The Study On Indica-Japonica Differentiation And Testing The Seeds Purity Of Hybrid Rice By SSRs And InDels

The rice genome (Oryza sativa ssp. japonica cultivar Nipponbare) was completely sequenced by the IRGSP in December, 2004. Another rice genome (Oryza sativa ssp. indica cultivar 93-11) also has had the fine map. Indica cultivar GLA 4 had been sequenced for 8.4Mb. Sequence information of these rice caltivars has begun to be greatly used in gene clone and functional genomics.The study on indica-japonica genetic diversity and inter-subspecific differentiation will be very helpful for us to further understand the origin of rice domestication, find new genes, better use of inter-subspecific heterosis. Here, the pedigrees of three sequenced rice cultivars were analyzed, the indica/japonica-specific markers were found from the selected markers, the seed purity were detected by SSR markers. Main results were summarized as follows:1. 46 typical indica and 47 typical japonica cultivars were selected from 443 materials judged by the total scores of Cheng's index. 152 markers (46 InDels and 106 SSRs) polymorphic between Nipponbare and 93-11 were selected based on the sequence information. Through the comparison of the genetic diversity of 53 SSRs and 47 InDels among 46 japonica and 47 indica rice varieties, we found that InDels' polymorphism had larger quantity and more stable amplification, and was easier to detect than SSRs.2. A method for simple detection of InDel ampification product was estabished, through multiple loading on the same agarose gel.3. The pedigrees of three sequenced rice cultivars were analyzed to show a majority of japonica components together with minor indica source in 'Nipponbare' and vice versa in '93-11', while all ancestors of 'Guang lu ai 4' seemed to be indica lines.4. Much higher InDel and SSR diversity between groups than within groups implies that the marker polymorphisms between 'Nipponbare' and '93-11' represent a large proportion of inter-subspecific diversity. All cultivars were divided into indica and japonica groups without overlapping when clustered by Cheng's index, InDels and SSRs. So does the AMONA anlysis.5. About 85% of indica cultivars and more than 90% of japonica cultivars were confirmed to have the same PCR banding patterns as '93-11' and 'Nipponbare', respectively. Some polymorphic loci between 'Nipponbare' and '93-11' cannot be validated in other indica and japonica cultivars. 17 inter-subspecific markers were found.6. Through bioinformatic anlysis of 17 inter-subspecific markers, 5 markers were located in the hypothetic genes.