QTL Mapping And Candidate Gene Analysis Of Tillering Ability In Rice Ratoon Season

Rice is a very important food crop,increasing its yield is the premise of food security.The ratooning rice cultivation pattern with the characteristics of saving land and resources could improve the multiple cropping index and yield.In recent years,the lack of varieties with strong regenerative capacity has become one of the main limiting factors for rice yield increase,and the strength of regenerative capacity affects the final yield by affecting the effective panicle number of regenerative rice.At present,there are few reports on gene mining that control tiller number of ratooning rice.Therefore,it is of great significance to explore QTL/genes that control tiller number of ratooning rice for improving yield of ratooning rice.In this study,we used the extreme phenotypic materials screened by the previous research group and the F₂isolation population and F_2:3lines constructed by the research group as test materials,and used GSR40K gene chip method to excavate QTLs for controlling tillering of ratooning rice,so as to detect more and more reliable loci.Then the complete interval mapping method（ICIM）of ICIMapping4.2 software was used to conduct QTL analysis on the candidate regions screened by QTL-seq method and the regions obtained by GSR40K gene chip method,and gene function annotation was used to screen candidate genes.It will lay a foundation for the analysis of the genetic mechanism of tiller,the breeding of rice varieties with high fertility,and the subsequent exploration and cloning of related major genes.The main results are as follows:（1）QTL mapping for tillering ability in rice ratoon seasonIn this study,f_2:3lines derived from F₂isolated population constructed from two materials with significant differences in the number of regenerated tillers were used as research materials.Phenotypic identification of the number of regenerated tillers of the parents and F_2:3lines was carried out in Jingzhou,Hubei province in 2020.The extreme mixed pool was constructed and sequenced using GSR40K gene array.Based on the genotyping and phenotypic identification results of the gene chip,it was speculated that the regenerated tiller of rice might be controlled by recessive genes,and finally three QTLs（q RTN2,q RTN3 and q RTN8）controlling tiller number of regenerated rice were mapped on chromosome 2,3 and 8.The total length of q RTN2（0.86-1.73 Mb）,q RTN3（3.05-6.08 Mb）and q RTN8（22.5-26.0 Mb）is 0.87 Mb,3.03Mb and 3.5 Mb respectively.Two QTLs（q RTN1-1 and q RTN1-2）controlling tiller number of ratooning rice were mapped on chromosome 1 by QTL-seq analysis.The total length of q RTN1-1（14.86-17.82 Mb）was 2.96 Mb.q RTN1-2（36.30-39.96 Mb）total length 3.66 Mb.（2）Mining of candidate genes for tillering ability in rice ratoon seasonIn this study,phenotypic identification of regenerated tiller number of parents and F₂lines was carried out in Jingzhou,Hubei and Lingshui,Hainan in 2021,using F₂populations constructed in the early stage to isolate the phenotypic characteristics of regenerated tiller number.Marker primers were designed according to the polymorphism of the genome sequence of the 5 target gene regions located by QTL-seq analysis and GSR40K gene chip analysis,and QTL analysis was performed on the candidate regions by complete interval mapping.q RTN1-1、q RTN1-2、q RTN3and q RTN8 were detected simultaneously in two environments.q RTN1-1 was reduced to 15.14-17.16 Mb,q RTN1-2 to 36.46-37.88 Mb and q RTN3 to 3.26-5.36 Mb.q RTN8 reduced to 24.77-25.82 Mb.Compared with previous QTLs for tillering traits,the results showed that q RTN1-2,q RTN3 and q RTN8 were all located in the range of mapped QTLs for tillering traits in rice,and were effective target loci for this study.Combined with gene annotation results,14 candidate genes were screened from q RTN1-2,q RTN3 and q RTN8.independently LOC＿Os01g63460、LOC＿Os01g63930、LOC＿Os01g64360、LOC＿Os01g64660（MOC2）、LOC＿Os01g65200（Os NPF5.16）、LOC＿Os03g07250（CYP704B2）、LOC＿Os03g07430（Os RLCK102）、LOC＿Os03g07530（Os FBK12）、LOC＿Os03g07540（Osb HLH153）、LOC＿Os03g08460（Os EBP-89）、LOC＿Os03g08754（Os MDP1）、LOC＿Os08g39640、LOC＿Os08g39730、LOC＿Os08g39890（Os SPL14）,LOC＿Os01g64660（MOC2）、LOC＿Os01g65200（Os NPF5.16）and LOC＿Os08g39890（Os SPL14）were previously studied genes controlling tillering of rice.