Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication
© Wang et al; licensee BioMed Central Ltd. 2010
Received: 9 September 2009
Accepted: 23 April 2010
Published: 23 April 2010
Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection.
Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process.
How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.
Gene duplication has long been recognized to be an important way to provide a substrate on which evolution acts. The classical models that predict the most possible fate of one of the duplicate genes is to degenerate to a pseudogene or get lost from the genome due to vagaries of chromosomal remodeling, locus deletion or point mutation [1–5]. A less frequent fate of the duplicate genes is to gain a new function (neo-functionalization) when the other copy still maintains its original function. However, recent studies have indicated that the newly duplicated genes are often sub-functionalized from their ancestral functions held by the parental genes [6–8]. The sub-functionalization model (also referred to as duplication-degeneration-complementation model) explains that the duplicate genes are maintained in the genome relying on complementary degenerative changes in a pair of duplicate genes, such that the duplicate genes together retain the original functions of their single ancestor [1–5, 9]. During this process, the expression domain shifting is the most common character of duplicate genes. As a consequence, the duplicates acquired sub-functionalization and then were less constrained by selection than the single ancestor, which had to maintain the capacity to fulfill all functions. Therefore, selection could act independently on each duplicate and increase the gene function specificity .
Sequence variation plays an essential role in functional renovation of genes, however, the relationship between DNA variation and functional consequence has been enigmatic for the vast majority of genes in plant and animal kingdoms, despite an increasing number of studies have been reported. Crop species and their wild relatives with available genome information are becoming fascinating subjects for study of correlation between cryptic genetic variation and functional evolution, because they have undergone rapid diversification under intense artificial selection [11–14]. Therefore, investigating crop domestication genes will shed meaningful light on genetic variation that drives cultivation adaptation . Rice was used by human about 11,000 years ago [16, 17]. It has been indicated that the divergence of indica and japonica predated rice domestication, suggesting that at least two genetically distinct gene pools of O. rufipogon were cultivated and subsequently domesticated [18–20]. During the long-term cultivation and domestication, tremendous diversity in rice has been selected by human, adapting to various ecosystems and agricultural management, in addition to high yielding characteristics, such as grain number and weight [12, 17].
Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, but little is known about the mechanisms of evolutionary change in duplicate genes leading to functional novelty. Rice has been recognized as a cereal model for such a study, and recent studies have discovered that some rice genes have undergone adaptive evolution under domestication selection [17, 21]. We previously reported that the rice grain-filling gene GIF1 (OsCIN2) encoding a cell wall invertase (CWI) was most likely subjected to domestication selection . Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function. Population genetic analysis showed that the two genes have experienced strong domestication selection, and interestingly, the target of selection in the GIF1 gene is the promoter region and that in OsCIN1 is the coding region.
Evolution of GIF1 and OsCIN1by gene duplication
Summary of nonsynonymous (Ka) and synonymous (Ks) substitutions in OsCIN1 and GIF1
Sub-functionalization of GIF1 and OsCIN1by expression differentiation
Sub-functionalization of GIF1 and OsCIN1 enzymes
The difference in the kinetics parameters of enzymatic activity might result from the amino acid substitutions, in particular the GIF1 and OsCIN1 proteins contain Ala and Gly residues in the NDPNG domain (motif), respectively (Figure 3C). Phylogenetic reconstruction (Figure 1A and 3C) revealed that the Gly-26-Ala substitution occurred after the GIF1 and OsCIN1 duplication. The crystal structure of the Arabidopsis CWI indicated that the conserved NDPNG domain is critical for CWI activity [30–32]. However, GIF1 and the homologous maize Mn1 contain a NDPNA motif instead of the NDPNG motif that presents in OsCIN1 and other CWIs, suggesting that the segmental duplication predates maize and rice differentiation. Furthermore, the crystal structure showed that Asp-239 interacted with Lys-242 and both the two amino acids played a crucial role in the transfructosylation process and interacted via H-bonds with the bound substrate . A Thr-241-Arg substitution in the Asp-239/Lys-242 region occurred in GIF1 as well as in Mn1. It is noteworthy that the mutation in the Mn1 gene also caused shrunk grains . The synteny between the GIF1 and Mn1 genome regions suggested that they could be orthologues (Additional file 3). These structure differences might contribute to different enzymatic kinetics of the GIF1 and OsCIN1 proteins. Together, these results suggested that GIF1 and OsCIN1 were subjected to sub-functionalization, or that GIF1 (probable Mn1 too) might have neofunctionalized, albeit we do not know the ancestral function of the CWIs.
