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Salinity is one of the major abiotic stresses limiting rice production worldwide. Understanding the genetic basis of salinity tolerance is key for rice breeding. In this study, a recombinant inbred line (RIL) population derived from a super hybrid rice Liang–You–Pei–Jiu (LYP9) parents 93-11 and PA64s, exhibited variation in phenotypes including shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW), and root dry weight (RDW) under 50 and 100 mM NaCl stress. QTL analysis identified a total of 38 QTLs for these 6 traits under two distinct concentrations of salt, distributing on chromosomes 1, 2, 3, 4, 5, 6, 7 and 10. A total of 21 QTLs were found in 6 stable loci. A novel major QTL,  qSL7  for shoot length on chromosome 7 was identified in two distinct concentrations. A chromosome segment substitution line (CSSL) harboring the  qSL7  locus from PA64s with 93-11 background was developed and exhibited higher SL value, higher K +  concentration, and lower Na +  concentration compared to 93-11. With BC 5 F 2:3  derived from CSSL- qSL7 /93-11, the  qSL7  was fine mapped within a 252.9 kb region on chromosome 7 where 40 annotated genes located including,  LOC_Os07g43530 , which encodes a DNA-binding domain containing protein reported previously as a transcription factor playing a positive role in salt stress tolerance. Our study provides new genetic resources for improvement of salinity tolerance in rice breeding.

QTL analysis for rice salinity tolerance and fine mapping of a candidate locus qSL7 for shoot length under salt stress