{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T11:16:34Z","timestamp":1784200594103,"version":"3.55.0"},"reference-count":69,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T00:00:00Z","timestamp":1781222400000},"content-version":"vor","delay-in-days":162,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-AC02-05CH11231"],"award-info":[{"award-number":["DE-AC02-05CH11231"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006235","name":"Lawrence Berkeley National Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006235","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R35GM148173"],"award-info":[{"award-number":["1R35GM148173"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Fast-neutron mutagenesis creates diverse genome-wide mutations, providing a powerful tool for crop functional genomics. Here, we present an expanded genomic and phenotypic analysis of 3268 fast-neutron (FN)-induced mutant rice lines (Oryza sativa L. cv. Kitaake). All FN lines were whole-genome sequenced, and mutations were identified by alignment in the Nipponbare and KitaakeX reference genomes. We cataloged over 428,000 mutations affecting 78.49% of Nipponbare genes and 70.38% of KitaakeX genes. In silico expression analysis indicates that 575 non-mutated Nipponbare genes are highly expressed and likely essential for viability. Each mutant carries, on average, 68.5 mutations in the Nipponbare alignments or 63.2 mutations for KitaakeX alignments, distributed randomly across all 12 chromosomes with no evident hotspots. FN lines have approximately 8.5% fewer mutations when using the KitaakeX alignment, underscoring the unique contributions of each reference genome and the importance of utilizing both for comprehensive mutation discovery. The majority of mutations are small deletions and single-base substitutions, with deletions predominating in their effect on genes. We found that 74.4% of all transcription factor Nipponbare genes were mutated at least once. Phenotypic characterization of over 2700 lines revealed a broad spectrum of variation in core agronomic traits (heading date, tiller number, plant height, panicle weight, seed yield components) and other morphological variants of interest. The integration of genomic and phenotypic data through the KitBase platform enabled the identification of candidate genes for several traits of interest. The KitBase website (https:\/\/kitbase.ucdavis.edu) has been updated to provide open access to all mutation data and seed stocks, as well as an intuitive query interface, facilitating forward and reverse genetic analyses in rice. This expanded resource enriches the rice functional genomics toolkit and highlights the value of coupling high-density mutation mapping with phenotypic data for rapid gene discovery and crop improvement.<\/jats:p>","DOI":"10.1093\/database\/baag024","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T11:33:19Z","timestamp":1777980799000},"source":"Crossref","is-referenced-by-count":0,"title":["KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants"],"prefix":"10.1093","volume":"2026","author":[{"suffix":"Jr","given":"Artur Teixeira","family":"de\u00a0Araujo","sequence":"first","affiliation":[{"name":"University of California Department of Plant Pathology, , Davis, CA ,","place":["United States"]},{"name":"The Genome Center, University of California , Davis, CA ,","place":["United States"]},{"name":"The Joint Bioenergy Institute , Emeryville, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rashmi","family":"Jain","sequence":"additional","affiliation":[{"name":"University of California Department of Plant Pathology, , Davis, CA ,","place":["United States"]},{"name":"The Genome Center, University of California , Davis, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deling","family":"Ruan","sequence":"additional","affiliation":[{"name":"University of California Department of Plant Pathology, , Davis, CA ,","place":["United States"]},{"name":"The Genome Center, University of California , Davis, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mawsheng","family":"Chern","sequence":"additional","affiliation":[{"name":"University of California Department of Plant Pathology, , Davis, CA ,","place":["United