Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

Genome-Wide Sequence Comparison Of Centromeric Regions And BAC-Landing On Chromosomes Provide New Insights Into Centromere Evolution Among Wheat, Brachypodium, And Rice

Lili Qi¹ , Bernd Friebe² , Yong Q. Gu³ , Chen Qian² , Bikram S. Gill²

¹  USDA-ARS, Northern Crop Science Laboratory, PO Box 5677, Fargo, ND 58105-5677 USA

²  Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506-5502, USA

³  USDA-ARS, Genomics and Gene Discovery Research Unit, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710 USA

As an emerging model system, the nearly finished sequence of Brachypodium distachyon will provide new insights into comparative and functional genomics of grass species. However, centromeres of B. distachyon are unlikely to be sequenced and assembled precisely similar to many other sequenced organisms because of their highly repeated structure. Three independent but complementary approaches were pursued to study centromeric region homologies among the chromosomes of wheat, Brachypodium, and rice. The genes present in pericentromeres of the basic set of seven chromosomes of wheat and the Triticeae, and the 80 rice centromeric genes spanning the CENH3 binding domain of centromeres 3, 4, 5, 7, and 8 were used as “anchor” markers to identify centromere locations in the B. distachyon chromosomes. Fifty-three B. distachyon BAC clones anchored by wheat pericentromeric ESTs were used as probes for BAC-FISH analysis of B. distachyon mitotic chromosomes. Integrated sequence alignment and BAC-FISH data were used to define the five possible centromere regions of B. distachyon corresponding to four wheat and five rice centromere regions. The following syntenic relationships of centromeres were evident for Brachypodium (Bd), wheat (W) and rice (R): Bd1-W2-R7, Bd2-W1-R5, Bd3-W7-R8, Bd4-W4-R11, and Bd5-R4. The positions of 30.2 Mb in chromosome Bd2, 19.5 Mb in Bd3, and 22.5 Mb in Bd4 may represent the core centers of centromeres for these three chromosomes. Five B. distachyon centromeres were traced back to the centromeres of the five ancestral chromosomes of grass genomes. This investigation provides a platform for studying the centromere evolution of grass genomes.