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Article

Genome-Wide Syntenic and Evolutionary Analysis of 30 Key Genes Found in Ten Oryza Species

by
Yeonghun Cho
1,
Insu Lim
1 and
Jungmin Ha
1,2,*
1
Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
2
Haeram Institute of Bakery Science, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
*
Author to whom correspondence should be addressed.
Agronomy 2023, 13(8), 2100; https://doi.org/10.3390/agronomy13082100
Submission received: 7 July 2023 / Revised: 1 August 2023 / Accepted: 7 August 2023 / Published: 10 August 2023
(This article belongs to the Special Issue Rice and Wheat Breeding: Conventional and Novel Approaches)
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Abstract

:
Rice is a vital staple food crop worldwide, providing nutrition and sustenance to a significant portion of the global population. The genetic diversity of cultivated rice species has been significantly reduced during domestication, resulting in the loss of favorable alleles. To overcome this limitation, wild rice species have been used in introgression breeding programs to introduce beneficial alleles. In this study, we performed syntenic and phylogenetic analyses for 10 Oryza species, comprising both cultivar and wild species. Pairwise syntenic analysis revealed 3885 synteny blocks containing 1,023,342 gene pairs among 10 species. O. nivara contained the most blocks that were syntenous with the other nine species. In total, 425 paralogous and orthologous genes were identified for 30 key genes involved in rice breeding. His1 (43), GS3 (28), and qSW5/GW5 (27) had the most paralogous and orthologous genes. For GS3 and qSW5/GW5, two gene transfer events were detected. These findings have implications for rice breeding strategies, particularly with respect to gene pyramiding and introgression breeding programs. This research will contribute to the development of elite cultivars with improved quality and yield to meet the growing global demand for high-quality rice.

1. Introduction

Rice is one of the major global staple food crops. Nearly half of the world’s population consumes rice as a primary source of food [1,2]. In Asian countries, rice production reached 6.9 billion tons in 2020 [3]. In addition to being rich in carbohydrates, rice contains various other nutrients, including proteins and vitamins [4]; moreover, the fact that rice does not contain gluten has made rice attractive to many people interested in a gluten-free diet [5,6]. Since the global population is predicted to reach 9.8–10.6 billion by the year 2050 (World Bank, 2022 [7]), new high-quality and high-yielding rice cultivars are required to meet the increasing global demand for rice production [8,9].
The genus Oryza is one of the most studied crop species due to its nutritional, social, and environmental importance [10]. This genus contains two groups: the cultivar group (e.g., O. glaberrima and O. sativa) and the wild rice group (e.g., O. australiensis, O. barthii, O. coarctata, O. glumipatula, O. meridionalis, O. nivara, O. punctata, and O. rufipogon). The genetic diversity of cultivated species has been highly decreased due to genetic bottlenecks; consequently, favorable alleles have been lost by existing elite cultivars during the process of domestication and breeding [11,12,13]. However, wild congeneric species have abundant genetic diversity and contain useful alleles not present in cultivated species. The rich diversity of wild species has therefore been used for trait introgression breeding in rice to improve resistance to abiotic and biotic stresses of cultivated species [14,15]. Previous studies have reported that the salt tolerance and blast resistance of O. sativa was enhanced by the introgression of the responsible genes PclNO1 and Pi-40(t) from O. coarctata and O. australiensis, respectively [16,17,18].
Theoretically, crossing over occurs randomly during meiosis, and alleles are exchanged between homologous chromosome pairs [19]. However, due to a variety of reasons, including chromosome structure, DNA methylation, and genetic drift, among others, recombination can be depressed at certain loci, leading to linkage disequilibrium (LD). LD refers to the non-random association of alleles at different loci produced during the recombination process [20,21]. In many plants, the recombination rate was highly suppressed in regions affected by chromosomal rearrangements such as inversions and segmental duplications [22,23]. Linkage drag is one of the most challenging problems to be solved by modern rice breeding programs [24]. Linkage drag causes several problems in rice breeding, including altering the segregation ratio and causing the co-inheritance of preferred and unpreferred loci. To overcome linkage drag, many breeding studies have transferred target alleles from wild species to cultivars; however, this process is cost- and labor-intensive [25,26]. To make the breeding process more efficient, the selection of parental materials with a high recombination rate at the target locus is important to reduce linkage drag during introgression breeding.
Syntenic analyses can reveal evolutionary history and quantify the genetic distance between genomes. In rice, syntenic analysis along with evaluation of the phylogenetic, evolutionary, and gene expansion mechanisms associated with resistance and defense response genes have been investigated in three Oryza species [27]. In addition, by combining syntenic analysis and gene expression analysis data, the identification of DDP genes and their evolutionary relationships among Oryza species and Arabidopsis have also been evaluated; this process was used to enhance salinity tolerance in rice [28]. However, previous syntenic analyses in rice have been mostly conducted on the gene level and have focused on wild species’ phylogenetic relationships to O. sativa, since it is the major cultivated species.
In contrast, Zeng et al. recently published an analysis of the most important 28 genes for rice breeding programs [29]. Here, we identified paralogs and orthologs of 30 key genes, including those associated with herbicide resistance (His1) [30] and rice fragrance (BADH2) [31], in ten Oryza species. Furthermore, we conducted synteny analysis among these ten Oryza species. This study can therefore provide insights into the evolutionary history of these focal genes and can inform rice breeding strategies based on introgression among Oryza species.

