Research On The Genetic Diversity And Origin Of Weedy Rice In China By SSR And Special Gene Sequence

As direct-seeding cultivation is prevalent in rice production areas, weedy red rice becomes the most harmful weed only second to barnyardgrass in the paddy field. It has shattering and seed dormancy as distinct character with variable morphological traits. Due to extreme similarity to the cultivated rice, it’s difficult to distinguish them in the field, especially at the early period of growth. Weedy rice varied largely in morphological characters, however, in some area the genetic diversity index based on genetic markers is very low. So it is necessary to study on the genetic diversity and relationship between different cultivated areas at a large geographic scale in order to enucidate the genetic diversity as well as origin and evolution of weedy rice. It is significant theoretically and practically to both research and practice of weedy rice control.The occurrence of weedy rice has been reported in several provinces in China. In order to understand the occurrence and distribution of weedy rice in China further, we investigated the main rice production area from 2006 autumn.1303 accessions of weedy rice samples were collected and planted in the experiment farm to observe their morphological traits. Based on the investigation. The investigation displayed that rice filed in middle of Jiangsu, west of Guangdong, Liaoning and Heilongjiang had been seriously infested by weedy rice, which increases the cost of farm management, decrease rice production and quality. The rice production was under threatened. In other regions there was suspecious weedy rice too. We found that the occurrence of weedy rice attributed to the labor-saving cultivation such as direct-seeding and wheat-rice interplanting. As continual application of the labor-saving cultivations, weedy rice infestation causes more serious damage to the rice production. The rice production areas planning to apply direct-seeding cultivation face the potential risk of weedy rice occurrence.Rice genetic markers of SSR were employed in the analysis of genetic diversity of weedy rice and uncertain samples. We had selected 21 pairs of SSR markers on nuclear genome and one pair of SSR marker on mitochondria genome. These markers produced 64 bands in the total. The results showed that the genetic diversity index of weedy rice is relatively low, but the genetic diversity index varied largely in different areas. The weedy rice populations in Liaoning have a low genetic diversity, the total genetic diversity index is h= 0.09, Tieling population show the highest index with 0.09. The index of weedy rice populations in Jiangsu province varied in a large scale, higher in Huaian, Yangzhou and Taizhou with diversity index h is 0.28,0.11,0.15 respectively; and lower in other areas, Jiangdu and Rugao populations have the least index h=0.02. The diversity index of Guangdong province is relatively higher with h= 0.16, except the Yangjiang population with h=0.07. The five weedy rice populations in the western area of China, Jiangyou, Kunming, Anshun, Changde and Liujiang, also had a relatively low diversity index. The analysis of genetic differentiation showed that contrast to less differentiation of Guangdong and Liaoning, in Jiangsu province weedy rice populations had more differentiation between each other. The Analysis of molecular variance (AMOVA) also displayed that the genetic diversity mainly exist among the three provinces. The differentiation between populations is low in populations which belong to the same province, except Jiangsu, in which there are two main ecotype of weedy rice with large differentiation each other. The cluster based on the Nei’s genetic distance between populations divide the whole weedy rice into two main group, correspondence to the two rice subspecies indica and japonica. The weedy rice from Liaoning and other northeast area, as well as Kunming and some samples from Lianyungang were involved in japonica-like group; the weedy rice populations from Guangdong province and Jiangsu middle area are involved in indica-like group, which also contain weedy rice collected from Liujiang, Jiangyou and Anshun. Based on the individual genetic information, Principle Component Analysis (PCA) gave the similar result, weedy rice and the cultivated rice overlap with each other. The wild rice individuals are distributed between indica and japonica group area. In the cluster tree we can found that weedy rice, like that from Guangdong, Liaoning and Kunming had a more short distance to the local cultivated rice. In Jiangsu province, the current cultivated rice mainly is japonica which is far away from the indica-like weedy rice found in the field. The application of STRUCTURE to analysis of population genetic structure and the relationship between weedy rice and cultivated rice showed when K=6, Liaoning and Guangdong weedy rice share genetic background with their local rice, distinct different to rice from other provinces. The weedy rice populations from Jiangsu province had a complex population structure, most of which are different to present cultivated rice, and some of which show close relationship to the Guangdong province weedy rice. Some japonica-like individuals in Jiangsu province show a close relationship to wild rice in the structure analysis. Based on the above results of genetic distance and cluster analysis, it may be concluded that weedy rice maybe originated from dedomestication of cultivated rice, possibalely without participation of wild rice and hybridization of indica and japonica rice, or hybridization of wild rice and cultivated rice.Furthermore, we analyzed the relationship of weedy rice and wild rice based on the sequence alignment of a region of nuclear pseudogene V-ATPase B-subunit (p-VATPase). The results showed that indica-like weedy rice and japonica-like weedy rice locate on separately clade of the phylogenetic tree constructed on the worldwide wild rice and rice, and the two ecotype of weedy rice maybe originated independently. In Liaoning and Guangdong, weedy rice and cultivated rice from the same province shared the same haplotype respectively, and the haplotype of the two ecotype of weedy rice had a more close relationship to other cultivated rice in public database. Korean weedy rice also showed a close relationship to three cultivated rice in the public database. Malaysia and Vietnam weedy rice was involved in the Guangdong evolution clade. The red pericarp gene of the weedy rice had been sequenced. The key deletion mutation in the sixth exon of red pericarp gene decided the change of red pericarp of wild rice to white pericarp of cultivated rice. The sequence results of the weedy rice show that all of them with red pericarp, including the samples selected from Liaoning, Guangdong, Jiangsu, Kunming, and the foreign weedy rice from Vietnam and Korean, got back the 14bp sequence that had been lost in the white rice, which are consistent with wild rice in the RC genotype. How those weedy rice got back this deletion sequence is still in puzzle. The main effect gene of shattering SH4 (Shattering 4), which is located on chromosome 4, was sequenced in an individual of Shenyang weedy rice of easy shattering. In rice genome, G/T mutation of 237 site on SH4 gene caused elimination of seed shattering. The sequence show a contrast result to the expectation, the weedy rice SH4 gene didn’t get the key mutation same to wild rice, still sharing the same genotype with rice. The gene controlling shattering of weedy rice maybe located on other chromosome. It is need to do more work to bring the genetic base of weedy traits of weedy rice to light.