Hybridization And Comparative Genomic Study Of Bamboo And Rice

Bamboos are members of the sub-family Bambusoideae within the grass family Poaceae. Bambusoideae is the most diversified subfamily in Gramineae, and can be distinguished from other groups of monocots by having woody culms, compound branching and highly developed root systems with very low frequencies of flowering. Bambusoideae is comprised of over 970 species, and is an important target of comparative genomic studies for understanding genetics, genomics and evolution of the Grass family.Previous studies have indicated that rice (oryza sativa) and bamboo are phytogenetically the closest among grasses. In fact, rice was oringinally classified into the subfamily Bambusoideae in the early studies, and was only recently considered as derived from an independent subfamily Ehrhartoideae. Rice has a relativley small genome and is the model plant for monocot species. There are sub-species for cultivated rice, namely japonica and indica.The genomes of both subspecies were fully sequenced in 2005.As bamboo rarely flowering, it is difficult to construct a genetic mapping population. The main of this study to carry out the genome-wide analysis of moso bamboo through comparative genomic approach using sequence information from rice (as well as sorghum) to identify candidate genes conserved both between bamboo and rice. Moreover, we intended to find bamboo-specific genes which will can be used in rice breeding. The main results are summarized as follows:(1) We generated hybrid seeds from the cross between rice (zhenshan 97A) and bamboo (Bambusa boniopsis). We used flow cytometry and SNP markers to demonstrate that the hybid seed contained DNA fragments derived from both bamboo and rice genomes.(2) This study is focused on analyzing the genome of moso bamboo(Phyllostachys pubesence), which is most widely grown with the highest economical value in China. Using flow cytometry we firstly estimated the genome size of moso bamboo as around 2034Mb, which is similar to that of maize (CV. B73) but significantly larger than that of rice. Furthermore, to evaluate the composition of the bamboo genome, approximately 1000 genome survey sequence were generated. Sequence analysis showed that the proportion of repeat element was 23.3% for the bamboo genome, which is significantly lower than that of the maize genome and similar to that of rice.(3) To validate the result from the GSS analysis,384 BAC clones were constructed using shoots of moso bamboo. We obtained 1.3Mb genomic sequences by sequencing 13 BAC clones with an insert size of over 100kb. A total of 112 non-transposable-element-related protein-coding genes were predicted in silico. We further estimated the amount and composition of repetitive elements in the bamboo genome using all of the large contigs (>10kb). The result showed that the content of repetitive elements in bamboo (36.2%) is similar to that in rice (39.5%), but significantly lower than that in maize (82.10%). This result is consistent with the evaluation based on GSS. Comparative genomic analysis indicated high levels of syntenies among bamboo, rice and soghum. The high levels of synteny between bamboo and rice suggest that rice is potentially a very useful model for decording Bambusoideae genome. It also suggests that the sorghum may be another useful reference for studying the bamboo genome.(4) We explored the use of rice SSR markers to study the genetic diversity in moso bamboo. Firstly,60 pairs of SSR primers were developed based on the moso bamboo genomic sequences obtained in this work. These primers subsequently used to assesse the genetic variability among 13 populaions of moso bamboo from 6 different provinces. The result showed that there is little genetic variability in moso bamboo. We then selected 120 rice SSR markers which distibuted evenly on the 12 chromosomes, and investigated their polymorphism in moso bamboo. Fourty-eight of these rice SSR primer pairs gave amplification product from the bamboo genome, representing a 40% success rate. These 48 primer pairs were then used to investigate the genetic diversity in 13 moso bamboo populations. Only five pairs of SSR primers gave polymorphic amplification bands, indicating again that the degree of genetic variability is very low in moso bamboo.