Preliminary Mapping Of QTL For Rice Sheath Blight Resistance And Candidate Gene Analysis Of QSB-9

Rice is one of the important food crops,providing staple food for nearly half of the world’s population.Sheath blight（ShB）,a fungal disease caused by Rhizoctonia solani（R.solani）,is one of the three major diseases of rice,seriously endangering the yield and quality of rice.Breeding resistant varieties is the most economical and effective strategy to reduce disease damage.However,rice resistance to ShB is a complex quantitative trait controlled by multiple genes.It is difficult to select resistant varieties through traditional breeding methods.Molecular marker assisted selection of QTLs（quantitative trait loci）for resistance to ShB is a feasible strategy for breeding resistant varieties,but the available resistance QTLs are still very limited.Previously,our research group achieved fine mapping of a ShB resistance QTL qSB-9TQ（the donor of resistance gene is Teqing/TQ）using the "TQ→Lemont（LE）"（Indicates that TQ chromosome fragment is imported into Le background）chromosome segment substitution lines and the field identification method.On this basis,this study further verified the QTL by screening the substitution lines with more consistent genetic background and using the greenhouse inoculation identification method.At the same time,the related genes were screened by whole genome sequencing and transcriptome analysis.In addition,two genomewide chromosome segment substitution line populations（hereafter named "YSBR1→LE" and"YSBR1→T394",respectively）was further constructed with YSBR1 as the donor and LE and Taijing 394（T394）as the acceptor.Some substitution lines were used to identify the resistance to ShB and important agronomic and yield related genes/QTLs.The main results are as follows:1.Validation of the major QTL qSB-9TQ for resistance to ShB.Using 210 polymorphic molecular markers that are relatively evenly distributed in the rice genome,three substitution lines with the closest genetic background to LE were screened from the 46 TQ→LE chromosome segment substitution lines constructed earlier covering the qSB-9TQ location interval（between molecular markers CY85-Y86）.The TQ substitution segments carried at the lower end of the long arm of chromosome 9 are:molecular markers（Y83）-Y84-CY85-Y86RM 6971-Y91.8-terminal（L5847）,（RM 6971）-Y91.8-terminal（L5859）and（Y91.8）terminal（L5864）.The resistance of the three substitution lines and the control to ShB in field,greenhouse and in vitro were identified,respectively.It was found that the resistance of each substitution line to ShB was significantly higher than that of LE in the three identification methods.However,there was no significant difference among the three lines in field identification,but there were significant differences in greenhouse and in vitro identification,that is,the resistance level of the substitution line L5847 was significantly higher than that of the other two lines（5859 and 5864）.This indicates that qSB-9TQ does exist between CY85 and Y86.At the same time,there is a resistance locus from Y91.8 to the end of chromosome,which was named qSB-9-2TQ,and the previous qSB-9TQ was renamed qSB-9-1 TQ.2.Interpretation gene analysis in qSB-9-1TQ and qSB-9-2TQ mapping interval.The whole genome resequencing analysis of the substitution line L5847 and LE showed that 13 and 45 interpretation genes with amino acid variation among the resistant and susceptible parents were screened in the qSB-9-1TQ and qSB-9-2TQ regions,respectively.Further,RNA-seq analysis found that there were 11 and 19 different expressed genes（DEGs）in the TQ interval of qSB-9-1TQ and qSB-9-2TQ,respectively,among resistant and susceptible varieties before and after the R.solani infection.Metabolic pathway analysis showed that phenylpropane biosynthesis pathway was significantly enriched in DEGs of the three substitution lines,and MAPK signal,flavonoid synthesis and fatty acid extension signal pathways were specifically enriched in the substitution line L5847,suggesting that these pathways may be related to the anti-ShB function of the two genes.By integrating whole genome sequencing and transcriptome data,25 and 42 candidate genes with or without differential expression but with amino acid variation were obtained in qSB-9-1TQ and qSB-9-2TQ,respectively,which will lay an important foundation for further isolation and cloning of target genes.3.Construction of introgression lines of YSBR1 related chromosome fragments and QTL mapping for resistance to ShB and important agronomic or yield related traits.280 pairs and 234 pairs of polymorphic molecular markers were used to detect and determine the marker genotypes of 59 BC4/5F5-6 YSBR1-T394 and 57 BC6F3 YSBR1→LE chromosome fragment introgression lines.At the same time,QTLs related to ShB resistance and phenotypic data of major agronomic or yield traits were located in combination with the phenotypic data of each substitution line.Two QTLs for resistance to ShB were detected in the population of YSBR1→T394,which were located on chromosomes 1 and 9 respectively.The resistance alleles of these two QTLs came from the susceptible variety T394.Two QTLs for resistance to ShB were detected in the population of YSBR1→LE substitution line,which were located on chromosomes 7 and 8 respectively.The resistance allele of these two QTLs came from YSBR1.Thirteen YSBR1→LE introgression lines covering the initial localization interval of qSB-12YSBR1 were further located between the molecular markers Indel25.8 and RM6306,with a spacing of 1.367Mb.A total of 45 QTLs affecting plant height,heading date,panicle length,primary branch number,secondary branch number,flag leaf length,flag leaf width,1000-grain weight and grain length were detected in the two populations,which were distributed on 12 chromosomes.One QTL of the same trait（qFLW4 for flag leaf width）was detected between the two populations.Location comparison showed that most agronomic or yield related QTLs were located in the same or similar interval as previously reported.