Rice Genetics IV - IRRI books - International Rice Research Institute

Monocots and eudicots: Is there still colinearity between rice and Arabidopsis?The close alignment of genes between genomes spread over 60 million years of cerealevolution begs the question as to whether synteny remains over the 140–200-million-year monocot-eudicot divide. Significant residual colinearity would mean thatmany cereal genomics approaches could be serviced by the Arabidopsis DNA sequence.This question has been addressed by several studies (Paterson et al 1996, Devoset al 1999, van Dodeweerd et al 1999). The consensus is that, although there is someevidence of residual synteny in some regions of the genome, gene sequences andorders have diverged so much that very little predictive power remains in the comparisons.The recent revelations of extensive local chromosome segment duplicationthat was preceded by a polyploidization event in Arabidopsis (The Arabidopsis GenomeInitiative 2000) would seem to definitely preclude the wide-scale use ofArabidopsis gene orders to approach cereal genetics. Nevertheless, the question shouldremain open a little longer as enough contiguous genomic rice sequence becomesavailable to compare directly with that of the model eudicot.ReferencesAhn SN, Tanksley SD. 1993. Comparative linkage maps of the rice and maize genomes. Proc.Natl. Acad. Sci. USA 90:7980-7984.Bennetzen JL. 2000. Comparative sequence analysis of plant nuclear genomes: microcolinearityand its many exceptions. Plant Cell 12:1021-1029.Chao S, Sharp PJ, Worland AJ, Warham EJ, Koebner RMD, Gale MD. 1989. RFLP-basedgenetic maps of wheat homoeologous group 7 chromosomes. Theor. Appl. Genet. 78:495-504.Chen M, San Miguel P, Bennetzen JL. 1998. Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. Genetics 148:435-443.Devos KM, Atkinson MD, Chinoy CN, Francis HA, Harcourt RL, Koebner RMD, Liu CJ,Masojc P, Xie DX, Gale MD. 1993. Chromosomal rearrangements in the rye genome relativeto that of wheat. Theor. Appl. Genet. 85:673-680.Devos KM, Beales J, Nagamura Y, Sasaki T. 1999. Arabidopsis-rice: Will colinearity allowgene prediction across the eudicot-monocot divide? Genome Res. 9:825-829.Devos KM, Pittaway TS, Reynolds A, Gale MD. 2000. Comparative mapping reveals a complexrelationship between the pearl millet genome and those of foxtail millet and rice.Theor. Appl. Genet. 100:190-198.Devos KM, Wang ZM, Beales J, Sasaki T, Gale MD. 1998. Comparative genetic maps offoxtail millet (Setaria italica) and rice (Oryza sativa). Theor. Appl. Genet. 96:63-68.Dufour M, Deu M, Grivet L, D’Hont A, Paulet F, Glaszmann JC, Hamon P. 1997. Constructionof a composite sorghum genome map and comparison with sugarcane, a related complexpolyploid. Theor. Appl. Genet. 94:409-418.Feuillet C, Keller B. 1999. High gene density is conserved at syntenic loci of small and largegrass genomes. Proc. Natl. Acad. Sci. USA 96:8265-8270.Foote T, Roberts M, Kurata N, Sasaki T, Moore G. 1997. Detailed comparative mapping ofcereal chromosome regions corresponding to the Ph1 locus in wheat. Genetics 147:801-807.86 Gale et al