| Dissecting the variations in population (including morphological variations and genetic variations) and corresponding divergent patterns is one of the central topics in population genetics and evolutionary biology. Isolation by distance (IBD) was considered to be the main factor driving population divergence. Recently, a bench of researches indicated local adaptation due to heterogeneous habitats would lead to population divergence as well. However, few works had surveyed the combined effects of IBD and DBA on population divergence. Oryza rufipogon Griff., the ancestor of Asia cultivated rice (O. sativa), has a wide distribution range across subtropical and tropical Asia where the biotic and abiotic factors vary in isolated marshlands of O. rufipogon populations. We have no idea whether the heterogeneity in habitats would lead to local adaptation that driving population divergence. Here, O. rufipogon was used as a model. We applied common garden trials, molecular marker assays and the next-generation resequencing technology to investigate the pattern of morphological and genetic variations between O. rufipogon populations. The aim was to reveal the effects of IBD and IBA on population divergence and the mechanism shaping the distribution pattern of population variations of O. rufipogon. The main results were listed below:1) We characterized the morphological variations of O. rufipogon 72 populations including 1102 samples across the whole distribution range under three common garden conditions. O. rufipogon showed significant phenotypic plasticity under different environmental conditions. Within the common garden, the divergent pattern of morphological variations of O. rufipogon was influenced by the climatic variables according to the population locations. Plant height, biomass, and heading date were the main differentiated traits among populations according to canonical correlation analyses (CCA). Plant height and heading date were significant correlated with annual mean temperature (r=0.638,p＜0.05; r=0.675,p<0.05); sexual reproduction traits, such as seeds production, the single spike weight and mature seed ratios were correlated with isothermality and the mean temperature of coldest month, respectively. The populations of O. rufipogon were divided into three groups according the PCA of climatic variables:subtropical monsoon climate group (SMCR), tropical monsoon climatic group (TMCR), and tropical climatic group (TCR). The traits variations of SMCR were affected mainly by temperature, the precipitation greatly influenced the pattern of traits variations of TMCR, whereas the morphological traits of TCR seemed to be less impacted by climate factors. Furthermore, the allometric exponents differed between the climatic groups, indicating trade-off between sexual reproductive and growth investments due to climatic changes. These results implied that the environmental factors correlating with morphological variations between O. rufipogon populations were different among the three climate groups, suggesting local adaptation.2) We used six microsatellites to estimate genetic divergence between O. rufipogon populations worldwide. We found relatively high differentiation (Fst=0.362) between populations. The populations could be briefly clustered into two main genetic groups (Ruf I and Ruf II), showing a clinal change from northeast to southwest. The genetic divergence pattern was identical to that of phenotypes; Ruf I was mainly in SMCR, and Ruf II was in TMCR and TCR. The Qst-Fst test indicated heading date was adaptively divergent.3) The fine-scale genetic structure, effective population size and outcrossing rate of 12 O. rufipogon populations from the subtropical monsoon climatic region (SMCR) were investigated with 12 microsatellites to detect the genetic variations. The distribution pattern of individuals of O. rufipogon is aggregative within population; a corresponding positive spatial genetic structure was detected by spatial autocorrelation analyses, indicating IBD at fine-scale. The effective population size Ne ranged from 35 to 4560; and was found to be significant correlated with the actual population size (r=0.969,p＜0.01), suggesting the importance of maintaining the size of local habit to hold the evolutionary potentials for O. rufipogon populations. The outcrossing rates varied greatly among populations (tm=0.053-0.616); and they were significantly correlated with population density (r=0.807,p＜0.01). The bottleneck effects due to population decline were not detected in most of the populations, implying little effect of recent habitat fragmentation on O. rufipogon populations.4) We investigated the genetic variation in 11 O. rufipogon populations from SMCR using 79 microsatellite loci to infer the effects of habitat fragmentation, IBD, and IBA on genetic structure. Significant population divergence had been found among populations (Fst=0.343); and historical and current gene flows were rare (mh=0.0002-0.0013, mc=0.007-0.029), indicating IBD and resulting in a high level of population divergence. Hierarchical AMOVA and partial Mantel tests indicated that population divergence of Chinese O. rufipogon was significantly correlated with environmental factors, especially habitat temperature (r=0.53, p<0.01). Eleven gene-linked microsatellite loci were identified as outliers, indicating local adaptation. Collectively, these findings implied that long term IBD, followed by local adaptation, have driven population divergence in O. rufipogon.5) Hdl and Hd3a were the key genes in controlling flowering time of rice. We have cloned the second exon of Hdl and the promoter region of Hd3a in 9 populations of O. rufipogon from SMCR, respectively. The nucleotide diversity was low in the two gene fragments. Hdl showed non-synonymous mutations mainly occurred in the southern population WC, it might lead to potential changes in heading date. The sequence of promoter region of Hd3a also showed a geographic variation pattern that two populations in south (FC and PS) had unique haplotypes, respectively. These findings implied that the changes of heading date in O. rufipogon populations might be involved in genetic variations.6) In order to find the signature of local adaptation at genome level, ten pooled DNA samples from ten populations of O. rufipogon were analyzed by using next-generation resequencing technology. We found clinal changes in the genome across the whole distribution range of O. rufipogon and the populations in tropical region seemed to be divergent early. Especially, these populations from SMCR (mainly from south China) could be divided into northern and southern groups. By comparing genome genetic differentiation, a total of 16610 SNPs had been identified responsible for the divergence between the two groups, of which 9804 SNPs located on 5796 genes and 1989 SNPs in the exons of 1274 genes. Based on these SNPs, we screened the genes involving in cold tolerance and flowering time, and finally we found eleven cloned genes might be related to population divergence, suggesting the potential molecular mechanisms underlying local adaptation. In addition, the finding SNPs, which were significant differentiation between northern and southern groups of O. rufipogon, would provided important clue for exploring the candidate genes of O. rufipogon population differentiation.Our research had dissected the mechanism shaping distribution pattern of population variations, and revealed the effects of IBD and IBA on population divergence. We provided a referenced scenario to study the mechanism underlying population divergence for those species with isolated populations located in patchy and heterogeneous habitats. |
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