States"]},{"name":"The Genome Center, University of California , Davis, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nguyen","family":"Ho","sequence":"additional","affiliation":[{"name":"University of California Department of Plant Pathology, , Davis, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rohan Bhushan","family":"Jhingan","sequence":"additional","affiliation":[{"name":"University of California Department of Plant Pathology, , Davis, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guotian","family":"Li","sequence":"additional","affiliation":[{"name":"University of California Department of Plant Pathology, , Davis, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phat Q","family":"Duong","sequence":"additional","affiliation":[{"name":"University of California Department of Plant Pathology, , Davis, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Florencia","family":"Ercoli","sequence":"additional","affiliation":[{"name":"University of California Department of Plant Pathology, , Davis, CA ,","place":["United States"]},{"name":"The Genome Center, University of California , Davis, CA ,","place":["United States"]},{"name":"The Innovative Genomics Institute, University of California , Berkeley, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4107-1345","authenticated-orcid":false,"given":"Pamela C","family":"Ronald","sequence":"additional","affiliation":[{"name":"University of California Department of Plant Pathology, , Davis, CA ,","place":["United States"]},{"name":"The Genome Center, University of California , Davis, CA ,","place":["United States"]},{"name":"The Joint Bioenergy Institute , Emeryville, CA ,","place":["United States"]},{"name":"The Innovative Genomics Institute, University of California , Berkeley, CA ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,12]]},"reference":[{"key":"2026071607015289500_bib1","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1080\/07352689.2011.554349","article-title":"Food for thought: a review of the role of energy in current and evolving agriculture","volume":"30","author":"Pimentel","year":"2011","journal-title":"Crit Rev Plant Sci"},{"key":"2026071607015289500_bib2","article-title":"Climate Change, Global Food Security, and the U.S. Food System [Internet]. U.S. Global Change Research Program","author":"Brown","year":"2015"},{"key":"2026071607015289500_bib3","doi-asserted-by":"publisher","first-page":"1971","DOI":"10.1073\/pnas.95.5.1971","article-title":"Comparative genetics in the grasses","volume":"95","author":"Gale","year":"1998","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026071607015289500_bib4","doi-asserted-by":"publisher","first-page":"S58","DOI":"10.1038\/514S58a","article-title":"Domestication: the birth of rice","volume":"514","author":"Callaway","year":"2014","journal-title":"Nature"},{"key":"2026071607015289500_bib5","doi-asserted-by":"publisher","first-page":"S2","DOI":"10.3177\/jnsv.65.S2","article-title":"Rice: importance for Global Nutrition","volume":"65","author":"Fukagawa","year":"2019","journal-title":"J Nutr Sci Vitaminol (Tokyo)"},{"key":"2026071607015289500_bib6","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1016\/j.molp.2022.03.009","article-title":"Twenty years of rice genomics research: from sequencing and functional genomics to quantitative genomics","volume":"15","author":"Wang","year":"2022","journal-title":"Mol Plant"},{"key":"2026071607015289500_bib7","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1111\/pce.12632","article-title":"Genetic resources offer efficient tools for rice functional genomics research","volume":"39","author":"Lo","year":"2016","journal-title":"Plant Cell Environ"},{"key":"2026071607015289500_bib8","doi-asserted-by":"publisher","first-page":"e163","DOI":"10.1371\/journal.pgen.0030163","article-title":"Genome-wide patterns of nucleotide polymorphism in domesticated rice","volume":"3","author":"Caicedo","year":"2007","journal-title":"PLoS Genet"},{"key":"2026071607015289500_bib9","article-title":"Development and Characterization of a Large Mutant Population of a Rice Variety Katy for Functional Genomics Studies and Breeding. Crop Breed Genet Genomics [Internet]","volume-title":"(26 March 2025, date last