2. Materials and Methods

2.1. Sequence Data

The complete genome sequences of Arabidopsis thaliana, Glycine max, Leersia perrieri, O. barthii, O. brachyantha, O. glaberrima, O. glumipatula, O. meridionalis, O. nivara, O. punctata, O. rufipogon, and O. sativa ssp. japonica were obtained from the EnsemblPlants online database (https://plants.ensembl.org/, accessed on 6 April 2023). The whole genome sequence of O. sativa ssp. indica was obtained from the Rice Genome Hub website (https://rice-genome-hub.southgreen.fr/, accessed on 6 April 2023). Bioinformatics analyses were performed using Python scripts.

2.2. Phylogenetic Analysis

Of the ten Oryza species, 50 orthologous genes in synteny blocks were used for phylogeny analysis. Amino acid sequences from orthologous genes were concatenated and aligned using ClustalOmega version 1.2.4 [32]. A phylogenetic tree was constructed using RAxML version 8.2.12 [33] and visualized with the Interactive Tree of Life (iTOL) version 6.7.5 [34].

2.3. Synteny Analysis

A synteny block was defined as set of grouped genes that was paired between chromosomes among species. Here, we identified synteny blocks among ten Oryza species using MCscanX version 1 November 2022 [35] with all settings set to default parameters. Synvisio (https://synvisio.github.io/#/, accessed on 25 April 2023) [36] was used to visualize synteny blocks.

2.4. Identification of Key Genes

Zeng D., Tian Z., Rao Y. et al. previously reported the paralogs and homologs of 28 key genes commonly used in rice breeding programs [29]. In addition, 30 key genes annotated to the Oryza sativa spp. japonica reference genome and their orthologs were also identified in the other nine Oryza species using BLASTP version 2.9.0 [37] and OrthoFinder version 2.5.4 [38] with all settings set to default parameters. Expression patterns of the 30 key genes were collected for developmental stages (10, 15, and 20 days after germination), abiotic stresses (dry, flood, and cold stress) (TENOR database, https://tenor.dna.affrc.go.jp/, accessed on 18 June 2023), and biotic stresses (rice black-streaked dwarf virus, rice blast, and bacterial leaf streak) [39,40,41,42] (Figure S1). The 30 key genes included: GRAIN NUMBER 1A (Gn1a, Os01g0197700), SOLUBLE STARCH SYNTHASE IVA (SSIV-1, Os01g0720600), SEMIDWARF 1 (sd1, Os01g0883800), HPPD INHIBITOR SENSITIVE 1 (His1, Os02g0280700), STARCH BRANCHING ENZYME 3 (SBE3, Os02g0528200), SOLUBLE STARCH SYNTHASE IIB (SSII-2, Os02g0744700), grain size 3 (GS3, Os03g0407400), ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 1(AGPL1, Os03g0735000), PULLULANASE (PUL, Os04g0164900), SOLUBLE STARCH SYNTHASE IIIB (SSIII-1, Os04g0624600), GRAIN WIDTH 5 (qSW5/GW5, Os05g0187500), SOLUBLE STARCH SYNTHASE IV-2 (SSIV-2, Os05g0533600), ADP-glucose pyrophosphorylase large subunit 1 (OsAGPL1, OsAPL3, Os05g0580000), Granule-bound starch synthase 1 (WX1, GBSSI, Os06g0133000), SOLUBLE STARCH SYNTHASE I (SSI, Os06g0160700), ALKALI DEGENERATION (ALK, Os06g0229800), HEADING DATE 1 (HD1, Os06g0275000), STRONG CULM 2(SCM2, Os06g0665400), STARCH BRANCHING ENZYME 1 (BEI, SBE1, Os06g0726400), ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT 4 (AGPL4, Os07g0243200), HEADING DATE 7 (Ghd7, Os07g0261200), GRANULE BOUND STARCH SYNTHASE II (GBSSII, Os07g0412100), DISPROPORTIONATING ENZYME 1 (DPE1, OsDPE1, Os07g0627000), Heading date (QTL)-5(t) (Ghd8, Os08g0174500), SOLUBLE STARCH SYNTHASE III-2 (SSIII-2, Os08g0191433), betaine aldehyde dehydrogenase 2 (BADH2, Os08g0424500), ADP-glucose pyrophosphorylase small subunit 2a (OsAGPS2a, Os08g0345800), pre-harvest sprouting 8 (OsPHS8, PHS8, ISA1, OsISA1, Os08g0520900), Tiller angle control 1 (TAC1, Os09g0529300), and SOLUBLE STARCH SYNTHASE IIC (OsSSII-1, Os10g0437600).

