Genome-Wide Meta-QTL Analysis and InDel Markers for Salt Tolerance in Rice: Bridging the Gap from Genomics to Breeding

Salt stress is a primary abiotic constraint on global rice productivity. To establish a robust genomic framework for breeding, we performed a genome-wide meta-QTL (MQTL) analysis integrating QTL data from both the seedling and reproductive stages. A high-density consensus map was constructed, and initial QTLs from independent studies were curated and filtered for redundancy. Confidence intervals were refined via meta-analysis to define stable MQTL regions. From 926 original QTLs at the seedling stage, 87 seedling MQTLs (SeMQTLs) were identified. Notably, SeMQTL1-5, which encompasses the major locus Saltol, and three additional high-confidence SeMQTLs (CI < 1 cM, physical interval ≤ 1 Mb, average PVE > 17%) were associated with ion homeostasis under salt stress. At the reproductive stage, 43 reproductive MQTLs (ReMQTLs) were consolidated from 241 QTLs, with PVE values ranging from 4.84% to 46.36%. Subsequent analysis nominated MQTLSIH1-2 (the most stable region) and MQTLSIH1-5 (containing SKC1) as key candidates for seedling tolerance, while MQTLPF11-1 (PVE > 28%) was prioritized for reproductive-stage breeding. A total of 39 MQTLs co-localized with SNP-based selection hotspots. Within these regions, we developed 21 InDel markers, of which 18 were validated as effective allele-specific markers for discriminating salt tolerance. This work delivers the first consolidated set of high-confidence, MQTL-derived InDel markers for salt tolerance in rice, providing a valuable resource for marker-assisted selection and the pyramiding of resilience loci into elite genetic backgrounds.