accessed)","author":"Jia","year":"2019"},{"key":"2026071607015289500_bib10","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1007\/s10142-002-0076-0","article-title":"Reverse genetics by fast neutron mutagenesis in higher plants","volume":"2","author":"Li","year":"2002","journal-title":"Funct Integr Genomics"},{"key":"2026071607015289500_bib11","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1039\/C3MB70349E","article-title":"Genome-wide analysis of radiation-induced mutations in rice (Oryza sativa L. ssp. indica)","volume":"10","author":"Cheng","year":"2014","journal-title":"Mol Biosyst"},{"key":"2026071607015289500_bib12","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/s12284-019-0274-1","article-title":"Identification of spontaneous mutation for broad-spectrum brown planthopper resistance in a large, long-term fast neutron mutagenized rice population","volume":"12","author":"Kamolsukyeunyong","year":"2019","journal-title":"Rice"},{"key":"2026071607015289500_bib13","doi-asserted-by":"publisher","first-page":"1326","DOI":"10.3389\/fpls.2019.01326","article-title":"Mutagenesis in rice: the basis for breeding a new super plant","volume":"10","author":"Viana","year":"2019","journal-title":"Front Plant Sci"},{"key":"2026071607015289500_bib14","doi-asserted-by":"crossref","DOI":"10.1007\/978-981-16-9720-3","volume-title":"Mutation Breeding for Sustainable Food Production and Climate Resilience","author":"Penna","year":"2023"},{"key":"2026071607015289500_bib15","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/1939-8433-6-39","article-title":"International consortium of rice mutagenesis: resources and beyond","volume":"6","author":"Wei","year":"2013","journal-title":"Rice"},{"key":"2026071607015289500_bib16","doi-asserted-by":"publisher","first-page":"1078","DOI":"10.1016\/j.molp.2016.03.009","article-title":"Genome-wide sequencing of 41 rice (Oryza sativa L.) mutated lines reveals diverse mutations induced by fast-neutron irradiation","volume":"9","author":"Li","year":"2016","journal-title":"Mol Plant"},{"key":"2026071607015289500_bib17","doi-asserted-by":"crossref","DOI":"10.1007\/978-981-19-9489-0","volume-title":"Induced Mutation Breeding","author":"Datta","year":"2023"},{"key":"2026071607015289500_bib18","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1046\/j.1365-313x.2001.01084.x","article-title":"A fast neutron deletion mutagenesis-based reverse genetics system for plants","volume":"27","author":"Li","year":"2001","journal-title":"Plant J"},{"key":"2026071607015289500_bib19","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1007\/s00122-006-0342-y","article-title":"Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley","volume":"113","author":"Zhang","year":"2006","journal-title":"Theor Appl Genet"},{"key":"2026071607015289500_bib20","first-page":"381","article-title":"Characterization of hemizygous deletions in citrus using array-comparative genomic hybridization and microsynteny comparisons with the poplar genome","volume":"9","author":"R\u00edos","year":"2008","journal-title":"Bmc Genomics [Electronic Resource]"},{"key":"2026071607015289500_bib21","doi-asserted-by":"publisher","first-page":"1261","DOI":"10.1071\/FP13147","article-title":"Exploiting a fast neutron mutant genetic resource in Pisum sativum (pea) for functional genomics","volume":"40","author":"Domoney","year":"2013","journal-title":"Funct Plant Biol"},{"key":"2026071607015289500_bib22","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1534\/genetics.114.170340","article-title":"Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean","volume":"198","author":"Bolon","year":"2014","journal-title":"Genetics"},{"key":"2026071607015289500_bib23","doi-asserted-by":"publisher","first-page":"1218","DOI":"10.1105\/tpc.17.00154","article-title":"The sequences of 1504 mutants in the model rice variety Kitaake facilitate rapid functional genomic studies","volume":"29","author":"Li","year":"2017","journal-title":"Plant Cell"},{"key":"2026071607015289500_bib24","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1186\/s12864-019-6262-4","article-title":"Genome sequence of the model rice variety KitaakeX","volume":"20","author":"Jain","year":"2019","journal-title":"Bmc Genomics [Electronic