{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T10:35:10Z","timestamp":1785839710587,"version":"3.56.0"},"reference-count":46,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2020,9,14]],"date-time":"2020-09-14T00:00:00Z","timestamp":1600041600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001503","name":"Indian Council of Agricultural Research","doi-asserted-by":"publisher","award":["NAHEP-CAAST"],"award-info":[{"award-number":["NAHEP-CAAST"]}],"id":[{"id":"10.13039\/501100001503","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>The semi-dwarfing allele, sd1-d, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), sd1-d, derived from a spontaneous mutation, has a 383-bp deletion in the SD1 gene. To date, as many as seven alleles of the SD1 gene have been identified and used in rice improvement, either with a functional single-nucleotide polymorphism (SNP), with insertion\u2013deletions (InDels), or both. Here, we report discovery of a novel SNP in the SD1 gene from the rice genotype, Pusa 1652. Genetic analysis revealed that the inheritance of the semi-dwarfism in Pusa 1652 is monogenic and recessive, but it did not carry the sd1-d allele. However, response to exogenous gibberellic acid (GA3) application and the subsequent bulked segregant and linkage analyses confirmed that the SD1 gene is involved in the plant height reduction in Pusa 1652. Sequencing of the SD1 gene from Pusa 1652 revealed a novel transition in exon 3 (T\/A) causing a nonsense mutation at the 300th codon. The stop codon leads to premature termination, resulting in a truncated protein of OsGA20ox2 obstructing the GA3 biosynthesis pathway. This novel recessive allele, named sd1-bm, is derived from Bindli Mutant 34 (BM34), a \u03b3-ray induced mutant of a short-grain aromatic landrace, Bindli. BM34 is the parent of an aromatic semi-dwarf cultivar, Pusa 1176, from which Pusa 1652 is derived. The semi-dwarfing allele, sd1-bm, was further validated by developing a derived cleaved amplified polymorphic sequence (dCAPS) marker, AKS-sd1. This allele provides an alternative to the most widely used sd1-d in rice improvement programs and the functional dCAPS marker will facilitate marker-assisted introgression of the semi-dwarf trait into tall genotypes.<\/jats:p>","DOI":"10.3390\/plants9091198","type":"journal-article","created":{"date-parts":[[2020,9,14]],"date-time":"2020-09-14T09:04:53Z","timestamp":1600074293000},"page":"1198","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5215-2079","authenticated-orcid":false,"given":"Shivashankar","family":"Bhuvaneswari","sequence":"first","affiliation":[{"name":"Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India"},{"name":"Division of Plant Breeding, ICAR RC NEH Region, Manipur Centre, Imphal 795004, Manipur, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Subbaiyan","family":"Gopala Krishnan","sequence":"additional","affiliation":[{"name":"Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ranjith Kumar","family":"Ellur","sequence":"additional","affiliation":[{"name":"Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8927-4590","authenticated-orcid":false,"given":"Kunnummal Kurungara","family":"Vinod","sequence":"additional","affiliation":[{"name":"Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haritha","family":"Bollinedi","sequence":"additional","affiliation":[{"name":"Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prolay Kumar","family":"Bhowmick","sequence":"additional","affiliation":[{"name":"Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vijay Prakash","family":"Bansal","sequence":"additional","affiliation":[{"name":"Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariappan","family":"Nagarajan","sequence":"additional","affiliation":[{"name":"Rice Breeding and Genetics Research Centre, ICAR- Indian Agricultural Research Institute, Aduthurai 612101, Tamil Nadu, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9777-8163","authenticated-orcid":false,"given":"Ashok Kumar","family":"Singh","sequence":"additional","affiliation":[{"name":"Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,9,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00425-017-2798-1","article-title":"The genetic and molecular basis of crop height based on a rice model","volume":"247","author":"Liu","year":"2018","journal-title":"Planta"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"a034645","DOI":"10.1101\/cshperspect.a034645","article-title":"The role of dwarfing traits in historical and modern agriculture with a focus on rice","volume":"11","author":"Cantos","year":"2019","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"4703","DOI":"10.1093\/jxb\/ery243","article-title":"Characterization of a new semi-dominant dwarf allele of SLR1 and its potential application in hybrid rice breeding","volume":"69","author":"Wu","year":"2018","journal-title":"J. Exp. Bot."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1642","DOI":"10.1104\/pp.103.033696","article-title":"An overview of gibberellin metabolism enzyme genes and their related mutants in rice","volume":"34","author":"Sakamoto","year":"2004","journal-title":"Plant Physiol."