title: The origin and evolution of fragrance in rice (Oryza sativa L.).
abstract: Fragrance in the grain is one of the most highly valued grain quality traits in rice, yet the origin and evolution of the betaine aldehyde dehydrogenase gene (BADH2) underlying this trait remains unclear. In this study, we identify eight putatively nonfunctional alleles of the BADH2 gene and show that these alleles have distinct geographic and genetic origins. Despite multiple origins of the fragrance trait, a single allele, badh2.1, is the predominant allele in virtually all fragrant rice varieties today, including the widely recognized Basmati and Jasmine types. Haplotype analysis allowed us to establish a single origin of the badh2.1 allele within the Japonica varietal group and demonstrate the introgression of this allele from Japonica to Indica. Basmati-like accessions were nearly identical to the ancestral Japonica haplotype across a 5.3-Mb region flanking BADH2 regardless of their fragrance phenotype, demonstrating a close evolutionary relationship between Basmati varieties and the Japonica gene pool. These results clarify the relationships among fragrant rice varieties and challenge the traditional assumption that the fragrance trait arose in the Indica varietal group.
authors.affiliation: Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Kovach
authors.forename: Mariafe N
authors.initials: MN
authors.lastname: Calingacion
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Fitzgerald
authors.forename: Susan R
authors.initials: SR
authors.lastname: McCouch
mesh_terms: D000483:Alleles; D001483:Base Sequence; D050728:Betaine-Aldehyde Dehydrogenase / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D005787:Gene Frequency; D014644:Genetic Variation; D005843:Geography; D006239:Haplotypes; D008969:Molecular Sequence Data; D009154:Mutation; D009812:Odorants; D012275:Oryza / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid
chemical_list: D010940:Plant Proteins; D050728:Betaine-Aldehyde Dehydrogenase
references.citation: Trends Genet. 2007 Nov;23(11):578-87
references.pmid: 17963977
references.citation: Theor Appl Genet. 2004 Sep;109(5):965-77
references.pmid: 15309297
references.citation: Nature. 2002 Oct 24;419(6909):832-7
references.pmid: 12397357
references.citation: Genetics. 2005 Mar;169(3):1631-8
references.pmid: 15654106
references.citation: Theor Appl Genet. 2008 Aug;117(3):353-68
references.pmid: 18491070
references.citation: Nature. 2006 Aug 10;442(7103):705-8
references.pmid: 16900200
references.citation: Genetics. 2009 Aug;182(4):1323-34
references.pmid: 19506305
references.citation: PLoS Genet. 2007 Sep;3(9):1745-56
references.pmid: 17907810
references.citation: Genetics. 2003 Oct;165(2):759-69
references.pmid: 14573486
references.citation: New Phytol. 2003 Mar;157(3):657-665
references.pmid: 33873418
references.citation: Curr Opin Plant Biol. 2009 Apr;12(2):185-92
references.pmid: 19185529
references.citation: Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15898-903
references.pmid: 12456878
references.citation: Plant Cell. 2008 Jul;20(7):1850-61
references.pmid: 18599581
references.citation: Genetics. 2002 Oct;162(2):941-50
references.pmid: 12399401
references.citation: Plant Biotechnol J. 2005 May;3(3):363-70
references.pmid: 17129318
references.citation: Theor Appl Genet. 1987 May;74(1):21-30
references.pmid: 24241451
references.citation: Plant Biotechnol J. 2008 May;6(4):416-23
references.pmid: 18331415
references.citation: Theor Appl Genet. 1996 Nov;93(7):1145-51
references.pmid: 24162494
references.citation: Ann Bot. 2004 Jan;93(1):67-73
references.pmid: 14602665
references.citation: Trends Plant Sci. 2009 Mar;14(3):133-9
references.pmid: 19230745
references.citation: Plant Sci. 2006 Oct;171(4):505-14
references.pmid: 25193648
references.citation: Plant Mol Biol. 2008 Nov;68(4-5):439-49
references.pmid: 18704694
references.citation: Theor Appl Genet. 1992 Sep;84(7-8):825-8
references.pmid: 24201481
references.citation: PLoS Genet. 2007 Aug;3(8):e133
references.pmid: 17696613