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Article

An Exploration of Candidate Korean Native Poaceae Plants for Breeding New Varieties as Garden Materials in the New Climate Regime Based on Existing Data

by
Sang Heon Kim
and
Wonwoo Cho
*
Division of Garden and Plant Resources, Korea National Arboretum, Pocheon 11186, Republic of Korea
*
Author to whom correspondence should be addressed.
Horticulturae 2024, 10(11), 1158; https://doi.org/10.3390/horticulturae10111158
Submission received: 30 September 2024 / Revised: 29 October 2024 / Accepted: 29 October 2024 / Published: 31 October 2024
(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)
Browse Figure
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Abstract

:
There is an increasing demand for low-maintenance public garden models, and environmental stress on plants due to climate change is growing. As a result, the demand for developing new plant varieties based on native species for use in gardens in response to climate change has increased significantly. Many plants in the Poaceae family are applied for various purposes, including food crops, fodder grasses, ornamental plants, and medicinal plants. Additionally, native plants provide economic and ecological benefits, making them advantageous for use in gardens. However, there are some difficulties in Poaceae breeding studies and the utilization of wild native plants for breeding. Model plants can be utilized in breeding studies of Poaceae plant species. In this study, to identify Korean native Poaceae species with the potential for use not only as garden materials but also as model plants for breeding research in response to climate change, candidate species were selected from the Korean Plant Names Index (KPNI). A total of three Korean native plants in the Poaceae family, including Brachypodium sylvaticum, Setaria viridis, and Zoysia japonica, were selected, and their properties and genome information were compared with the existing representative model plants, Arabidopsis thaliana and Brachypodium distachyon. The current research status of B. sylvaticum, S. viridis, and Z. japonica has been summarized, and the genome size and other characteristics of these model plants have been compared and discussed. As a result, both A. thaliana (2n = 2x = 10) and B. distachyon (2n = 2x = 10) are annual C3 plants, but B. sylvaticum (2n = 2x = 18) is a perennial C3 plant, and S. viridis (2n = 2x = 18) is an annual C4 plant. Thus, B. sylvaticum and S. viridis can be utilized as model plants for perennial C3 plants and annual C4 plants, respectively. Z. japonica (2n = 4x = 40) is a perennial C4 plant, but it can be unsuitable as a model plant because it is an allotetraploid. The application of these newly selected candidate plants in breeding research can build a foundation for breeding native Poaceae plants in Korea in the new climate regime.

1. Introduction

The role of gardens in biodiversity conservation is expanding due to rapid urban growth, which has increased the need for low-maintenance public garden models [1,2]. Native plants can be used as garden materials for effective maintenance because they are good materials for gardens, restoration, and erosion control [3,4]. Recently, environmental stress on plants due to climate change is growing, and to cope with its brunt, plant breeding is valuable [5,6]. Therefore, the demand for developing new plant varieties based on native plants as garden materials against climate change has increased.
Many plants in the Poaceae family are used as food crops, fodder grasses, ornamental plants, and medicinal plants [7]. Souza et al. [8] described the capability of native Poaceae plants for usage as garden materials. Moreover, Dunster [9] argued that Poaceae should be used not only for ornamental purposes but also for a variety of functions in the age of climate change. However, some Poaceae species are polyploid or have large and complex genomes, which pose challenges for breeding studies [10]. To overcome this problem, model plants, which have many advantages, such as short life cycles and small genome sizes [11,12], can be utilized in breeding studies of Poaceae plant species.
Model plants are extensively researched in plant science or agriculture [11,13]. Arabidopsis thaliana has been widely applied as a model plant since the 1980s [14]. However, Arabidopsis is a dicotyledon in the Brassicaceae family, which is not advisable in some areas as a model plant of principal plants in the Poaceae family [15,16]. Brachypodium distachyon, which is distributed in the Mediterranean region, has been broadly investigated since the late 2000s by researchers and breeders on cereal crops, notably wheat and barley, which are valuable crops in the Triticeae tribe [17]. However, B. distachyon is not native to Korea, so it is not suitable for use as a garden material in Korea.
B. sylvaticum and Setaria viridis have been recently proposed for use as model plants in the Poaceae family [18]. B. sylvaticum can be utilized as a model plant for perennial grasses [19]. S. viridis has the potential to be applied as a model plant for C4 photosynthesis exploration [20]. Both B. sylvaticum and S. viridis are native to Korea, so they are suitable for use as not only model plants but also garden materials in Korea.
Zoysia japonica, which is a perennial C4 grass, is the most popular warm-season turfgrass in Korea [21,22]. The reference genome of Z. japonica and Z. matrella was assembled and available [23]. Also, transgenic Z. japonica accessions were obtained using the genetic transformation method [24]. Therefore, Z. japonica has not yet been referred to as a model plant, but it seems that it can be used as a model plant for both perennial C4 plants and garden materials.
In this study, to identify Korean native Poaceae species with the potential to be used not only as garden materials but also as model plants for breeding research on abiotic stress tolerance in response to climate change, candidate species were selected from the Korean Plant Names Index (KPNI) based solely on previous research. The current research status of B. sylvaticum, S. viridis, and Z. japonica, which were finally selected from the KPNI, has been summarized, and their genome size, life cycle, and other characteristics have been compared with those of A. thaliana and B. distachyon, existing representative model plants, to evaluate their applicability. The main goals of this study are to establish criteria for selecting suitable candidate species for full-scale breeding research without incurring costs from expensive experiments and to review their applicability.

