A Preliminary Investigation Into Some Regions Of The Rice Genome With The Support Of Physical Maps

As the most planted crop in China, rice (Oryza sativa L.) is also an important model plant in scientific research. The cultivated rice in China belongs to two subspecies:Oryza sativa L. japonica and Oryza sativa L. indica. Comparative genomics is an important method to unlock the potential of Oryza genome, and physical map is a useful tool for it. In this study we did a preliminary investigation into a QTL region and some other regions of the rice genome with the support of physical maps.Physical maps for both rice varieties Zhenshan 97 and Minghui 63 have been constructed in our laboratory, and were integrated with the genetic maps which were made using the two varieties as mapping parents. According to the initegrated maps, some structural differences at the long arm end of chromosome 3 have been found which are aligned to numerous QTLs reported as well as a QTL for grain yield that Professor Yu Sibin of our University is currently studying. There remain some gaps in this region on both physical maps. After the sizes of the gaps were analyzed, two ways were taken to fill the gaps. For a small gap, PCR method was used to clone the sequence with a primer pair designed according to the BAC end sequences (BES). For the bigger ones, hybridization method was used to screen the 10×coverage BAC library with 9 probes. Twenty four positive clones for Minghui 63, which closed one gap, and 31 clones for Zhenshan 97, which closed two gaps, have been obtained. Fingerprint analysis confirmed the continuity of these clones. At the same time, alignment between BAC end sequences and Nipponbare reference sequence reveals some putative SNPs in this region. Different methods were used to verify them. Our results showed that the putative Zhenshan 97 SNPs are not the real SNPs and come from BES errors, while the 23 putative Minghui 63 SNPs/InDels were all validated, of which 18 aligned to Nipponbare unique sequences located in ORFs, which may cause functional changes.Comparative analysis of rice variety Zhonghua 11 BES revealed many putative SNPs and specific repetitive sequences in the genome of Zhonghua 11. Verification results showed that more than 99.2% of putative SNPs are correct and only about 0.8% are false. Blast analysis demonstrated that about 44.2% of these SNPs are located in coding regions which may play roles in gene functions. Some representative putative Zhonghua 11 specific repetitive sequences were analyzed via Southern hybridization. The results showed a high accordance with what the computer predicted.