Genome assembly and predicted gene BUSCO scores.
<div><p>Rice (<i>Oryza sativa</i> L.) is a staple for more than half of the world’s population, and grain quality strongly influences consumer preference and market value. Udai21, also referred to as Ohkome21, and previously designated as Yudai21, is a Japanese japonica culti...
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| _version_ | 1849927626805739520 |
|---|---|
| author | Hiroki Ikeda (510280) |
| author2 | Masatsugu Tamura (22683631) Takayuki Ohnishi (816437) Kenta Shirasawa (586327) |
| author2_role | author author author |
| author_facet | Hiroki Ikeda (510280) Masatsugu Tamura (22683631) Takayuki Ohnishi (816437) Kenta Shirasawa (586327) |
| author_role | author |
| dc.creator.none.fl_str_mv | Hiroki Ikeda (510280) Masatsugu Tamura (22683631) Takayuki Ohnishi (816437) Kenta Shirasawa (586327) |
| dc.date.none.fl_str_mv | 2025-11-25T18:39:11Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pone.0324304.t002 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Genome_assembly_and_predicted_gene_BUSCO_scores_/30714745 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Genetics Evolutionary Biology Ecology Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified sampling two breeder oryza sativa </ likely parental origins impact variants relative annotate predicted impacts 522 predicted genes superior eating quality excellent eating quality distinctive quality traits carried introgressed aus div >< p curated genome resource aus maternal origin rice </ p aus × koshihikari organelle genome analysis grain quality aus cluster wide analysis rice (< organelle single hybrid origin breeding origin genome resequencing world ’ trace ancestry storage performance starch metabolism results support representative accessions previously designated paternal contribution market value map polymorphisms maintained lines l .) informed crossing identified 1 genomic composition genetic basis enable marker derived segments cultivar uniformity conducted whole chromosomes 1 candidate loci assisted selection assessed within among 37 also referred |
| dc.title.none.fl_str_mv | Genome assembly and predicted gene BUSCO scores. |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | <div><p>Rice (<i>Oryza sativa</i> L.) is a staple for more than half of the world’s population, and grain quality strongly influences consumer preference and market value. Udai21, also referred to as Ohkome21, and previously designated as Yudai21, is a Japanese japonica cultivar noted for excellent eating quality and storage performance, yet its breeding origin and genomic basis remain unclear. Here, we aimed to resolve the genomic composition and likely parental origins of Udai21, and to identify candidate genes related to its distinctive quality traits. We generated a chromosome-scale assembly using PacBio HiFi long reads and assessed within-cultivar uniformity by sampling two breeder-maintained lines. We then profiled population structure using double digest restriction-site associated DNA sequencing together with representative accessions and conducted whole-genome resequencing and organelle genome analysis to trace ancestry, map polymorphisms, and annotate predicted impacts. Udai21 was predominantly japonica but carried introgressed aus-derived segments on chromosomes 1, 2, 3, 6, 7, and 10. Organelle single-nucleotide polymorphisms placed Udai21 with the aus cluster, consistent with an aus maternal origin and a japonica (Koshihikari) paternal contribution. The two maintenance lines showed high genetic uniformity. Among 37,522 predicted genes, we identified 1,017 non-redundant genes harboring high- or moderate-impact variants relative to Koshihikari, including loci previously implicated in grain quality and starch metabolism. These results support a hybrid origin for Udai21 (aus × Koshihikari) and provide a curated genome resource and candidate loci that can enable marker-assisted selection and informed crossing to combine superior eating quality with postharvest stability.</p></div> |
| eu_rights_str_mv | openAccess |
| id | Manara_73cc81b3b224002d0e94562507d2b250 |
| identifier_str_mv | 10.1371/journal.pone.0324304.t002 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30714745 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Genome assembly and predicted gene BUSCO scores.Hiroki Ikeda (510280)Masatsugu Tamura (22683631)Takayuki Ohnishi (816437)Kenta Shirasawa (586327)GeneticsEvolutionary BiologyEcologyEnvironmental Sciences not elsewhere classifiedBiological Sciences not elsewhere classifiedsampling two breederoryza sativa </likely parental originsimpact variants relativeannotate predicted impacts522 predicted genessuperior eating qualityexcellent eating qualitydistinctive quality traitscarried introgressed ausdiv >< pcurated genome resourceaus maternal originrice </ paus × koshihikariorganelle genome analysisgrain qualityaus clusterwide analysisrice (<organelle singlehybrid originbreeding