2. Materials and Methods

The list of Poaceae plant species was downloaded from the KPNI (http://www.nature.go.kr/kpni/, accessed on 11 July 2024). The scientific names of all plants were modified to remove information about authority, subspecies, or variety, leaving only the genus and species names. Since reference genomes are usually provided on a species basis, in the ‘Classification’ column, only ‘Species’ was selected, whereas ‘Variety’, ‘Subspecies’, ‘Horticultural cultivar’, and ‘Cultivar’ were deselected to filter the list (Supplementary Table S1). Furthermore, plant species with assembled reference genomes were investigated from the Published Plant Genomes database (https://www.plabipd.de/, accessed on 11 July 2024). A list of Poaceae plant species with assembled reference genomes was created based on the flowering plant cladogram, and their genome sizes were examined (Supplementary Table S2). Poaceae plant species with available reference genomes were selected from the KPNI list, and their characteristics, including life cycle and photosynthetic type, were investigated (Table 1). Since securing, cultivating directly, and evaluating all of the selected species take time and labor and is expensive, the analysis was conducted preferentially based on existing data. The life cycles of the selected plant species were investigated by the Korean Biodiversity Information System (http://www.nature.go.kr/, accessed on 12 July 2024) and the USDA PLANTS Database (https://plants.usda.gov/, accessed on 12 July 2024), and they were classified as annual or perennial. The photosynthetic types of the selected plants were investigated from previous studies, and they were classified as C3 or C4.
Small genome size is one of the criteria for model plants [11]. The genome sizes of Brachypodium distachyon, the model plant for monocots but not native in Korea, and rice (Oryza sativa), which is the representatively cultivated crop but not native in Korea, are 270 Mbps and 430 Mbps, respectively. Rice is one of the major food crops in the world, and many studies have already been conducted. Some researchers have suggested the use of rice as a model plant for monocots due to its relatively small genome size. Thus, if the genome size of a candidate species is larger than rice, the species is not worth being used as a model plant. To add to this point, Korean native plant species with genome sizes smaller than that of rice were selected as candidate model plants. The current research states of the candidate model species were investigated. The candidate model plants were compared with the representative model plants, Arabidopsis thaliana and Brachypodium distachyon, and the properties of these plants were compared and analyzed (Table 2). Also, based on Phytozome 13 (https://phytozome-next.jgi.doe.gov/, accessed on 18 July 2024), the genomes of the 2 existing representative model plants and the 2 newly suggested model plants were summarized (Table 3). For each plant species, two versions of genomes were selected and compared. Because it had no genome information in Phytozome 13, it was hard to analyze Zoysia japonica directly with the other 4 plants. Therefore, based on other studies [23,38], the genome of Zoysia japonica was analyzed separately from those of other species in the Zoysia genus, such as Z. matrella and Z. pacifica, which are cultivated plants in Korea (Table 4).

