Linkage Analysis And GWAS Reveal QTL Controlling Salt Tolerance In Rice And Candidate Genes Discovery

Soil salinization is an important restrictive factor that hinders the normal growth of crops,affects high and stable crop Fields and the expansion of planting area.Rice planting is one of the economical and effective ways to improve and utilize saline soil,and genetic improvement of rice salt tolerance is the basis for planting rice in saline soil.The mapping of rice salt-tolerance genes is a necessary condition for rice salt-tolerance gene cloning and molecular breeding,and is of great significance for promoting rice salt-tolerance breeding.In previous study,there are many reports about the preliminary location of QTL for rice salt tolerance,but it is difficult to discover salt tolerance genes.Through the salt tolerance gradient test of rice,a salt tolerance identification evaluation method was established;RIL groups and related groups were used as research materials,To carry out multi-year repeated identification and evaluation of salt tolerance at the tillering stage in the greenhouse and field salt stress environment;use genome-wide resequencing technology,through linkage analysis and GWAS analysis strategy,to explore the QTL locus of rice salt tolerance;in salt stress and normal Under the environment,RNA-seq analysis was carried out on two parents of RIL population and families with significant differences in salt tolerance,and bioinformatics methods were used to predict and analyze rice salt tolerance candidate genes.The research results are as follows:(1)The optimum salt stress concentration for identification of salt tolerance at rice tillering stage is 0.5%.The best time for phenotypic investigation is 4-5 weeks after salt stress treatment.Using salt damage level as an evaluation index,rice germplasm can be accurately identified difference in salt tolerance.This identification method was used to identify the salt tolerance of 2886 rice germplasm resources,and 137 relatively salt-tolerant germplasms were screened,which provided important resource support for the study of the genetic mechanism of rice salt tolerance and the selection of new varieties.(2)In the RIL population constructed by Jileng 1 × Milyang 23,1.81 M high-quality SNP markers were detected,and the “sliding window” strategy was used to simplify the above SNP markers to 3061 Bin markers.A high-density genetic map with a total length of 1408.03 cM and an average spacing of 0.48 cM was constructed.The genetic map has high collinearity with the rice reference genome,and can quickly and accurately locate genes related to high heritability traits such as plant height and growth period.Based on the above salt tolerance identification results of the RIL population,12 salt tolerance related QTL were located,6 of which were stable QTLs that could be repeatedly detected in different environments.Searching for stable detection of cloned genes within the QTL confidence interval,four rice salt tolerance related genes were screened: OsNAPL6,OsRR22,ONAC106 and ONAC063.(3)A 1.31 M high-quality SNP marker was developed using the associated population.The estimated LD attenuation distance of the population is about 445 kb,and the population can be divided into 2 subgroups.Combined with the identification data of population salt tolerance,145 rice salt tolerance related SNP markers were screened and located on 19 QTLs.Four of them are stable QTLs that can be repeatedly detected in different environments.Near the stable QTL,two cloned rice salt tolerance related genes: OsDREB1 D and OsRR22,five uncloned osmoregulatory transport-related genes,which can be used as candidate genes for rice salt tolerance.(4)Through rice salt tolerance differential transcriptome analysis,515 rice salt-tolerance-related specific transcripts were screened and distributed on 480 genes,of which 10 genes have been cloned,further verifying that these genes are differentially expressed Affect the salt stress response of rice.Among the specific differential expressions of salt tolerance in rice screened by comparative transcriptome analysis,two genes are located within the confidence interval of the QTL site(Os02g0574100 and Os11g0256300),which can be used as candidate genes affecting the genetic regulation of rice salt tolerance,and further genes need to be developed functional verification.