Different phenotypes of GIF1-OE and CIN1-OE plants support sub-functionalization of GIF1 and OsCIN1
Evidence of OsCIN1domestication-selection
Cultivars and wild rice germplasm used in this study
Sample name/IRGC no.
Canella De Ferro
Southern Asian indica
Southern Asian indica
Southern Asian indica
Papua New Guinea
HKA tests of the OsCIN1 and GIF1 locia
polymorphism site number
To narrow down the selection target in the OsCIN1 gene, we examined all the variations in the OsCIN1 genome regions, and found that an amino acid substitution (Arg-212-Leu) almost fixed in the rice cultivars, indicating that, unlike GIF1 which was selected in the promoter region, this site in the coding region could be the target of artificial selection in the OsCIN1 gene (Figure 5B). Further functional characterization of this site will provide more evidence to address how this site has contributed to OsCIN1 function in cultivated rice.
Gene duplication and adaptive conflict
Gene duplication plays a fundamental role in organism evolution by providing genetic materials from which novel functions can arise. Large numbers of duplicate genes were found in genomes, which contributed greatly to the genome structure and function evolution [1–5, 39]. In general, the duplicate genes have two fates: first, the duplicate gene lost its function due to chromosome remodeling, deletion, and point mutation (known as non-functionalization); second, the duplicate gene retained for the maintenance of ancestral functions [1–5]. According to adaptive conflict model, adaptive mutations could be prohibited in the case of multifunctional genes, or one mutation that can optimize one function, may compromise the other functions, this mutation will be prohibited [6, 40]. The adaptive conflict could be solved by sub-functionalization of duplicate genes. In this case, the duplicate genes would be less constrained and be able to evolve new functions under selection [41, 42]. With this scenario, it is common that one gene could have multifunction in nature [40, 43].
Independent selection of GIF1 and OsCIN1mutations
The sequenced genomes of Oryza sativa, Arabidopsis thaliana and Populus trichocarpa all contain a family of cell wall invertases [44–46], some members of these gene families were reported to be involved in growth and development, disease resistance, stress responses and cell death, suggesting that the CWI gene families might have undergone sub- or neo-functionalized in these species.
Through genomic synteny analysis, we showed that GIF1 and OsCIN1 derived from a segmental duplication from an ancestor, most likely during genome duplication in grass species. After duplication, GIF1 and OsCIN1 have evolved to gain divergent functions with different expression patterns and enzymatic kinetics parameters through accumulating mutations in cultivated rice. In contrast to GIF1 on which domestication selection mainly occurred in the cis-regulatory region (Figure 5A), the artificial selection occurred mainly in the coding region of OsCIN1 (Figure 5B). Therefore, both GIF1 and OsCIN1 were most likely subjected to domestication selection, resulting in a cultivated GIF1 locus for better harvest, although the biological importance of OsCIN1 in domestication remains enigmatic. With this scenario, GIF1 and OsCIN1 may provide a good genetic model to demonstrate how duplicate genes could evolve and be artificially selected independently during crop domestication with divergent functions derived from accumulation of mutations in the regulatory and coding regions respectively, adding to those systems reported [47, 48].
Differential biological functions of GIF1 and OsCIN1
GIF1 is mainly expressed in seed vascular tissues and controls sucrose unloading for starch synthesis at the early grain-filling stage . Overexpression of the GIF1 gene produced plants with marked defects both in grain-filling and development, indicating that over-activity of the GIF1 enzyme disrupts sugar homeostasis, a process important to normal grain and plant development. In contrast, OsCIN1 has lower CWI activity compared to GIF1 in the transgenic plants (Figure 3). Consistent with this, no obvious phenotype was observed in CIN1-OE plants except pre-harvest sprouting (Figure 4). Interestingly, OsCIN1 might be involved in pathogen defense and stress response . It has been reported that sugars interact with signaling pathways mediated by phytohormones such as GA and ABA during seed germination and seedling development [34, 49], which are also involved in stress responses. Preharvest sprouting of the CIN1-OE seeds may implicate a role for OsCIN1 in sugar-mediated alpha amylases activation . However, detailed experiments are needed to dissect the OsCIN1 function.