3. Results

Of the 494 Poaceae plants listed in the KPNI, 352 were registered as species (Supplementary Table S1), and 38 were selected for analysis in this study (Table 1). The number of Korean native plants was 14, the number of cultivated plants was 12, and the number of exotic plants was 12, respectively. The number of plants with genome sizes less than 1 Gbps was 16. The number of annual plants was 20, whereas the number of perennial plants was 18. The number of the C3 plants was 16, whereas the number of the C4 plants was 22. Plants with genome sizes smaller than that of rice (O. sativa) were selected, resulting in five species chosen for analysis. Of them, three plants (Brachypodium sylvaticum, Setaria viridis, and Zoysia japonica) were native to Korea, whereas two plants (Z. matrella and Z. pacifica) were cultivated in Korea.
Thus, three Korean native plants were selected as the candidate model plants, and their properties and the two representative model plants (Arabidopsis thaliana and Brachypodium distachyon) were analyzed (Table 2). A. thaliana was determined to be eudicots in the Brassicaceae family, whereas the others were monocots in the Poaceae family. A. thaliana, B. distachyon, and S. viridis were annual, but B. sylvaticum and Z. japonica were perennial. A. thaliana, B. distachyon, and B. sylvaticum were C3 plants, whereas S. viridis and Z. japonica were C4 plants. Both A. thaliana and B. distachyon were diploids with 10 chromosomes, but both B. sylvaticum and S. viridis were diploids with 18 chromosomes. Also, Z. japonica was a tetraploid with 40 chromosomes. Except for B. distachyon, the others were native plants in Korea.
The information on the genomes of the four plants (A. thaliana, B. distachyon, B. sylvaticum, and S. viridis) was obtained from Phytozome 13 and their reference publications (Table 3). Within the same species, assembled genome sizes sometimes varied depending on the genome version but were approximately the same. The genome size of A. thaliana was the smallest, followed by B. distachyon, B. sylvaticum, and S. viridis. Compared to A. thaliana and S. viridis, B. distachyon and B. sylvaticum showed relatively high differences in the number of contigs between the genome versions. As the genome versions were updated, the number of contigs decreased, indicating increased genome completeness through gap-filling. No constant trend was found in either the protein-coding transcripts or the protein-coding genes. As the genome versions were updated, the protein-coding transcripts of A. thaliana, B. distachyon, and B. sylvaticum increased, whereas those of S. viridis decreased. As the genome versions were updated, the protein-coding genes of A. thaliana and B. distachyon increased, whereas those of B. sylvaticum and S. viridis decreased.
The genome of Z. japonica was analyzed based on other studies (Table 4). There were large differences in the genomes of Z. japonica between Yang et al. [38] and Tanaka et al. [23]. Yang et al. [38] used the PacBio long-read sequencing, so the average length and maximum length they found were longer than those found by Tanaka et al. [23]. Also, Tanaka et al. [23] estimated the genome sizes of Z. japonica, Z. matrella, and Z. pacifica using flow cytometry as 390 Mbps, 380 Mbps, and 370 Mbps, respectively. The obtained genome sizes of Z. matrella and Z. pacifica were larger than the estimated genome sizes, whereas the obtained genome size of Z. japonica was smaller than the estimated genome size.

