QTL Analysis For Rice Salinity Tolerance And Fine Mapping Of A Candidate Locus QSL7 For Shoot Length Under Salt Stress

Salinity is one of the major abiotic stresses limiting rice production worldwide.Long-term salt stress causes chronic ion toxicity and water osmosis imbalance in rice plants,and leads to death.As rice is one of the three major food for the world's population,study of the genetic mechanism of salinity tolerance of rice with different stress levels would be beneficial for rice breeding.In present study,we investigated rice salt tolerance in 132 recombinant inbred lines?RILs?derived from a cross between the two indica rice varieties 93-11 and Pei-ai64s?PA64s?,parents of the super hybrid rice,Liang-You-Pei-Jiu?LYP9?.We carried out phenotyping,quantitative trait loci?QTL?analysis,genome wide transcriptome analysis and fine mapping of a novel major QTL.The results obtained in this study are as follows:1.38 QTLs controlling salt tolerance were identified under two salt stress conditions.To determine the genetic basis of the salinity stress tolerance attributes in rice,QTLs were mapped.Based on the high-density genetic map of 132 RILs,we did QTL analysis for 6 agronomical important traits 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 stresses.QTL analysis identified a total of38 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 19 stable QTLs were found in 5 QTL clusters in both levels.Especially,one novel major QTL qSL7 for shoot length was detected in two distinct stress levels.2.Identification of candidate genes involved in salinity tolerance using comparative transcriptome.We investigated salinity-responsive transcriptomic changes in PA64s and 93-11 to identify the differentially expressed genes in stable QTLs flanking regions.Compared to differentially expressed genes?DEGs?of both parents between salt stress and normal condition,a total of 3,047 and 1,008 genes were detected specifically expressed in 93-11 and PA64s,respectively.Functional characterization by KEGG along with the GO enrichment results suggested that differentially expressed genes were mainly involved in regulation of transcription factors,salt stress responses,oxidation-reduction responses,and photosynthesis.A total of 1,048 expressed genes harbored in 5 loci containing 19 QTLs.We found 29 parent specific genes expression co-localized with the 5 stable loci.3.Fine mapping of a novel major QTL qSL7 controlling shoot length under salt stresses.A novel major QTL,qSL7 for an important agronomic trait shoot length on chromosome 7 was identified in two distinct concentrations.A chromosomal 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.The soluble sugar and proline were highly accumulated in CSSL-qSL7 than 93-11.With BC₅F_2:3:3 derived from CSSL-qSL7/93-11,the qSL7 was fine mapped within a 252.9 kb region on chromosome 7 where 40annotated genes located including,LOC?Os07g43530,which encode a DNA-binding domain containing protein and reported previously as a transcription factor,plays a positive role in salt stress tolerance.Our study provides new genetic resources for the improvement of salinity tolerance in rice breeding.