Resource]"},{"key":"2026071607015289500_bib25","doi-asserted-by":"publisher","first-page":"e1004809","DOI":"10.1371\/journal.ppat.1004809","article-title":"Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses","volume":"11","author":"Schwessinger","year":"2015","journal-title":"PLOS Pathog"},{"key":"2026071607015289500_bib26","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1038\/nbt.2050","article-title":"Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes","volume":"30","author":"Xu","year":"2012","journal-title":"Nat Biotechnol"},{"key":"2026071607015289500_bib27","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1939-8433-6-4","article-title":"Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data","volume":"6","author":"Kawahara","year":"2013","journal-title":"Rice"},{"key":"2026071607015289500_bib28","article-title":"Aligning Sequence Reads, Clone Sequences and Assembly Contigs with BWA-MEM [Internet]. arXiv. 2013","author":"Li"},{"key":"2026071607015289500_bib29","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2026071607015289500_bib30","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1038\/nmeth.1363","article-title":"BreakDancer: an algorithm for high-resolution mapping of genomic structural variation","volume":"6","author":"Chen","year":"2009","journal-title":"Nat Methods"},{"key":"2026071607015289500_bib31","doi-asserted-by":"publisher","first-page":"2865","DOI":"10.1093\/bioinformatics\/btp394","article-title":"Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads","volume":"25","author":"Ye","year":"2009","journal-title":"Bioinformatics"},{"key":"2026071607015289500_bib32","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res"},{"key":"2026071607015289500_bib33","doi-asserted-by":"publisher","first-page":"i333","DOI":"10.1093\/bioinformatics\/bts378","article-title":"DELLY: structural variant discovery by integrated paired-end and split-read analysis","volume":"28","author":"Rausch","year":"2012","journal-title":"Bioinformatics"},{"key":"2026071607015289500_bib34","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1038\/nature14649","article-title":"Parent\u2013progeny sequencing indicates higher mutation rates in heterozygotes","volume":"523","author":"Yang","year":"2015","journal-title":"Nature"},{"key":"2026071607015289500_bib35","doi-asserted-by":"publisher","first-page":"D1104","DOI":"10.1093\/nar\/gkz1020","article-title":"PlantRegMap: charting functional regulatory maps in plants","volume":"48","author":"Tian","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026071607015289500_bib36","doi-asserted-by":"publisher","first-page":"1630","DOI":"10.1101\/gr.094607.109","article-title":"JBrowse: a next-generation genome browser","volume":"19","author":"Skinner","year":"2009","journal-title":"Genome Res"},{"key":"2026071607015289500_bib37","doi-asserted-by":"publisher","first-page":"2334","DOI":"10.1093\/bioinformatics\/btm331","article-title":"ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user\u2019s datasets","volume":"23","author":"Deng","year":"2007","journal-title":"Bioinformatics"},{"key":"2026071607015289500_bib38","doi-asserted-by":"publisher","first-page":"D883","DOI":"10.1093\/nar\/gkl976","article-title":"The TIGR rice genome annotation resource: improvements and new features","volume":"35","author":"Ouyang","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2026071607015289500_bib39","doi-asserted-by":"publisher","first-page":"1232","DOI":"10.1016\/j.molp.2023.08.003","article-title":"A complete assembly of the rice Nipponbare reference genome","volume":"16","author":"Shang","year":"2023","journal-title":"Mol Plant"},{"key":"2026071607015289500_bib40","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1146\/annurev-genom-091212-153423","article-title":"Unraveling the tangled skein: the evolution of transcriptional regulatory networks in development","volume":"16","author":"Rebeiz","year":"2015","journal-title":"Annu Rev Genomics Hum Genet"},{"key":"2026071607015289500_bib41","doi-asserted-by":"publisher","first-page":"jkae274","DOI":"10.1093\/g3journal\/jkae274","article-title":"Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions","volume":"15","author":"Ellison","year":"2025","journal-title":"G3 Genes Genomes