3. Results

3.1. Phylogenetic Analysis of the Genus Oryza

A phylogenetic tree was constructed using ten different Oryza species as well as A. thaliana, G. max, and L. perrieri as outgroups (Figure 1). This analysis revealed that Asian species, including O. nivara, O. rufipogon, O. sativa ssp. Indica, and O. sativa ssp. Japonica, were grouped on one branch, with African species, including O. barthii and O. glaberrima, grouped together on a different branch. In the Asian group, wild species such as O. nivara and O. rufipogon were separated from cultivated species, including O. sativa.

3.2. Syntenic Analysis within the Asian Group

Pairwise syntenic analysis was then conducted among the ten Oryza species (Figure 2). In total, 3885 synteny blocks were identified, containing 1,023,342 gene pairs. On average, 50.3 genes were located in each block. Between O. sativa ssp. japonica and O. sativa ssp. indica, we identified 901 synteny blocks, the most of any species pair (Table 1A). O. nivara is the species that contained the most blocks that were syntenous with another species, while O. rufipogon and O. barthii was the pair with the highest average number of genes within synteny blocks with 90.1. This was followed by 84.4 between O. sativa ssp. japonica and O. rufipogon, and 83.3 between O. sativa ssp. japonica and O. barthii (Table 1B). In terms of physical length, the synteny blocks between O. rufipogon and O. punctata were the longest, with a total length of 744,092 kbp, including duplication (Table 1C).

3.3. Identification of Orthologs and Paralogs of Target Genes

Next, we identified paralogous and orthologous genes for the 30 target genes among the ten Oryza species. These 30 genes have been much studied because of their essential roles in rice breeding (Figure S1). In total, 425 paralogs and orthologs were identified. Based on copy number variation, the 30 target genes were then separated into four groups: High Variation (HV), Single Duplication (SD), Single Loss (SL), and No Variation (NV) (Table 2, Figure 3).
We identified His1, GS3, and GW5 as members of the HV group. Among these three genes, His1 had the most (43) paralogous and orthologous genes, followed by GS3 (28) and GW5 (27). O. sativa ssp. japonica and O. punctata had seven paralogous His1 genes, followed by O. glaberrima (six) and O. nivara (five). For GS3, O. sativa ssp. indica had the most paralogs (five). O. rufipogon, O. nivara, and O. sativa ssp. japonica all contained the most paralogs of GW5, each with four.
We identified TAC1, PUL, SSIII-1, SSI, and Gn1a as members of the SD group. While most Oryza species had a single copy of the TAC1 gene, O. brachyantha, O. glaberrima, and O. sativa ssp. Japonica all had another paralogous gene of TAC1. Likewise, PUL, SSIII-1, SSI, and Gn1 each had an additional copy in O. glaberrima, O. meridionalis, O. sativa ssp. Indica, and O. brachyantha. In contrast, the SL group included nine genes (i.e., AGPS2a, SBE3, BADH2, SSII-2, HD1, Ghd7, GBSSII, Ghd8, and DPE1), each of which had lost a single copy in at least one of the ten Oryza species.
Finally, we identified 13 genes (i.e., SSIV-1, SSIV-2, AGPL1, AGPL4, Wx1(GBSSI), sd1, OsAGPL1(OsAPL3), ALK, SCM2, BE1(SBE1), SSIII-2, OsPHS8(PHS8, ISA1, OsISA1), and OsSSII-1) as members of the NV group. Each of these genes had same gene copy number in all ten Oryza species, although the syntenic relationships among these genes was not conserved.