},{"key":"ref_5","first-page":"309","article-title":"Rice yielding and plant hormones","volume":"Volume 62","author":"Hirano","year":"2008","journal-title":"Rice Biology in the Genomics Era. Biotechnology in Agriculture and Forestry"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Castorina, G., and Consonni, G. (2020). The Role of Brassinosteroids in Controlling Plant Height in Poaceae: A Genetic Perspective. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21041191"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1016\/j.molp.2020.03.009","article-title":"A Strigolactone Biosynthesis Gene Contributed to the Green Revolution in Rice","volume":"13","author":"Wang","year":"2020","journal-title":"Mol. Plant"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/416701a","article-title":"Green revolution: A mutant gibberellin-synthesis gene in rice","volume":"416","author":"Sasaki","year":"2002","journal-title":"Nature"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"9043","DOI":"10.1073\/pnas.132266399","article-title":"Semi-dwarf sd-1, \u201cgreen revolution\u201d rice, contains a defective gibberellin 20-oxidase gene","volume":"99","author":"Spielmeyer","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1093\/dnares\/9.1.11","article-title":"Positional Cloning of Rice Semi dwarfing Gene, sd-1: Rice \u201cGreen Revolution Gene\u201d Encodes a Mutant Enzyme Involved in Gibberellin Synthesis","volume":"9","author":"Monna","year":"2002","journal-title":"DNA Res."},{"key":"ref_11","unstructured":"Chandler, R. (1972). The impact of the improved tropical plant type on rice yields in South and Southeast Asia. Rice Breeding, International Rice Research Institute."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Tomita, M., and Ishimoto, K. (2019). Rice novel semidwarfing gene d60 can be as effective as green revolution gene sd1. Plants, 8.","DOI":"10.3390\/plants8110464"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.molp.2017.12.004","article-title":"Shortened basal internodes encodes a Gibberellin 2-Oxidase and contributes to lodging resistance in rice","volume":"11","author":"Liu","year":"2018","journal-title":"Mol. Plant"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1270\/jsbbs.57.53","article-title":"Genetic and molecular analysis of the utility of sd1 alleles in rice breeding","volume":"57","author":"Asano","year":"2007","journal-title":"Breed. Sci."},{"key":"ref_15","first-page":"1","article-title":"Growth habit of the plant in the tropics and its effect on nitrogen response","volume":"3","author":"Tanaka","year":"1964","journal-title":"Tech. Bull. IRRI"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1601-5223.2010.02168.x","article-title":"Differentiation in wild-type allele of the sd1 locus concerning culm length between indica and japonica subspecies of Oryza sativa (rice)","volume":"148","author":"Murai","year":"2010","journal-title":"Hereditas"},{"key":"ref_17","unstructured":"Singh, R.K., and Singh, U.S. (2003). Aromatic rices of Manipur. A Treatise on the Scented Rices of India, Kalyani Publishers."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1186\/2193-1801-2-228","article-title":"Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India","volume":"2","author":"Choudhury","year":"2013","journal-title":"Springerplus"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1017\/S1479262119000273","article-title":"Population genetics analyses of North-East Indian indigenous rice landraces revealed divergent history and alternate origin of aroma in aus group","volume":"17","author":"Chakraborty","year":"2019","journal-title":"Plant Genet. Resourc."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Roy, S., Marndi, B.C., Mawkhlieng, B., Banerjee, A., Yadav, R.M., Misra, A.K., and Bansal, K.C. (2016). Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the North-Eastern Himalayas of India. BMC Genet., 17.","DOI":"10.1186\/s12863-016-0414-1"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1270\/jsbbs.52.143","article-title":"Loss-of-function of a rice Gibberellin Biosynthetic gene, GA20 oxidase (GA20ox-2), led to the rice \u2018Green revolution\u2019","volume":"52","author":"Ashikari","year":"2002","journal-title":"Breed. Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1007\/s10528-013-9584-y","article-title":"Identification of an Isogenic Semi-dwarf Rice Cultivar Carrying the Green Revolution sd1 Gene by Multiplex Codominant ASP-PCR and SSR Markers","volume":"51","author":"Naito","year":"2013","journal-title":"Biochem. Genet."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1111\/j.1744-7909.2006.00248.x","article-title":"Genetic analysis and mapping of the dominant dwarfing gene D-53 in rice","volume":"48","author":"Wei","year":"2006","journal-title":"J. Integr. Plant. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1111\/j.1439-0523.2008.01495.x","article-title":"High-resolution mapping revealed a 1.3-Mbp genomic inversion in Ssi1, a dominant semidwarf gene in rice (Oryza sativa)","volume":"128","author":"Miura","year":"2009","journal-title":"Plant Breed."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/j.1439-0523.2007.01444.x","article-title":"Characterizations and molecular mapping of a novel dominant semi-dwarf gene Sdd(t) in rice (Oryza sativa)","volume":"127","author":"Liu","year":"2008","journal-title":"Plant Breed."