Genetic Differentiation Of Indica, Japonica Rice And Its Relationship With Geographical Distribution

Indica-japonica variation represents the most significant genetic differentiation in Asian cultivated rice, and it has also been the focus of how to use genetic differentiation of cultivated rice. Based on the differentiation in characteristics of morphology, physiology, genetics and their habitat, especially when significant differentiated varieties shows obvious reproductive isolation and sterility in F1 hybrids, Asian cultivated rice was classified into two sub-species Oryza sativa L. subsp. indica Kato and subsp. japonica Kato. In this study Insertion/Deletion molecular markers (InDel) was first used in indica-japonica genetic differentiation of cultivated rice and identification of the degree of indica-japonica differentiation. Based on that indica rice and japonica rice adapt to different environmental conditions we analyzed the differentiation and distribution patterns of cultivated rice along altitude and latitude gradients, and also accurately identified the type of rice. In order to exploring the difference in genome of typical indica and typical japonica, we analyzed gene sequence which is located near to the InDel molecular markers. This research will facilitate indica-japonica differentiation theoretical research, strategic utilization and conservation of rice germplasm, and provide scientific data for introducing different type of rice to certain place to achieve better agronomic characteristics. The mainly results of this study are:1. In this study, we analyzed 203 varieties and 14 wild accessions of rice collected from localities across an altitude gradient between 450 and 2,350 m above sea level in Yunnan, China, applying the "InDel molecular index" developed recently. Results from PCA of the InDel data demonstrated significant genetic differentiation of rice varieties from Yunnan into indica and japonica types. A few cultivars and nearly all wild rice accessions showed only moderate or no differentiation. Further analyses demonstrated a clear distribution pattern of the rice varieties in the mountainous region:indica varieties were grown across the entire altitude gradient in the sampling areas, but most japonica varieties were found above 1,400 m. These results clearly indicated that indica rice could be cultivated in areas at much higher altitudes than those categorized by the traditional methods. The knowledge opens a new dimension for introducing indica rice varieties to mountainous regions at higher altitudes and for selecting rice germplasm in these regions. In addition, the pattern of significant indica-japonica differentiation in rice varieties from Yunnan suggested the exotic origin of cultivated rice, which did not support the hypothesis that Yunnan is a part of the center of origin of rice, although it is certainly one of the centers of genetic diversity for rice.2. Asian cultivated rice has significantly differentiated into indica and japonica subspecies that have extensive distribution worldwide. To determine genetic differentiation of Asian cultivated rice across a latitudinal gradient, a total of 387 Asian cultivated rice varieties, five African rice varieties, and 52 wild rice accessions collected from a wide range of Asian countries and other regions were analyzed applying the InDel molecular index. The principal component analysis classified Asian cultivated rice into two distinct groups, which demonstrated significant molecular genetic differentiation of Asia cultivated rice, while all wild rice and African cultivated rice showed no evident differentiation. The results clearly indicated that Asian cultivated rice has differentiated profoundly since its domestication and during its adaptation to various environments, contrasting with wild rice and African rice. Analysis of the geographic distribution indicated a clear pattern for the different types of rice, in which indica rice varieties were found across a wide range of latitudes from -2°S to 40°N and japonica varieties were mostly focused in the high latitude areas greater than 15°N. Most intermediate types of rice originated in regions at latitudes lower than 27°N. Correlation patterns between rice types and temperature along the latitude gradients suggested that indica rice was considerably less sensitive to temperature along the latitude ranges, but japonica rice was highly sensitive to the temperature at different latitudes. The molecular genetic intermediate type of rice was also sensitive to temperature. We conclude that the distribution pattern of different types of Asian rice across large latitudinal ranges is the consequence of their adaptation in relation to ecological factors of the environment, especially temperature. This has an important implication in breeding of hybrid rice by selecting properly differentiated indica and japonica parents.3. In order to understand the indica-japonica differentiation information in genome which linked with InDel molecular marker and to learn the molecular mechanism of indica-japonica differentiation, in this study we analyzed sequence approached closely to 34 InDel molecular markers and found:there are 50 sequences have functional domain which means these sequence could be real gene. Based on the PCR we get these sequences separately from typical indica and typical japonica. Further alignment of sequencing result showed that there are molecular variation between the sequence from typical indica 93-11 and typical japonica niponbare:Near the molecular marker R2M10, the sequences from 93-11 and niponbare have 90 bases change; R4M43, there are 19 bases change; R8M46, there are 18 variation in sequence; R3M10, there is one variation in sequence, there is one deletion mutation in japonica at the position of 420bp which make one shift mutation in related protein sequence; it was a termination beforehand in indica at the position of 609bp. Understanding these predicted gene sequences and further analysis of their domain and function, will help us to understand the selection process of indica-japonica variation. This study has very important implication in indicating the origin, differentiation and dimension of indica-japonica variation, and also in providing the genetic information for the mechanism of indica-japonica variation.