Genet"},{"key":"2026071607015289500_bib42","doi-asserted-by":"publisher","first-page":"2133","DOI":"10.1105\/tpc.15.00051","article-title":"Characteristics of plant essential genes allow for within- and between-species prediction of lethal mutant phenotypes","volume":"27","author":"Lloyd","year":"2015","journal-title":"Plant Cell"},{"key":"2026071607015289500_bib43","article-title":"Identification of essential genes in Caenorhabditis elegans through whole genome sequencing of legacy mutant collections. Genetics","author":"Li-Leger","year":"2021"},{"key":"2026071607015289500_bib44","doi-asserted-by":"publisher","first-page":"1306","DOI":"10.1101\/gr.131474.111","article-title":"Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana","volume":"22","author":"Belfield","year":"2012","journal-title":"Genome Res"},{"key":"2026071607015289500_bib45","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1186\/s13073-019-0656-4","article-title":"Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population","volume":"11","author":"Wong","year":"2019","journal-title":"Genome Med"},{"key":"2026071607015289500_bib46","doi-asserted-by":"publisher","first-page":"eabo7676","DOI":"10.1126\/sciadv.abo7676","article-title":"Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing","volume":"8","author":"Park","year":"2022","journal-title":"Sci Adv"},{"key":"2026071607015289500_bib47","doi-asserted-by":"publisher","first-page":"e2018940118","DOI":"10.1073\/pnas.2018940118","article-title":"Mechanism and function of root circumnutation","volume":"118","author":"Taylor","year":"2021","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026071607015289500_bib48","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1186\/s12284-019-0308-8","article-title":"Whole-genome sequencing identifies a rice grain shape mutant, gs9\u20131","volume":"12","author":"Jiang","year":"2019","journal-title":"Rice"},{"key":"2026071607015289500_bib49","doi-asserted-by":"publisher","first-page":"100215","DOI":"10.1016\/j.xplc.2021.100215","article-title":"Paladin, a tyrosine phosphatase-like protein, is required for XA21-mediated immunity in rice","volume":"2","author":"Chen","year":"2021","journal-title":"Plant Commun"},{"key":"2026071607015289500_bib50","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1111\/tpj.15692","article-title":"Silencing of Dicer-like protein 2a restores the resistance phenotype in the rice mutant, sxi4 (suppressor of Xa21-mediated immunity 4)","volume":"110","author":"Liu","year":"2022","journal-title":"Plant J"},{"key":"2026071607015289500_bib51","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1038\/s41586-023-06205-2","article-title":"Genome editing of a rice CDP-DAG synthase confers multipathogen resistance","volume":"618","author":"Sha","year":"2023","journal-title":"Nature"},{"key":"2026071607015289500_bib52","doi-asserted-by":"publisher","first-page":"0175","DOI":"10.34133\/plantphenomics.0175","article-title":"Fast and efficient root phenotyping via pose estimation","volume":"6","author":"Berrigan","year":"2024","journal-title":"Plant Phenomics"},{"key":"2026071607015289500_bib53","doi-asserted-by":"crossref","DOI":"10.1101\/2022.05.28.493846","article-title":"The H3K4me1 Histone Mark Recruits DNA Repair to Functionally Constrained Genomic Regions in Plants. Genomics","author":"Quiroz","year":"2022"},{"key":"2026071607015289500_bib54","doi-asserted-by":"publisher","first-page":"2410","DOI":"10.1093\/plcell\/koae089","article-title":"H3K4me1 recruits DNA repair proteins in plants","volume":"36","author":"Quiroz","year":"2024","journal-title":"Plant Cell"},{"key":"2026071607015289500_bib55","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1186\/s12284-022-00585-1","article-title":"Whole-genome sequencing of rice mutant library members induced by N-methyl-N-nitrosourea mutagenesis of fertilized egg cells","volume":"15","author":"Kubo","year":"2022","journal-title":"Rice."