- Campbell et al. - Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa). - Results: The transcriptomes of the two subspecies of rice are highly divergent. - Cultivated rice consists of two subspecies: Indica and Japonica. - 2 Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, 175 West Campus Drive, 24060 Blacksburg, VA, USA Full list of author information is available at the end of the article. - [2] showed considerable reduc- tion in genetic diversity in Indica and Japonica compared with O. - rufipogon to the autogamous breeding system of cul- tivated rice likely led to greater partitioning of genetic diversity among the two subspecies, and further differen- tiation of the two groups. - [4] showed that approximately 10% of the genes in the Indica and Japonica genomes showed evidence of presence-absence variation or asym- metrical genomic locations. - While the morphological and genetic differences of Indica and Japonica have received considerable attention, few studies have investigated the divergence between the two subspecies at transcriptome level [13–15]. - Walia et al. - [13] utilized genome-wide expression profiling to char- acterize the transcriptional responses for two Indica and Japonica cultivars to salinity. - Lu et al. - Jung et al. - The objective of this study is to examine the genetic basis of the transcriptional variation at a population level within the O. - Here, we show that transcrip- tional diversity between Indica and Japonica subspecies is consistent with diversity at the genetic level. - 10 read counts) in at least one or more of the 91 accessions. - This equates to about 46% of the genes present in the rice genome (total of 55,986 genes in MSUv7 build).. - Divergence between the Indica and Japonica subspecies are evident at the genetic and transcriptional levels To examine patterns of variation within the transcrip- tomics data, we performed principle component analysis (PCA) of transcript levels for the 91 accessions. - 10 reads) in at least 20% of the samples.. - PCA analysis of the expression matrix resulted in a clear. - separation between the two subspecies along PC1, sug- gesting a significant transcriptional divergence between Indica and Japonica (Fig. - The first PC accounted for approximately 26.8% of the variation in gene expression.. - These results suggest that the two subspecies of cultivated rice have divergent transcriptomes, but the transcriptomes of the subpopulations are more similar. - Zhao et al. - To further explore the differences and identify genes that display divergent expression between the two subspecies, the 91 accessions were first classified into Indica and Japonica-like groups, using the program STRUCTURE with the assumption of two groups and no admixture [19]. - The top four principle components from PCA analysis of the genotypic data are pictured in A and B to illustrate the divergence of the major subpopulations in rice. - Next, a linear mixed model was fit for each of the 26,675 genes, where subspecies was considered a fixed effect and accession as a random effect. - This divergent expression levels observed between the two subspecies could be the result of the presence or absence of genes within the subspecies. - of the samples were retained for downstream analyses. - Collectively, these results sug- gest that the divergence between Indica and Japonica. - Several studies have shown that the unique domestica- tion history of the two subspecies has resulted in large differences in the overall genetic diversity between the two subspecies, with Indica being more genetically diverse than Japonica [2, 20–22]. - Genetic diversity within each subspecies was estimated using π for 33,543 SNPs in randomly selected 35 Indica and 35 Japonica accessions. - 2 Genetic and expression diversity within Indica and Japonica accessions. - a The coefficient of variation was used as an estimate of the diversity in gene expression within each subspecies. - b Site-wise nucleotide diversity ( π ) was used as an estimate of the genetic diversity within each of the subspecies using 36,901 SNPs described by [16]. - To estimate the extent to which vari- ation in gene expression is under genetic control, a mixed model was fit to the expression of each of the 22,675 genes and the variance between accessions was estimated. - The significance of the random between − accession term was determined using a likelihood-ratio test. - The broad-sense heritability (H 2 ) was estimated as the proportion of the total variance explained by between-accession variance to total variance. - H which accounts for approximately 53% of the genes expressed in at least 20% of the samples (Fig. - Here, a gene was consid- ered as expressed if 10 or more reads mapped to the gene in 20% or more of the samples. - A total of 22,444 genes were found to be expressed in at least 20% of the samples for the Japonica subspecies, while 22,068 were found to be expressed in the Indica subspecies. - A total of 5,005 genes exhibited significant H 2 in Indica and 3,338 genes in Japonica (FDR <. - For instance, only 1,681 and 2,644 genes were found to have significant H 2 and h 2 , respectively, in both Indica and Japonica.. - were considerably different between Indica and Japonica (Fig. - Thus, to further examine the potential causes of the observed differences in heritability, we quantified the expression diversity (CV), genetic variation and environmental vari- ation within each subspecies for genes exhibiting H 2 and h 2 , as well as those with shared heritable vari- ation. - Mizuta et al. - a Comparison of broad-sense heritability between Indica (H I 2 ) and Japonica (H 2 J. - b Comparisons of narrow sense heritability between the two subspecies. - Differences in broad (c) and narrow sense heritability (d) between Indica and Japonica. - et al. - Moreover, many genes exhibit large differences in genetic variability between the Indica and Japonica, suggesting that these genes may be regulated by divergent genetic mechanisms.. - For each gene, associations were tested for SNPs within 100kb of the transcription start site. - This equates to approximately 81% of the genes displaying heritable expression, and indicates that a large portion of genes with heritable expression are regulated by variants in close proximity to the gene.. - Of the 5,097 eQTL genes detected genes;. - The presence or absence of cis-regulatory variants within a given subspecies may be the result of the unique domes- tication histories that have shaped Indica and Japonica, and/or