origingenome resequencingworld ’trace ancestrystorage performancestarch metabolismresults supportrepresentative accessionspreviously designatedpaternal contributionmarket valuemap polymorphismsmaintained linesl .)informed crossingidentified 1genomic compositiongenetic basisenable markerderived segmentscultivar uniformityconducted wholechromosomes 1candidate lociassisted selectionassessed withinamong 37also referred<div><p>Rice (<i>Oryza sativa</i> L.) is a staple for more than half of the world’s population, and grain quality strongly influences consumer preference and market value. Udai21, also referred to as Ohkome21, and previously designated as Yudai21, is a Japanese japonica cultivar noted for excellent eating quality and storage performance, yet its breeding origin and genomic basis remain unclear. Here, we aimed to resolve the genomic composition and likely parental origins of Udai21, and to identify candidate genes related to its distinctive quality traits. We generated a chromosome-scale assembly using PacBio HiFi long reads and assessed within-cultivar uniformity by sampling two breeder-maintained lines. We then profiled population structure using double digest restriction-site associated DNA sequencing together with representative accessions and conducted whole-genome resequencing and organelle genome analysis to trace ancestry, map polymorphisms, and annotate predicted impacts. Udai21 was predominantly japonica but carried introgressed aus-derived segments on chromosomes 1, 2, 3, 6, 7, and 10. Organelle single-nucleotide polymorphisms placed Udai21 with the aus cluster, consistent with an aus maternal origin and a japonica (Koshihikari) paternal contribution. The two maintenance lines showed high genetic uniformity. Among 37,522 predicted genes, we identified 1,017 non-redundant genes harboring high- or moderate-impact variants relative to Koshihikari, including loci previously implicated in grain quality and starch metabolism. These results support a hybrid origin for Udai21 (aus × Koshihikari) and provide a curated genome resource and candidate loci that can enable marker-assisted selection and informed crossing to combine superior eating quality with postharvest stability.</p></div>2025-11-25T18:39:11ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.1371/journal.pone.0324304.t002https://figshare.com/articles/dataset/Genome_assembly_and_predicted_gene_BUSCO_scores_/30714745CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/307147452025-11-25T18:39:11Z |
| spellingShingle | Genome assembly and predicted gene BUSCO scores. Hiroki Ikeda (510280) Genetics Evolutionary Biology Ecology Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified sampling two breeder oryza sativa </ likely parental origins impact variants relative annotate predicted impacts 522 predicted genes superior eating quality excellent eating quality distinctive quality traits carried introgressed aus div >< p curated genome resource aus maternal origin rice </ p aus × koshihikari organelle genome analysis grain quality aus cluster wide analysis rice (< organelle single hybrid origin breeding origin genome resequencing world ’ trace ancestry storage performance starch metabolism results support representative accessions previously designated paternal contribution market value map polymorphisms maintained lines l .) informed crossing identified 1 genomic composition genetic basis enable marker derived segments cultivar uniformity conducted whole chromosomes 1 candidate loci assisted selection assessed within among 37 also referred |
| status_str | publishedVersion |
| title | Genome assembly and predicted gene BUSCO scores. |
| title_full | Genome assembly and predicted gene BUSCO scores. |
| title_fullStr | Genome assembly and predicted gene BUSCO scores. |
| title_full_unstemmed | Genome assembly and predicted gene BUSCO scores. |
| title_short | Genome assembly and predicted gene BUSCO scores. |
| title_sort | Genome assembly and predicted gene BUSCO scores. |
| topic | Genetics Evolutionary Biology Ecology Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified sampling two breeder oryza sativa </ likely parental origins impact variants relative annotate predicted impacts 522 predicted genes superior eating quality excellent eating quality distinctive quality traits carried introgressed aus div >< p curated genome resource aus maternal origin rice </ p aus × koshihikari organelle genome analysis grain quality aus cluster wide analysis rice (< organelle single hybrid origin breeding origin genome resequencing world ’ trace ancestry storage performance starch metabolism results support representative accessions previously designated paternal contribution market value map polymorphisms maintained lines l .) informed crossing identified 1 genomic composition genetic basis enable marker derived segments cultivar uniformity conducted whole chromosomes 1 candidate loci assisted selection assessed within among 37 also referred |