Oryza sativa Japonica Group
Rice (Oryza sativa L.) is a major cereal crop and also a model grass plant for functional genomic study. Here, we resequenced the genomes of Wu-Yun-Geng7, one landrace of East China to ~34x raw data coverage. We identified 34,794 InDels (6-100 bp) from re-sequencing data of rice cultivars: Wu-Yun-Geng7 and Guang-Lu-Ai4. Furthermore, we developed 205,659 InDels in 8 japonica and 9 indica cultivars and 2,681 InDels showed subgroup-specific pattern. PCR analysis of subgroup-specific markers indicated that the precision reached 90% (86 of 95). Finally, we integrated the InDels/markers information into a website (Rice InDel Marker Database, RIMD, http://202.120.45.71/) for the researchers. The subgroup markers we have identified should be valuable for identifying agronomically important genes and for breeding in rice.
cultivar
japonica
dev_stage
reproduction
geo_loc_name
China: Shanghai
tissue
leaf
biomaterial_provider
Zhanglab, Shanghai Jiao Tong University
BioSampleModel
Plant