Abstract
BackgroundUnderstanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing.ResultsThe genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment.ConclusionsOur findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal.
Highlights
Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces
The result of Principal component analysis (PCA) showed geographic structure in the japonica group: we found that the rice accessions from northern locations were assigned to one cluster, the rice accessions from southern locations were assigned to one cluster, and rice accessions from locations in the middle were assigned to one cluster (Fig. 3a)
We found the average haplotype diversity, gene diversity, and polymorphism information content (PIC) were 0.655, 0.755, and 0.725, respectively (Table S3-4), which indicated there was a high level of genetic diversity in landraces from Yunnan and these landraces were extremely important for enriching the rice gene pool
Summary
Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. We examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. Over the past 30 years, the phenomenon of large areas planted with single breeding varieties has increased the use of improved rice varieties, which has led to a narrow genetic base and an overall reduction in the genetic diversity of rice varieties grown in China (Xu et al 2016). Landrace diversity is found throughout the cultivated range for rice, making the landraces a rich source of genetic variation that includes such characteristics as high grain quality, wide adaptability, strong environmental tolerance, disease and insect resistance, and cultural uses, and can provide a valuable gene pool for the discovery and utilization of favorable genes. Over the past 50 years, local rice landraces have been largely replaced by genetically uniform, high-yielding modern varieties in many parts of China. Rice landraces are generally no longer planted in China, there are exceptions in some ethnic minority regions in Yunnan or Guizhou
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