QTL Mapping and Transcriptome Sequencing Analysis of Heading Date in Rice

Xiong Jiaming; Zhang Luqian; Yuan Hongliang; Yi Shiwu; Zhou Yu; Ruan Binzhou; Zhang Liying; Wang Yue

doi:10.14083/j.issn.1001-4942.2025.08.001

Abstract：Heading date is a critical period determining the number of filled grains in rice,significantly influencing its growth process.Timely heading is a prerequisite for stable rice yield.To analyze the genetic characteristics of rice heading date,this study established three sowing date treatments on May 7,17 and 27(labeled as M7,M17 and M27,respectively).The heading date of two rice varieties,RT and SC,which ex-hibited a large difference in heading date,and their F7 generation recombinant inbred lines(RILs)population were investigated.The genetic variation characteristics of the heading date trait were analyzed.Simultaneously,quantitative trait locus(QTL)mapping for the heading date trait in the RILs population using a previously constructed genetic linkage map were performed,and the candidate genes regulating rice heading date were i-dentified combined with RNA-seq analysis.The results showed that heading dates under different sowing treat-ments exhibited continuous variation characteristics.The coefficients of variation(CV)for the heading date trait in both the parental varieties and the RILs population increased with delayed sowing dates,and the CV values for M7,M17 and M27 treatments were 9.08％,9.29％and 14.69％,respectively.Through QTL analysis of the heading date trait in the RILs population under M7,M17 and M27 treatments,a total of four associated QTLs were detected,which were located on chromosomes 3 and 7 with the logarithm of odds(LOD)scores ranging from 3.47 to 18.63 and the phenotypic variance explained(PVE)ranging from 7.46％to 26.57％.Through anal-ysis of RNA-seq results from the flag leaves of the two parental varieties,70 differentially expressed genes(DEGs)within the QTL intervals were detected,among which,31 genes were up-regulated and 39 genes were down-regulated.The result of Gene Ontology(GO)functional annotation indicated that the majority of DEGs were involved in regulation of rice heading date by participating in biological processes,including cellular processes and metabolic processes and so on.The results of Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis revealed that the DEGs were primarily associated with regulatory pathways such as non-homologous end joining repair,vitamin B6 metabolism,and photosynthesis.These QTLs and candidate genes could be used for further fine mapping and functional analysis,which are of great importance for guiding molecu-lar breeding practices aimed at precise regulation of heading date and for informing rice production.