3.4. Syntenic Analysis of His1, qSW5/GW5, and GS3 in the HV Group

Next, we further investigated the syntenic relationship of orthologous genes in the high variation group for His1, qSW5/GW5, and GS3. A total of 43 His1 genes were widely distributed on rice chromosomes 2, 3, and 6 (Figure 4). In most Oryza species, two His1 genes were evenly identified in different syntenic blocks on chromosome 2; this pattern was not observed for O. brachyantha. For O. punctata, two additional His1 genes were identified on chromosome 3. On chromosome 6, the numbers of His1 genes present varied among species. Here, O. sativa ssp. Japonica had the largest number of His1 genes, with five; moreover, four His1 genes were present for O. glamipatula, three for O. punctata and O. nivara, two for O. brachyantha and O. barthii, and one for O. rufipogon and O. sativa ssp. Indica, respectively.
For qSW5/GW5, which is present on chromosome 1, 5, and 6, at most, three qSW5/GW5 orthologs or paralogs were found in chromosome 1 among the ten species. For instance, qSW5/GW5 paralogous genes on chromosomes 1 and 5 showed a syntenic relationship, and only O. brachyantha lacked a paralogous gene on chromosome 5.
Finally, syntenic blocks, including genes orthologous to GS3, were identified on chromosomes 3, 8, and 9. On chromosome 3, all species contained GS3 orthologs except O. glamipatula. Next, the orthologous genes on chromosomes 8 and 9 were located in syntenic blocks in most Oryza species. However, in O. sativa ssp. Indica, two paralogous genes were also identified on chromosome 3.

4. Discussion

Genetic diversity plays a crucial role in crop breeding programs. Since modern breeding programs have been performed using limited genetic pools, current elite cultivars of most major crops have a significantly lower genetic diversity relative to landrace and wild species [43,44]. To address the genetic bottlenecks created by using a limited genetic pool, incorporating genes from closely related wild species is a viable strategy. However, the presence of genome incompatibility barriers among different rice varieties remains one of the biggest challenges to rice breeders for developing new rice cultivars that have high yield and high quality [45].
Genome compatibility is one of the most critical factors during introgression breeding [46]. Although functional variations of orthologous genes depend on sequence variations in functional domains, genomic compatibility relies on chromosome structural variation. For this reason, syntenic analysis on the level of the genome is critical for providing evidence of genome compatibility among species [47]. In addition, synteny analysis has been successful in identifying chromosomal regions that are conserved among rice species [48,49]. It has been demonstrated that these conserved regions contain important genes related to yield, disease resistance, and nutritional quality [50]. Therefore, via synteny analysis, breeders can design an effective strategy to transfer genes of interest to target varieties, which leads to the development of improved rice cultivars. On the level of the genome, O. nivara and O. rufipogon, two wild Asian species, represent the most promising breeding materials for elite cultivars since their genomic backgrounds are mostly compatible with O. sativa.
Although general genome compatibility can be predicted based on genome-wide syntenic relationships, a syntenic analysis on the level of genes is required for gene pyramiding during introgression, since orthologous genes at different loci must be targeted. Next, we conducted a syntenic analysis of the orthologous and paralogous genes identified based on sequence similarity, focusing on genes showing a high copy number variation (CNV). With the exception of O. brachyantha, two His1 genes present on chromosome 2 were conserved within a syntenic block among the other nine species, indicating that the His1 genes on chromosome 2 were duplicated from chromosome 6 after speciation from O. punctata (Figure 1). With respect to resistance genes, dosage effects have been reported that suggest that CNV is highly associated with resistance [51,52,53,54]. In rice, resistance to the herbicide benzobicyclon varies among cultivars, depending on the copy number of His1. For the two subspecies of O. sativa, O. sativa ssp. Japonica, which has seven copies of His1, has been reported to show greater resistance than O. sativa ssp. Indica, which has three copies of His1 [55,56]. Similarly, in soybean, a high copy number of Rhg1, an R-gene against Heterodera glycines, is associated with an increased expression of a set of genes that confer resistance to soybean cyst nematodes [51]. Therefore, Oryza species with high His1 copy numbers, including O. punctata, O. glaberrima, and O. nivara, are candidate genetic resources to breed highly resistant rice cultivars.
For qSW5/GW5, paralogous genes on chromosomes 1 and 5 have been identified as a syntenic block in the genomes of most Oryza species. Since a qSW5/GW5 paralog was not identified in O. brachyantha, the paralogous gene on chromosome 5 may reflect a duplication, following speciation from O. punctata.
With respect to GS3, paralogous genes on chromosomes 8 and 9 were identified as a syntenic block in the genomes of most Oryza species. Since GS3 paralogs are not identified in O. brachyantha, a paralogous gene on chromosome 9 may have been duplicated, following speciation from O. punctata. However, only O. sativa ssp. indica possesses an additional paralogous gene of GS3 on chromosome 3.
Since qSW5/GW5 and GS3 both affect grain weight and grain size [57], an introgression of extra copies at different loci—e.g., the locus on chromosome 6 in O. rufipogon and chromosome 4 in O. sativa ssp. indica—may be a promising candidate for the genetic enhancement of rice yield and quality [58].
In addition to CNV, other quantitative traits of rice that can be affected by the number of effective alleles can be improved via the introduction of additional genetic factors through inter-species crossing. To improve each trait by the introduction of genes and/or alleles from different loci, gene pyramiding through introgression breeding may be an effective strategy for developing elite rice cultivars [59].

