Mapping Of Resistance QTL To False Smut In Rice Cv.MR183-2 And Expression Profiling Of Resistant/susceptible Rice Varieties During Ustilaginoidea Virens Infection

False smut of rice(Oryza sativa L.),caused by the ascomycetous fungus Ustilaginoidea virens(Cooke)Takahashi,is a grain disease with typical symptoms in panicles.False smut causes significant loss in yield and quality.In addition,a great amount of mycotoxins produced by false smut balls on rice panicles pose health threats to human and animals.However,little is known about the inheritance of resistance to rice false smut and molecular mechanisms of rice resistance to false smut.To elucidate molecular basis of rice resistance to false smut,resistance QTLs were mapped using the rice variety MR183-2 with high field resistance to false smut in this study.First,we,in collaboration with Sichuan Agricultural University,developed F2,F6 and F7 mapping populations derived from the cross of MR183-2 and a susceptible variety 08R2394.Subsequently,160 polymorphic markers were screened from-4000 SSR markers.The genotypes of individual lines in three mapping populations were determined using these polymorphic markers and then molecular genetic maps were constructed for F2,F6 and F7 populations using Mapmaker/EXP.Version 3.0.Resistance phenotypes to false smut of these populations were evaluated in disease miseries by natural infection in three different years.The recorded disease indices,together with genetic maps,were subsequently used for resistance QTL mapping through Window QTL Cartographer 2.5.Two QTLs were mapped to chromosomes 2 and 8 in F2 and F6 populations,respectively,while four QTLs were mapped to chromosome 2,4,and 8(2)in the F7 population.A QTL on chromosome 8 was detected in all of three mapping populations with the phenotypic variance of?8%,?12%and?27%.The QTL significantly reduced disease indices and increased false smut resistance,which may be utilized for marker-assisted disease resistance breeding in rice.To elucidate molecular mechanisms underlying false smut resistance in rice,expression profiles of resistant and susceptible varieties in response to U.virens infection were determined by RNA-Seq technology.Alignment statistics,quality assessment of sequencing reads and sequencing saturation analysis indicated that transcriptome data were reliable and suitable for further analyses.Differentially expressed genes(DEGs)in resistant and susceptible varieties were analyzed and screened in RNA-seq data.Among common DEGs shared by both varieties,138 and 335 genes were up-regulated in IR28 at 24 and 48 h post inoculation(hpi),respectively,more than those in LYP9(88 and 78).In contrast,fewer DEGs(67 and 54)in IR28 were down-regulated than those(117 and 311)in LYP9 at the two time points.Through GO enrichment analyses,a set of genes encoding receptor-like kinases and cytoplasmic kinases were found to be specifically induced in the resistant variety and suppressed in the susceptible cultivar,indicating that plant perception of conserved pathogen-associated molecular signatures and subsequent triggering of defence signalling pathways are essential for resistance to false smut.In addition,many pathogenesis-related(PR)genes in PR2-6,PR8 and PR9 families,genes involved in diterpene phytoalexin(PA)and phenylpropanoid biosynthesis pathways and OsWRKY53,OsWRKY69 andOsWRKY71 were specifically induced in the resistant variety and suppressed in the susceptible cultivar revealed by cluster and KEGG pathway enrichment analyses.The data suggest that basal defense responses including induced PA production,elevated PR gene expression and some WRKY transcription factors contribute to false smut resistance.Third,analyses of cis-acting regulatory elements revealed that the RY repeat motif was significantly more abundant in the 5'-regulatory regions of these differentially regulated PR genes,particularly in the up-regulated chitinase gene cluster at the early stages of U.virens infection.The finding suggests that the cis element might be involved in the regulation of resistance reaction in rice.Lastly,expression profiles of 9 differentially regulated genes were also investigated by quantitative real-time PCR.The consistency between qRT-PCR data and transcriptome data indicates the reliability of RNA-Seq data.In summary,the results in the study will facilitate fine mapping and eventual isolation of resistance QTL to false smut.Meanwhile,the findings provided valuable information to elucidate resistance signaling pathways and molecular mechanisms of disease resistance in rice.