1b19fa699cf26d38f18c7ce94bda53b7 pmc_10667994.pdf 857c7c0792ef4d356104f50c8422ee69426d039d pmc_10667994.pdf 4e7f2b4858c2a47aa940936d9c4a305902e90e1970420c59b1068bbd41b12bc7 pmc_10667994.pdf Title: Development and Genome-Wide Analysis of a Blast-Resistant japonica Rice Variety Subject: Rice is one of the most important crops in the world, and its production is severely affected by the rice blast disease caused by the fungus Magnaporthe oryzae. Several major blast resistance genes and QTLs associated with blast resistance have been described and mostly identified in indica rice varieties. In this work, we report the obtention of a blast-resistant rice breeding line derived from crosses between the resistant indica variety CT13432 and the japonica elite cultivar JSendra (highly susceptible to blast). The breeding line, named COPSEMAR9, was found to exhibit resistance to leaf blast and panicle blast, as demonstrated by disease assays under controlled and field conditions. Furthermore, a high-quality genome sequence of the blast-resistant breeding line was obtained using a strategy that combines short-read sequencing (Illumina sequencing) and long-read sequencing (Pacbio sequencing). The use of a whole-genome approach allowed the fine mapping of DNA regions of indica and japonica origin present in the COPSEMAR9 genome and the identification of parental gene regions potentially contributing to blast resistance in the breeding line. Rice blast resistance genes (including Pi33 derived from the resistant parent) and defense-related genes in the genome of COPSEMAR9 were identified. Whole-genome analyses also revealed the presence of microRNAs (miRNAs) with a known function in the rice response to M. oryzae infection in COPSEMAR9, which might also contribute to its phenotype of blast resistance. From this study, the genomic information and analysis methods provide valuable knowledge that will be useful in breeding programs for blast resistance in japonica rice cultivars. Keywords: breeding; defense; genome mapping; japonica; Magnaporthe oryzae; microRNA (miRNA); Oryza sativa; resistance Author: Glòria Escolà, Víctor M. González-Miguel, Sonia Campo, Mar Catala-Forner, Concha Domingo, Luis Marqués and Blanca San Segundo Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Wed Oct 11 13:39:54 2023 CEST ModDate: Wed Oct 11 14:28:27 2023 CEST Custom Metadata: no Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 19 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 1915522 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- IEFSKB+VnURWPalladioL Type 1 Custom yes yes no 10 0 SHSBJD+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 PRXCQE+URWPalladioL-Roma Type 1 Custom yes yes no 20 0 JRLCFG+URWPalladioL-Ital Type 1 Custom yes yes no 24 0 GUKTPO+URWPalladioL-BoldItal Type 1 Custom yes yes no 28 0 SARIAE+VnURWPalladioL-Bold Type 1 Custom yes yes no 32 0 VTLKDP+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 51 0 TELXLI+CMSY10 Type 1 Builtin yes yes no 84 0 GOOHMW+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 98 0 NUVNGI+PalatinoLinotype-Italic TrueType WinAnsi yes yes yes 106 0 TCEMMW+PalatinoLinotype-Bold TrueType WinAnsi yes yes yes 110 0 DCWKWC+PalatinoLinotype-Roman TrueType WinAnsi yes yes yes 114 0 GOOHMW+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 127 0 NUVNGI+PalatinoLinotype-Italic TrueType WinAnsi yes yes yes 135 0 TCEMMW+PalatinoLinotype-Bold TrueType WinAnsi yes yes yes 139 0 DCWKWC+PalatinoLinotype-Roman TrueType WinAnsi yes yes yes 143 0 GOOHMW+PalatinoLinotype-Roman CID TrueType Identity-H yes yes yes 161 0 NUVNGI+PalatinoLinotype-Italic TrueType WinAnsi yes yes yes 169 0 TCEMMW+PalatinoLinotype-Bold TrueType WinAnsi yes yes yes 173 0 DCWKWC+PalatinoLinotype-Roman TrueType WinAnsi yes yes yes 177 0 OVNEXW+EURM10 Type 1 Builtin yes yes no 195 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2024-09-01 08:22:02 CEST RepresentationInformation: pmc_10667994.