5. Conclusions

Here, have identified conserved syntenic regions that can facilitate the transfer of important genes between different rice varieties, which can lead to the development of improved rice varieties. This approach may ultimately contribute to a greater food security and an improved nutrition for the growing global population.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agronomy13082100/s1, Figure S1. Expression patterns of 30 key genes in Oryza sativa ssp. japonica.

Author Contributions

Conceptualization, Y.C., I.L. and J.H.; data collection, formal analysis, and investigation, Y.C. and I.L.; visualization and writing—original draft, Y.C.; writing—review and editing, Y.C., I.L. and J.H.; supervision, J.H.; All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by two National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT; Grant No. 2021R1C1C1004233 and No. 2022R1A4A1030348).

Data Availability Statement

No new data were created in this study. All analyzed data can be found in the article. Data sharing is not applicable.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Phylogenetic tree of ten Oryza species. This tree is based on the amino acid sequence similarity for 50 orthologous genes and was constructed using the maximum likelihood method (RAxML). A. thaliana, G. max and L. perrieri were used as outgroups. Numbers above lines indicate branch length.
Figure 1. Phylogenetic tree of ten Oryza species. This tree is based on the amino acid sequence similarity for 50 orthologous genes and was constructed using the maximum likelihood method (RAxML). A. thaliana, G. max and L. perrieri were used as outgroups. Numbers above lines indicate branch length.
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Figure 2. Genome-wide syntenic analysis of ten Asian Oryza species. Only syntenic relations between the closest related species in the phylogenetic tree (Figure 1) were visualized. Gray lines indicate syntenic relations between the same chromosome, while red lines indicate syntenic relations between different chromosomes. Genomes are located according to their position on the phylogenetic tree. In total, 3885 synteny blocks were identified, which included 1,023,342 gene pairs. Only those synteny blocks with 50 or more gene pairs were included.
Figure 2. Genome-wide syntenic analysis of ten Asian Oryza species. Only syntenic relations between the closest related species in the phylogenetic tree (Figure 1) were visualized. Gray lines indicate syntenic relations between the same chromosome, while red lines indicate syntenic relations between different chromosomes. Genomes are located according to their position on the phylogenetic tree. In total, 3885 synteny blocks were identified, which included 1,023,342 gene pairs. Only those synteny blocks with 50 or more gene pairs were included.
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Figure 3. Schematic visualization of the High Variation, Single Duplication, Single Loss, and No Variation groups. Thirty genes were separated into four groups based on variation characteristics. (A) The High Variation (HV) group contains His1, GS3, and GW5. Genes in HV had high gene copy numbers in different species. (B) Single Duplication (SL) group contains TAC1, PUL, SSIII-1, SSI, and Gnla. Each gene in the Single Duplication group had extra copies in at least one of the Oryza species. (C) The Single Loss (SL) group contained a total of 9 genes (i.e., AGPS2a, SBE3, BADH2, SSII-2, HD1, Ghd7, GBSSII, Ghd8, and DPE1). Genes in the SL group lost a single copy among the Oryza species. (D) The No Variation (NV) group contains 13 genes (i.e., SSIV-1, SSIV-2, AGPL1, AGPL4, Wx1(GBSSI), sd1, OsAGPL1(OsAPL3), ALK, SCM2, BE1(SBE1), SSIII-2, OsPHS8(PHS8, ISA1, OsISA1), and OsSSII-1). All genes had the same number of gene copies in all ten Oryza species.
