali tolerance index under alkaline stress were identified, which were distributed across chromosomes 1, 2, 3, 4, 5, 7, and 8. All of these QTLs formed two QTL clusters for alkali tolerance on chromosome 5 and chromosome 7, designated AT5 and AT7, respectively. Nine QTLs were identified for the relative alkaline damage rate of the root number, root length, seedling height, seedling dry weight, and root dry weight under alkali stress. These QTLs were located on chromosome 2, 4, 6, 7, 8, 9, and 12. In conclusion, these findings further strengthen our knowledge about rice's genetic mechanisms for alkaline tolerance. This research offers clues to accelerate breeding programs for new alkaline-tolerance rice varieties.

Introduction: Soil salinity poses a severe threat to rice production, resulting in stunted growth, leaf damage, and substantial yield losses. This study focuses on developing an early maturing seedling stage salinity tolerant rice variety by integrating conventional breeding methods with marker assisted breeding (MAB) approaches.Methods: Seedling-stage salinity tolerance Quantitative Trait Locus (QTL) Saltol from the salt-tolerant parent FL478 was introduced into the high-yielding but salt-sensitive rice variety ADT 45. This was achieved through a combination of conventional breeding and MAB. The breeding process involved rigorous selection, screening, and physiological parameter assessments.Results: KKL(R) 3 (KR 15066) identified as the top performing Recombinant Inbred Line (RIL), consistently demonstrating maximum mean grain yields under both salinity (3435.6 kg/ha) and normal (6421.8 kg/ha) conditions. In comparison to the early maturing, salt-tolerant national check variety CSR 10, KKL(R) 3 exhibited a substantial yield increase over 50%.Discussion: The notable improvement observed in KKL(R) 3 positions it as a promising variety for release, offering a reliable solution to maximize yields, ensure food security, and promote agricultural sustainability in both saline and non-saline environments. The study highlights the effectiveness of MAB in developing salt-tolerant rice varieties and emphasizes the significance of the Saltol QTL in enhancing seedling stage salinity tolerance. The potential release of KKL(R) 3 has the capacity to revolutionize rice production in salt affected regions, providing farmers with a reliable solution to maximize yields and contribute to food security while ensuring agricultural sustainability.