Gene duplication and functional divergence contribute greatly to genetic novelty and adaptive evolution. However, molecular basis of selection and functionalization of duplicate genes remains largely unknown. Based on a set of data including population genetic analysis, fine sequencing of wild rice BACs, phenotyping of transgenic plants and analysis of gene expression and enzymatic activity, we provide a line of evidence that the two rice CWI genes GIF1 and OsCIN1 are a pair of duplicate genes and have been subjected to sub-functionalization during evolution or domestication selection. Therefore, duplicate genes could be independently selected towards different functional specificity, either on promoter for different expression pattern or on coding region for different protein function/activity. Our study provides a vivid example for evolution of genetic novelties in a model crop. The interesting phenotype of preharvest sprouting OsCIN1-OE plants suggests that OsCIN1 overaccumulation might disturb sugar balance during seed germination.
Duplication and synteny analysis
The 500-kb radiuses of the GIF1 and OsCIN1 regions were scanned for homologous pairs. A homolog pair was defined as a single nr-KOME cDNA and its blastn homolog. A total of 18 homologous genes in both sides of the GIF1 and OsCIN1 loci were compared to establish linearity.
Sequencing and evolution analysis
To investigate the selective forces acting on GIF1 and OsCIN1 on the molecular evolution scale, we estimated the statistic Ka/Ks using the re-sequencing data (see below) and the maize Mn1 and Incw1-1 as the outgroup sequence, where Ka was the number of nonsynonymous substitutions per nonsynonymous site and Ks was the number of synonymous substitutions per synonymous site . Ka/Ks values significantly less than 1 were often taken as evidence of constraint. The mean Ks of nine pair homolog genes, including GIF1 and other eight genes (Additional file 2), in the GIF1 and OsCIN1 regions were used to estimate the duplication time. Two BAC clones of O. punctata (BB genome) from the OMAP project http://www.omap.org/ containing GIF1 and OsCIN1 respectively, were sequenced.
Analysis of OsCIN1 and GIF1 domestication
We deeply analyzed the OsCIN1 and GIF1 sequences from the re-sequenced genomes of 25 rice cultivars and 25 wild rice germplasm (Table 2), which has been done in Dr. Wen Wang's group, using Solexa technology (data not shown). Haplotype diversity was calculated for nucleotide diversity (π), and Tajima's D- statistics were calculated with DnaSP version 4.0. The gene tree was created using MEGA software . The sequences then were aligned. The 2-kb up-/downstream genome sequences and the GIF1, OsCIN1 coding sequences were used for HKA test as described . Sequences from wild rice O. punctata (BB genome) from the OMAP project http://www.omap.org/ were used as outgroups for the HKA test. The DNA phylogenetic tree was constructed by neighbor-joining method using MEGA. The known or predicted CWI genes with high sequence similarity to GIF1 from Oryza sativa, Lolium perenne, Hordeum vulgare, Dendrocalamopsis oldhamii and the recently released Zea mays and Sorghum bicolor genomes were used in this study.
Development and growth of OsCIN1-OEtransgenic plants
The full-length OsCIN1 coding sequence was PCR-amplified from ZH11 cDNA by using the primers 5'-TCTAGTACAAAACAATGGGGACTC-3' and 5'-CGGAAAACCTCTTTATTATCTGTA-3'. The amplified fragment was subsequently cloned into the vector 35S-C1301 and transformed into ZH11 to generate 25 independent ectopic expression lines as described . All transgenic materials were assayed in the second (T1) or third (T2) generations with 10-24 sibling plants grown in the paddy field to ensure agronomic traits.
Invertase activity assay
The caryopses were ground in the extraction buffer, and the extraction was centrifuged at 12,000 g for 10 min. The pellet was washed twice then re-suspended in the extraction buffer. Insoluble invertase activity was assayed as described .
RNA preparation and analysis
Total RNA was prepared from rice tissues using TRIzol reagent according to the manufacture's protocol (GIBCO BRL). For RT-PCR, 1-5 ug total RNA was used for the first-strand cDNA synthesis with the SuperScript III System (Invitrogen). RT-PCR analysis of GIF1 and OsCIN1 was performed with the primers [22, 23].
All sequences have been deposited in GenBank under accession numbers GU797900-GU798049.
We thank M. Long and W. Capoen for critical reading of the manuscript and helpful suggestions; R. A. Wing for O. punctata BAC clones. X. Zhang, L. Zeng and S. Ye for rice growth. This work was supported by grants from the Ministry of Science and Technology of China (2007AA02Z162, 2007AA10Z187), grants from the National Natural Science Foundation of China (30721061) to Z. He
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