Figure 3. Schematic visualization of the High Variation, Single Duplication, Single Loss, and No Variation groups. Thirty genes were separated into four groups based on variation characteristics. (A) The High Variation (HV) group contains His1, GS3, and GW5. Genes in HV had high gene copy numbers in different species. (B) Single Duplication (SL) group contains TAC1, PUL, SSIII-1, SSI, and Gnla. Each gene in the Single Duplication group had extra copies in at least one of the Oryza species. (C) The Single Loss (SL) group contained a total of 9 genes (i.e., AGPS2a, SBE3, BADH2, SSII-2, HD1, Ghd7, GBSSII, Ghd8, and DPE1). Genes in the SL group lost a single copy among the Oryza species. (D) The No Variation (NV) group contains 13 genes (i.e., SSIV-1, SSIV-2, AGPL1, AGPL4, Wx1(GBSSI), sd1, OsAGPL1(OsAPL3), ALK, SCM2, BE1(SBE1), SSIII-2, OsPHS8(PHS8, ISA1, OsISA1), and OsSSII-1). All genes had the same number of gene copies in all ten Oryza species.
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Figure 4. Syntenic relations among HV group genes for ten Oryza species. Colors (i.e., blue, orange, yellow, green, and gray) indicate true orthologs located within the same syntenic blocks. Black indicates no syntenic relationship. Black outlines indicate true paralogs with a syntenic relationship. (A) A total of 43 His1 genes were identified on rice chromosomes 2, 3, and 6. (B) A total of 27 qSW5/GW5 genes were identified on rice chromosomes 1, 5, and 6. qSW5/GW5 on chromosome 5 had a syntenic relationship with one of the paralogous genes on chromosome 1. (C) A total of 28 GS3 genes were identified on rice chromosomes 3, 4, 8, and 9. Paralogous genes on chromosome 8 and on chromosome 9 also had a syntenic relationship.
Figure 4. Syntenic relations among HV group genes for ten Oryza species. Colors (i.e., blue, orange, yellow, green, and gray) indicate true orthologs located within the same syntenic blocks. Black indicates no syntenic relationship. Black outlines indicate true paralogs with a syntenic relationship. (A) A total of 43 His1 genes were identified on rice chromosomes 2, 3, and 6. (B) A total of 27 qSW5/GW5 genes were identified on rice chromosomes 1, 5, and 6. qSW5/GW5 on chromosome 5 had a syntenic relationship with one of the paralogous genes on chromosome 1. (C) A total of 28 GS3 genes were identified on rice chromosomes 3, 4, 8, and 9. Paralogous genes on chromosome 8 and on chromosome 9 also had a syntenic relationship.
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Table 1. Summary statistics for syntenic analysis among ten Oryza species. (A) Numbers of synteny blocks between species pairs. (B) Average number of genes in each synteny block. (C) Total length of synteny blocks, including duplication (kbp). Obra = O. brachyantha; Opun = O. punctata; Omer = O. meridionalis; Oglu = O. glumipatula; Ogla = O. glaberrima; Obar = O. barthii; Oruf = O. rufipogon; Oniv = O. nivara; Oind = O. sativa ssp. indica; Ojap = O. sativa ssp. japonica.
Table 1. Summary statistics for syntenic analysis among ten Oryza species. (A) Numbers of synteny blocks between species pairs. (B) Average number of genes in each synteny block. (C) Total length of synteny blocks, including duplication (kbp). Obra = O. brachyantha; Opun = O. punctata; Omer = O. meridionalis; Oglu = O. glumipatula; Ogla = O. glaberrima; Obar = O. barthii; Oruf = O. rufipogon; Oniv = O. nivara; Oind = O. sativa ssp. indica; Ojap = O. sativa ssp. japonica.