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1266\/ggs.84.209","article-title":"Dominant mutation of TWISTED DWARF1 encoding an alpha-tubulin protein causes severe dwarfing and right helical growth in rice","volume":"84","author":"Sunohara","year":"2009","journal-title":"Genes Genet. Syst."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1111\/j.1744-7909.2011.01031.x","article-title":"Genetic analysis and fine mapping of a novel semidominant dwarfing gene LB4D in rice","volume":"53","author":"Liang","year":"2011","journal-title":"J. Integr. Plant Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1007\/s00438-008-0406-6","article-title":"Isolation and characterization of dominant dwarf mutants, Slr1-d, in rice","volume":"281","author":"Asano","year":"2009","journal-title":"Mol. Genet. Genom."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Piao, R., Chu, S.-H., Jiang, W., Yu, Y., Jin, Y., Woo, M.O., Lee, J., Kim, S., and Koh, H.J. (2014). Isolation and Characterization of a Dominant Dwarf Gene, D.-h, in Rice. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0086210"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"14357","DOI":"10.1038\/srep14357","article-title":"A gain-of-function Bushy dwarf tiller 1 mutation in rice microRNA gene miR156d caused by insertion of the DNA transposon nDart1","volume":"5","author":"Maekawa","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/j.pld.2018.09.001","article-title":"Mapping and breeding value evaluation of a semi-dominant semi-dwarf gene in upland rice","volume":"40","author":"Chen","year":"2018","journal-title":"Plant Divers."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1270\/jsbbs.63.164","article-title":"Genetic analysis and fine mapping of a semi-dwarf gene in a centromeric region in rice (Oryza sativa L.)","volume":"63","author":"Chen","year":"2013","journal-title":"Breed. Sci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1007\/s12041-019-1131-0","article-title":"Genetic diversity and population structure analysis of Asian and African aromatic rice (Oryza sativa L.) genotypes","volume":"98","author":"Mishra","year":"2019","journal-title":"J. Genet."},{"key":"ref_34","unstructured":"Sharma, S.D., and Rao, U.P. (2004). Role of Indian Agricultural Research Institute in genetic improvement of rice varieties in India. Genetic Improvement of Rice Varieties in India, Today & Tomorrow\u2019s Printers and Publ."},{"key":"ref_35","unstructured":"IRRI (2013). Standard Evaluation System for Rice, International Rice Research Institute. [5th ed.]."},{"key":"ref_36","first-page":"134","article-title":"A rapid method for identifying different dwarfing genes in rice","volume":"1","author":"Kumar","year":"1984","journal-title":"Rice Genet. Newsl."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"4321","DOI":"10.1093\/nar\/8.19.4321","article-title":"Rapid isolation of high molecular weight DNA","volume":"8","author":"Murray","year":"1980","journal-title":"Nucleic Acids Res."},{"key":"ref_38","first-page":"13","article-title":"\u201cPerfect\u201d markers for the rice sd-1 semi-dwarfing gene","volume":"27","author":"Ellis","year":"2002","journal-title":"Int. Rice Res. Notes."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1093\/dnares\/9.6.199","article-title":"Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.)","volume":"9","author":"McCouch","year":"2002","journal-title":"DNA Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"9829","DOI":"10.1073\/pnas.88.21.9828","article-title":"Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations","volume":"88","author":"Michelmore","year":"1991","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1016\/0888-7543(87)90010-3","article-title":"Mapmaker: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations","volume":"1","author":"Lander","year":"1987","journal-title":"Genomics"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler Transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence alignment\/map (SAM) format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e115","DOI":"10.1093\/nar\/gks596","article-title":"Primer3\u2014New capabilities and interfaces","volume":"40","author":"Untergasser","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1016\/S0168-9525(02)02820-2","article-title":"Web-based primer design for single nucleotide polymorphism analysis","volume":"18","author":"Neff","year":"2002","journal-title":"Trends Genet."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1016\/j.plantsci.2015.08.020","article-title":"Improvement of Basmati rice varieties for resistance to blast and bacterial blight diseases using marker assisted backcross breeding","volume":"242","author":"Ellur","year":"2016","journal-title":"Plant Sci."}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/9\/9\/1198\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:09:43Z","timestamp":1760177383000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/9\/9\/1198"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,9,14]]},"references-count":46,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2020,9]]}},"alternative-id":["plants9091198"],"URL":"https:\/\/doi.org\/10.3390\/plants9091198","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,9,14]]}}}