},{"key":"2026071607015289500_bib56","doi-asserted-by":"publisher","first-page":"310","DOI":"10.3390\/plants8090310","article-title":"Insertional mutagenesis approaches and their use in rice for functional genomics","volume":"8","author":"Ram","year":"2019","journal-title":"Plants"},{"key":"2026071607015289500_bib57","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1079\/9781789249095.0030","article-title":"National repository of EMS induced mutants of an upland rice cultivar Nagina 22: progress update on characterization and utilization","volume-title":"Mutation Breeding, Genetic Diversity and Crop Adaptation to Climate Change","author":"Sevanthi","year":"2021"},{"key":"2026071607015289500_bib58","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/s11103-004-5112-0","article-title":"Chemical- and irradiation-induced mutants of indica rice IR64 for forward and reverse genetics","volume":"59","author":"Wu","year":"2005","journal-title":"Plant Mol Biol"},{"key":"2026071607015289500_bib59","doi-asserted-by":"publisher","first-page":"1238","DOI":"10.1016\/j.molp.2017.06.006","article-title":"Construction of a genome-wide mutant library in rice using CRISPR\/Cas9","volume":"10","author":"Meng","year":"2017","journal-title":"Mol Plant"},{"key":"2026071607015289500_bib60","doi-asserted-by":"publisher","first-page":"1771","DOI":"10.1105\/tpc.012559","article-title":"Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome","volume":"15","author":"Miyao","year":"2003","journal-title":"Plant Cell"},{"key":"2026071607015289500_bib61","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1038\/386388a0","article-title":"Evidence for a selectively favourable reduction in the mutation rate of the X chromosome","volume":"386","author":"McVean","year":"1997","journal-title":"Nature"},{"key":"2026071607015289500_bib62","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1016\/S0960-9822(99)80334-0","article-title":"Do essential genes evolve slowly?","volume":"9","author":"Hurst","year":"1999","journal-title":"Curr Biol"},{"key":"2026071607015289500_bib63","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1093\/genetics\/152.2.661","article-title":"The causes of synonymous rate variation in the rodent genome: can substitution rates be used to estimate the sex bias in mutation rate?","volume":"152","author":"Smith","year":"1999","journal-title":"Genetics"},{"key":"2026071607015289500_bib64","doi-asserted-by":"publisher","first-page":"1540","DOI":"10.1111\/nph.17706","article-title":"Intergenic spaces: a new frontier to improving plant health","volume":"232","author":"Tonnessen","year":"2021","journal-title":"New Phytol"},{"key":"2026071607015289500_bib65","doi-asserted-by":"publisher","first-page":"1543","DOI":"10.1111\/tpj.16582","article-title":"A large sequenced mutant library\u2014valuable reverse genetic resource that covers 98% of sorghum genes","volume":"117","author":"Jiao","year":"2024","journal-title":"Plant J"},{"key":"2026071607015289500_bib66","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1111\/tpj.14291","article-title":"Genome-wide analysis of flanking sequences reveals that Tnt1 insertion is positively correlated with gene methylation in Medicago truncatula","volume":"98","author":"Sun","year":"2019","journal-title":"Plant J"},{"key":"2026071607015289500_bib67","doi-asserted-by":"publisher","first-page":"e11","DOI":"10.1093\/pcp\/pcv194","article-title":"TOMATOMA update: phenotypic and metabolite information in the Micro-Tom mutant resource","volume":"57","author":"Shikata","year":"2016","journal-title":"Plant Cell Physiol"},{"key":"2026071607015289500_bib68","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/s13007-021-00765-y","article-title":"Rapid identification of mutations caused by fast neutron bombardment in Medicago truncatula","volume":"17","author":"Du","year":"2021","journal-title":"Plant Methods"},{"key":"2026071607015289500_bib69","volume-title":"Plant Molecular Breeding in Genomics Era: Concepts and Tools (Advances in Plant Breeding Strategies; vol. 3)","author":"Al-Khayri","year":"2024"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baag024\/68516991\/baag024.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baag024\/68516991\/baag024.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T11:02:07Z","timestamp":1784199727000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baag024\/8706849"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":69,"URL":"https:\/\/doi.org\/10.1093\/database\/baag024","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"baag024"}}