(A) Numbers of Synteny Blocks
ObraOpunOmerOgluOglaObarOrufOnivOindOjap
Obra115353486378344300331645440305
Opun 159551458410379420745515394
Omer 137595510513571823658523
Oglu 150427404436824509421
Ogla 134337387710487358
Obar 140350729419328
Oruf 149818448342
Oniv 160901706
Oind 155443
Ojap 155
(B) Average number of genes per synteny block
ObraOpunOmerOgluOglaObarOrufOnivOindOjap
Obra24.568.940.963.163.478.273.434.961.680.7
Opun 21.440.458.958.669.565.634.449.667.8
Omer 14.839.940.845.243.027.534.742.9
Oglu 20.461.474.772.535.757.365.9
Ogla 19.879.070.935.653.571.2
Obar 20.390.139.969.483.4
Oruf 21.338.470.184.4
Oniv 14.132.337.5
Oind 16.962.3
Ojap 22.0
(C) Total length of synteny blocks, including duplication (kbp)
ObraOpunOmerOgluOglaObarOrufOnivOindOjap
Obra102,259482,879424,226470,842431,825535,282459,779431,573421,875461,883
Opun 165,853601,179688,557524,906557,918744,092567,689563,041682,892
Omer 95,698599,219467,896491,808597,297552,403483,530598,173
Oglu 135,462522,483563,117688,523640,215620,922675,950
Ogla 101,031511,157509,612492,492483,220513,075
Obar 107,814551,033527,107511,753545,746
Oruf 118,095571,611584,100662,749
Oniv 80,763513,998616,664
Oind 89,577577,416
Ojap 141,898
Table 2. Orthologous and paralogous genes for thirty key genes among ten Oryza species. The thirty target genes were members of one of four groups: the High Variation (HV), Single Duplication (SD), Single Loss (SL), and No Variation (NV) groups. Obra = O. brachyantha; Opun = O. punctata; Omer = O. meridionalis; Oglu = O. glumipatula; Ogla = O. glaberrima; Obar = O. barthii; Oruf = O. rufipogon; Oniv = O. nivara; Oind = O. sativa ssp. Indica; Ojap = O. sativa ssp. Japonica.
Table 2. Orthologous and paralogous genes for thirty key genes among ten Oryza species. The thirty target genes were members of one of four groups: the High Variation (HV), Single Duplication (SD), Single Loss (SL), and No Variation (NV) groups. Obra = O. brachyantha; Opun = O. punctata; Omer = O. meridionalis; Oglu = O. glumipatula; Ogla = O. glaberrima; Obar = O. barthii; Oruf = O. rufipogon; Oniv = O. nivara; Oind = O. sativa ssp. Indica; Ojap = O. sativa ssp. Japonica.
Gene NameObraOpunOmerOgluOglaObarOrufOnivOindOjapsum
His1274264353743HV
GS3232313335328
qSW5/GW5122331444327
TAC1211121111213SD
PUL111121111111
SSIII-1112111111111
SSI111111112111
Gn1a210111111110
OsAGPS2a221222222219SL
SBE3222222221118
BADH2210222222217
SSII-211011111119
HD111110111119
Ghd711011111119
GBSSII01011111118
Ghd801111011118
DPE1, OsDPE101111110118
SSIV-1111111111110NV
SSIV-2111111111110
AGPL1111111111110
AGPL4111111111110
WX1, GBSSI111111111110
sd1111111111110
OsAGPL1, OsAPL3111111111110
ALK111111111110
SCM2111111111110
BEI, SBE1111111111110
SSIII-2111111111110
OsPHS8, PHS8, ISA1, OsISA1111111111110
OsSSII-1111111111110
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Cho, Y.; Lim, I.; Ha, J. Genome-Wide Syntenic and Evolutionary Analysis of 30 Key Genes Found in Ten Oryza Species. Agronomy 2023, 13, 2100. https://doi.org/10.3390/agronomy13082100

AMA Style

Cho Y, Lim I, Ha J. Genome-Wide Syntenic and Evolutionary Analysis of 30 Key Genes Found in Ten Oryza Species. Agronomy. 2023; 13(8):2100. https://doi.org/10.3390/agronomy13082100

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Cho, Yeonghun, Insu Lim, and Jungmin Ha. 2023. "Genome-Wide Syntenic and Evolutionary Analysis of 30 Key Genes Found in Ten Oryza Species" Agronomy 13, no. 8: 2100. https://doi.org/10.3390/agronomy13082100

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