Plant & Animal Genomes XIV Conference Plant & Animal Genomes XIV ConferenceJanuary 14-18, 2006
Town & Country Convention Center
San Diego, CA
Hiroyuki Kanamori , Jianzhong Wu , Shoko Saji , Takahito Bito , Wataru Karasawa , Rie Yoshihara , Satomi Hosokawa , Michie Shibata , Yukiyo Ito , Mayu Yamamoto , Kanako Kurita , Ari Kikuta , Nobukazu Namiki , Takashi Matsumoto , Takuji Sasaki
A comprehensive molecular characterization of rice germplasm will be indispensable in developing novel rice breeding strategies in the future. The International Rice Genome Sequencing Project (IRGSP) has completed the sequencing of Oryza sativa L. ssp. japonica cv. Nipponbare genome that must now be used as a fundamental tool for developing new breeding materials from various rice genetic resources. The genus Oryza consists of the two cultivated species (O. sativa and O. glaberrima) and 21 wild species with a wide range of variation, which has not been explored at the genome level. In this study, we analyzed the phylogenetic relationship among species based on the distribution pattern of SINEs and the genome diversity at the nucleotide level using EST markers. In particular, p-SINE1 is known to be a good candidate to estimate the phylogenetic relationship within the AA genome of Oryza. We selected and designed primer pairs specific for 31 p-SINE1 members with particular loci on the rice chromosomes and 943 EST primer pairs (designed from 3'-UTR) located at 500 kb interval in each chromosome of Nipponbare. A total of 21 species (more than 60 strains) of the wild rice (AA-HHJJ genomes) were screened using the above primers. We found that most of the primer pairs specific for the 31 p-SINE1 members showed insertion polymorphism among the closely related wild rice species belonging to the O. sativa complex (AA genome) while no polymorphism or even no corresponding fragments of PCR amplification could be obtained for the other wild rice species (BB-HHJJ genomes). On the other hand, the degree of conservation of 3'-UTR regions is more than 90% for the AA genome, 50-70% for BB, BBCC, CC, CCDD and EE genomes that comprise the O. officinalis complex, and less than 40% for the FF, GG and HHJJ genomes. These results clarify the utility of p-SINE1 members and the Nipponbare EST markers for understanding the evolutionay history as well as genome diversity of the genus Oryza. This study was supported by grants from the Ministry of Agriculture, Forestry and Fisheries of Japan (GC1108, GD2007).