title: The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica.
abstract: Common wild rice (Oryza rufipogon) plays an important role by contributing to modern rice breeding. In this paper, we report the sequence and analysis of a 172-kb genomic DNA region of wild rice around the RM5 locus, which is associated with the yield QTL yld1.1. Comparative sequence analysis between orthologous RM5 regions from Oryza sativa ssp. japonica, O. sativa ssp. indica and O. rufipogon revealed a high level of conserved synteny in the content, homology, structure, orientation, and physical distance of all 14 predicted genes. Twelve of the putative genes were supported by matches to proteins with known function, whereas two were predicted by homology to rice and other plant expressed sequence tags or complementary DNAs. The remarkably high level of conservation found in coding, intronic and intergenic regions may indicate high evolutionary selection on the RM5 region. Although our analysis has not defined which gene(s) determine the yld1.1 phenotype, allelic variation and the insertion of transposable elements, among other nucleotide changes, represent potential variation responsible for the yield QTL. However, as suggested previously, two putative receptor-like protein kinase genes remain the key suspects for yld1.1.
authors.affiliation: School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia. song.beng.kah@artsci.monash.edu.my
authors.forename: Beng-Kah
authors.initials: BK
authors.lastname: Song
authors.forename: Ingo
authors.initials: I
authors.lastname: Hein
authors.forename: Arnis
authors.initials: A
authors.lastname: Druka
authors.forename: Robbie
authors.initials: R
authors.lastname: Waugh
authors.forename: David
authors.initials: D
authors.lastname: Marshall
authors.forename: Kalaivani
authors.initials: K
authors.lastname: Nadarajah
authors.forename: Soon-Joo
authors.initials: SJ
authors.lastname: Yap
authors.forename: Wickneswari
authors.initials: W
authors.lastname: Ratnam
mesh_terms: D020029:Base Pairing / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial; D002999:Clone Cells; D018744:DNA, Plant / Q000235:genetics*; D005091:Exons / Q000235:genetics; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics*; D007438:Introns / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D018744:DNA, Plant