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2024-07-12 02:35:36 CEST Size: 1915522 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 517 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: section.1 Item: Title: Results Destination: section.2 Children: Item: Title: Resistance to Infection by the Rice Blast Fungus Magnaporthe oryzae in the Breeding Line COPSEMAR9 Destination: subsection.2.1 Item: Title: Sequencing, Assembly and Annotation of the COPSEMAR9 Genome Destination: subsection.2.2 Item: Title: Resistance Genes in COPSEMAR9 Destination: subsection.2.3 Item: Title: Mining of Blast-Associated miRNAs in the Genome of COPSEMAR9 Destination: subsection.2.4 Item: Title: Discussion Destination: section.3 Item: Title: Materials and Methods Destination: section.4 Children: Item: Title: Plant Material and DNA Extraction Destination: subsection.4.1 Item: Title: Phenotyping for Resistance to Leaf Blast in Rice Seedlings under Controlled Conditions Destination: subsection.4.2 Item: Title: Field Experiments Destination: subsection.4.3 Item: Title: Whole-Genome Sequencing on the PacBio and Illumina Platforms, De Novo Assembly and Reference-Based Annotation Destination: subsection.4.4 Item: Title: Mapping of Indica Regions Destination: subsection.4.5 Item: Title: Mining of Blast Disease Resistance and Blast-Associated MIR Genes Destination: subsection.4.6 Item: Title: References Destination: section.A. Info: Title: Development and Genome-Wide Analysis of a Blast-Resistant japonica Rice Variety Author: Glòria Escolà, Víctor M. González-Miguel, Sonia Campo, Mar Catala-Forner, Concha Domingo, Luis Marqués and Blanca San Segundo Subject: Rice is one of the most important crops in the world, and its production is severely affected by the rice blast disease caused by the fungus Magnaporthe oryzae. Several major blast resistance genes and QTLs associated with blast resistance have been described and mostly identified in indica rice varieties. In this work, we report the obtention of a blast-resistant rice breeding line derived from crosses between the resistant indica variety CT13432 and the japonica elite cultivar JSendra (highly susceptible to blast). The breeding line, named COPSEMAR9, was found to exhibit resistance to leaf blast and panicle blast, as demonstrated by disease assays under controlled and field conditions. Furthermore, a high-quality genome sequence of the blast-resistant breeding line was obtained using a strategy that combines short-read sequencing (Illumina sequencing) and long-read sequencing (Pacbio sequencing). The use of a whole-genome approach allowed the fine mapping of DNA regions of indica and japonica origin present in the COPSEMAR9 genome and the identification of parental gene regions potentially contributing to blast resistance in the breeding line. Rice blast resistance genes (including Pi33 derived from the resistant parent) and defense-related genes in the genome of COPSEMAR9 were identified. Whole-genome analyses also revealed the presence of microRNAs (miRNAs) with a known function in the rice response to M. oryzae infection in COPSEMAR9, which might also contribute to its phenotype of blast resistance. From this study, the genomic information and analysis methods provide valuable knowledge that will be useful in breeding programs for blast resistance in japonica rice cultivars. Keywords: breeding; defense; genome mapping; japonica; Magnaporthe oryzae; microRNA (miRNA); Oryza sativa; resistance Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Wed Oct 11 13:39:54 CEST 2023 ModDate: Wed Oct 11 14:28:27 CEST 2023 ID: 0x25bc5067eeeb66f2181b40ebfb98a67f, 0x25bc5067eeeb66f2181b40ebfb98a67f Filters: FilterPipeline: FlateDecode Fonts: Type1: Font: BaseFont: SARIAE+VnURWPalladioL-Bold FontSubset: true FirstChar: 160 LastChar: 225 FontDescriptor: FontName: SARIAE+VnURWPalladioL-Bold Flags: Symbolic FontBBox: -152, -301, 1000, 935 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: OVNEXW+EURM10 FontSubset: true FirstChar: 22 LastChar: 22 FontDescriptor: FontName: OVNEXW+EURM10 Flags: Symbolic FontBBox: -32, -243, 1060, 720 FontFile: true Font: BaseFont: PRXCQE+URWPalladioL-Roma FontSubset: true FirstChar: 2 LastChar: 241 FontDescriptor: FontName: PRXCQE+URWPalladioL-Roma Flags: Symbolic FontBBox: -166, -283, 1021, 943 FontFile: true 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95, 193, 132, 203 Checksum: 968a8d66 Type: CRC32 Checksum: 1b19fa699cf26d38f18c7ce94bda53b7 Type: MD5 Checksum: 857c7c0792ef4d356104f50c8422ee69426d039d Type: SHA-1 Checksum: 4e7f2b4858c2a47aa940936d9c4a305902e90e1970420c59b1068bbd41b12bc7 Type: SHA-256