Study On Waxy Gene Diversity In Rice From China

Rice farming in the world could trace back to 10,000 years ago, which has a long history. The rice is the staple food of Chinese people, but due to the continuous improvement of food production and the people's living standards, people's demand for rice shift from quantity to quality requirements gradually, therefore, the quality traits of rice is concerned by consumers and breeders more and more. The starch is the main component in rice, and the amylose content is one of the most important index for measuring the quality of rice, the gene which controlls the amylose content is Waxy gene. China is rich in cultivated rice (Oryza sativa L.) and common wild rice (Oryza rufipogon Griff.) germplasm resources, by studying the diversity of Waxy gene in the rice germplasm, we can explore the route of the origin and evolution about this gene, and the result of association analysis between the nucleotide polymorphism and the amylose content can be applied into breeding practice, which can provide an important theoretical basis for protecting and utilizing superior genetic resources in China.Ninety-eight accessions of cultivated rice (Oryza sativa L.) and 134 accessions of common wild rice(Oryza rufipogon Griff.) from the previous established micro-core collection of Chinese rice germplasm resources were studied by amplifying the Waxy gene using segmental designed primers, sequencing the fragment, assembling the contigs and aligning the entire gene (about 4953bp) aiming to examining the sequence polymorphisms and diversity. The Waxy gene sequence diversity in different cultivated rice and common wild rice strains was analyzed to study the relationship of origin and evolution, meanwhile the association analysis between the Waxy gene sequence polymorphisms and amylose content phenotype was carried out to identify the certain genotype that are closely related to the phenotype. The results are as follows:1. Total 51 nucleotide polymorphism loci were identified in 98 cultivated rice accessions on average one polymorphism per 98bp; and total 226 nucleotide polymorphism loci in 134 common wild rice accessions on average one polymorphism per 24bp; the sequence polymorphism in common wild rice was about fourfold as that in cultivated rice, this is due to common wild rice as the ancestors of cultivated rice undergoing a low selection pressure and keep rich allele variations.2. The analysis of gene diversity between the glutinous rice and non-glutinous rice, indica rice and japonica rice,cultivated rice and common wild rice showed that the nucleotide diversity (π) in wild rice accessions was about two times as that in the cultivated rice accessions, theπin non-glutinous rice accessions was about sixfold as that in the glutinous rice accessions, theπin indica rice was equal to that in japonica rice, which indicated that the glutinous rice suffered strong selection pressure during the domestication, and the parallel evolution relationship may exist between indiaca and japonica.3. Based on the analysis of linkage disequilibrium about the sequence polymorphisms of Waxy gene in the cultivated rice accessions, strong LD structure was identified through the entire region of this gene. Then this sequence polymorphisms were used into downstream association analysis with the phenotype trait, 23bp InDel and G/T polymorphism loci were found that they significantly correlated with amylose content, which can be applied into the MAS breeding program. 4. The relationship between the variation sites and the geographic location, the amylose content and the geographic location were carried out in cultivated rice accessions respectively, it showed that Chinese cultivated rice existed the evolution trends that from low to high latitude. The haplotype analysis, the phylogenetic and cluster analysis results indicated that the waxy mutations in Chinese rice germplasm derived from the provinces of Guangdong, Guangxi, and Hainan; the southern district of China was the origin center of Chinese cultivated rice.5. Many low frequency alleles were detected in common wild rice and cultivated rice landraces accessions which reflected these variations could reach the point of extinction at any time; common wild rice and cultivated rice landraces were rich in so many excellent genes and allele variations, which had great significance for enriching the narrowed genetic basis of cultivated rice modern variety and ensuring the food security; therefore, the protection to the common wild rice and cultivated rice landraces germplasm resources is a very important task.