driven by environmental adaptation of the wild progenitors from which they were derived. - The absence of variation at the eQTL SNP could be due to sam- pling during differentiation of the wild progenitors or during domestication (e.g. - In the case of selection, we expect to see reduced genetic diversity around the eQTL compared to the rest of the genome. - while the Japon- ica subspecies consists of the japonica-X, subtropi- cal japonica, temperate japonica, and tropical japonica subpopulations.. - For instance, approximately 11% of the 880 Indica-specific. - For each, subpopulation and class of eQTL (e.g.Indica-specific, Japonica-specific, and shared) π was calculated for each SNP within 100 kb of the most significant eQTL SNP. - Collectively these results suggest that selective pressures may have shaped the cis-regulatory divergence of the Indica and Japonica subspecies.. - The differentiation between the Indica and Japonica sub- species of cultivated rice has been intensively character- ized at the morphological, biochemical, and genetic levels. - Here, we provide a comprehensive analysis of the transcriptional and cis- regulatory divergence between the major subspecies of rice, and show that the presence or absence of cis regula- tory variants within the subspecies is a component of this divergence.. - Of the 25,732 genes showing evidence of expression in the current study, approximately 29% showed significant differences. - in expression levels between the two subspecies. - While few studies have examined the differences in expression levels between diverse populations of Indica and Japon- ica, recent studies have utilized whole genome sequencing to shed light on the genetic differentiation between the subspecies of cultivated rice [2, 27]. - [27] found that on average approximately 15% of all genes showed evidence of PAV between the genomes of Indica and Japonica accessions, further indi- cating that PAV is pervasive between the subspecies of cultivated rice. - Therefore, while the expression data provides considerable insight into transcriptional varia- tion in cultivated rice, it likely captures only a portion of the total transcriptome given the lack of temporal and spa- tial resolution. - [27] captured PAV using 3,010 resequenced rice genomes, while the current study utilized only a fraction of the variation of Wang et al. - The current study highlights many differences between the Indica and Japonica subspecies, but does so under the assumption that the genomes of the two subspecies should not be too different. - The over- all high colinearity of the genomes of the two subspecies and the ability to recover fertile F1 individuals from Indica-Japonica hybrids suggests that this is a reasonable assumption.. - Potential causes of transcriptional divergence between Indica and Japonica. - The availability of high density SNP information for RDP1 allowed us to begin to elucidate the genetic basis of the observed transcrip- tional divergence between the subspecies of cultivated. - Therefore, it is possible that many more DE or PAV genes have different genetic architectures in the two subspecies, but were missed because of the stringency of statistical threshold. - A second possibility is that many of the genes showed divergent expression are influenced greatly by the environment, and thus have low heritability. - The heritable transcriptional divergence may be due to genetic variants that influence gene expression and are divergent between Indica and Japonica. - The availability of high density SNP information for RDP1 allowed us to begin to elucidate the genetic basis of the observed transcriptional divergence between the sub- species of cultivated rice, and classify genetic effects into those that are common between subspecies, or unique to a given subspecies. - reflect a portion of the differences in genetic variation between the two subspecies. - the cis-regulatory variant was shared between both subspecies, indicating that much of the cis-regulatory variation is common between the two subspecies. - For one, both Indica and Japonica originate from populations of the same species, Oryza rufipogon.. - Moreover, crosses between Indica and Japonica often pro- duce viable offspring, indicating a high degree of colinear- ity and functional similarity between the genomes. - Moreover, the patterns of genetic variability for these genes are consistent with their potential role in the adaptation of flowering in different environments for Indica and Japonica.. - The morphological and genetic differences between sub- species of cultivated rice have been studied extensively, however the divergence of Indica and Japonica at the transcriptional and regulatory levels is largely unresolved.. - The pH of the solution was monitored twice daily and was recirculated from a reservoir beneath the tubs to the growth tubs. - Ten days after transplant, aerial parts of the seedlings were excised from the roots and frozen immediately in liquid nitrogen. - The significance of the fixed effect of subspecies was determined by comparing the full model above with a reduced model that lacked subspecies using a likelihood-ratio test. - The coefficient of variation (CV) was used to estimate the diversity in gene expression within the Indica and Japonica subspecies. - of the samples) were removed, leaving a total of 22,503 genes in Japonica and 21,719 genes in Indica. - was estimated across subspecies for 22,675 genes that were expressed in both Indica and Japonica. - However, due to the unequal sample size for the Indica and Japonica sub- species, a random set of 35 Japonica accessions were selected. - These permutations were used to estimate π 0 , the probability for a gene to have no eQTL in any subspecies. - 0.1 in both Indica and Japon- ica). - For each eQTL SNP, all SNPs within 100kb of the eQTL SNP was extracted from the 4.8M core SNP data. - The MAF was determined for each of the 12 subpopulations in the 3kg data, and SNPs that had low diversity (MAF <. - 0.01) in 10 of the 12 subpopulations were excluded from fur- ther analyses. - Additional file 1: Genetic and expression diversity within Indica and Japonica accessions.. - Funds were used for the design of the study, as well as the collection and analyses of the data.. - A draft sequence of the rice genome (Oryza sativa L. - Registration of the rice diversity panel 1 for genomewide association studies. - numerical evaluation of the indica-japonica differentiation
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