4. Discussion

Plants in the Poaceae family can be utilized in various ways [7]. However, most plant breeders focus on cereal crops such as rice, wheat, and maize, and only a few researchers have performed breeding programs for ornamental purposes [43]. Ornamental grasses in the Poaceae family are utilized in garden design and landscaping; these gardens are economically important in climate change acclimatization and extenuation [44,45]. Also, native plants have some economic and ecological benefits, and the utilization of native plants is advantageous in gardens [46,47]. Thus, although there is a need to study more diverse Korean native Poaceae species for garden plant breeding in response to increasingly severe and frequent abnormal climate damage by climate change, basic breeding studies on wild native plants in Korea are relatively scarce compared to cultivated crops.
Nowadays, breeders can utilize genomic resources such as reference genomes for molecular breeding for crop improvement [48]. Many species persist uncharted even though thousands of genomes have been explored [49]. Due to recent technological developments, various sequencing methods have been developed, and their cost is cheaper than before [50]. However, assembling the reference genome is still a costly, energy-demanding, and protracted task [51]. Furthermore, due to insufficient information, there are difficulties in utilizing wild plants for breeding [52]. Information obtained from model plants can be hypothesized for application to the target species of breeding, making it easier for researchers to conduct studies on those plant species [53]. Thus, building a foundation through research using model plants may play an important role in the breeding of wild native plants, which has not yet been explored. Additionally, if the model plant itself can be used as a garden material, it would be economically beneficial because it could be developed for a cultivar, not only for research purposes but also for practical use as a garden material.
Conducting experiments with actual plants requires significant time and money, and it is not feasible to include all plant species native to Korea. Therefore, it is crucial to select plant species for study using reasonable criteria before starting a full-scale experiment. In this study, to identify some Korean native Poaceae species with the potential to be used not only as garden materials but also as model plants for breeding research on abiotic stress tolerance in response to climate change, candidate species were explored from the KPNI based solely on previous research. A total of three native Korean Poaceae plants, including Brachypodium sylvaticum, Setaria viridis, and Zoysia japonica, were ultimately selected, and their characteristics and genome information were compared with those of representative model plants Arabidopsis thaliana and Brachypodium distachyon. Additionally, based on previous studies and existing data, the potential for using these plant species as garden materials in Korea will be discussed.
Brachypodium distachyon was first suggested as a model plant for cereals and forage grasses in 2001 [54]. B. distachyon is an annual C3 grass and is primarily distributed in the Mediterranean region (Figure 1A). Meanwhile, in Japan, a country geographically close to Korea, B. distachyon was first discovered at the Shimizu Port in 1953, and it is classified as a naturalized plant [55,56]. In Korea, however, although B. distachyon has been used in studies since the late 2000s [57,58], the discovery of B. distachyon in the wilds of Korea has not yet been reported. According to the Köppen–Geiger climate classification system, B. distachyon mainly distributes in Bsh, Csa, Csb/Bsk, and Cfa/Cfb regions [59]. Also, most parts of Japan belong to the Cfa region [60], so B. distachyon can survive there. However, most of the Korean Peninsula is composed of the Dwa climate, and Cfa is mainly observed in some southern regions, including Wando and Jeju [61,62]. Actually, in some island regions of the southern part of the Korean Peninsula, mainly Jeju Island, there are some plant species that are not distributed in the Korean Peninsula but are instead distributed in China, Japan, and Taiwan [63]. Therefore, it is reasonable to judge that B. distachyon would be able to adapt naturally and survive only in some southern regions of Korea, and it is inevitable that it will require significant effort and high costs to artificially cultivate B. distachyon as a garden material in most regions of Korea. For this reason, even though B. distachyon is a model plant for Poaceae plants, it is inefficient to use it for breeding purposes as a garden material in Korea.
Unlike B. distachyon, B. sylvaticum is a perennial C3 grass native to Korea (Figure 1B). Both B. sylvaticum and B. distachyon are plants in the Brachypodium genus of the Pooideae subfamily, so they are genetically close to each other [64]. Genetically close species can be utilized for breeding with hybridization and introgression [65]. The first version of the reference genome of B. distachyon was announced in 2010 [66]; by comparison, the reference genome of B. sylvaticum was recently reported [41]. Steinwand et al. [19] suggested B. sylvaticum for use as a model plant for perennial grasses. Also, according to Kim [67], B. sylvaticum was one of the potential candidates for ornamental grasses, and it was applied abroad but not in Korea. Therefore, B. sylvaticum can be utilized not only as a model plant for perennial C3 grasses but also as a garden material in Korea.
In the Brachypodium genus of the Pooideae subfamily, there is no species that is native or cultivated in Korea apart from B. sylvaticum. In the Pooideae subfamily, there are many significant C3 perennial grasses, such as bentgrasses (Agrostis spp.), bluegrasses (Poa spp.), fescues (Festuca spp.), and ryegrasses (Lolium spp.), applied as turf in temperate zones [68]. Except for annual cereal crops such as wheat, barley, and oat, and their relatives, only a few plants for a perennial turf in the Pooideae subfamily, such as Poa pratensis and Lolium perenne, have been studied for reference genome assembly [69,70]. Therefore, B. sylvaticum can be utilized as a model plant for perennial cool-season grasses whose reference genomes have not been reported, such as bentgrasses (Agrostis spp.) and fescues (Festuca spp.) in Korea.
S. viridis is an annual C4 grass in the Panicoideae subfamily, which includes many economically valuable C4 species such as maize, sorghum, and sugarcane [71]. Brutnell et al. [20] suggested the use of S. viridis as a model plant for C4 photosynthesis. The reference genomes of S. viridis were first reported in 2020 [42,72]. Therefore, compared to B. distachyon, S. viridis received attention relatively late as a model plant. However, S. viridis can be transformed using the floral-dip method, which has not yet been reported in B. distachyon [73]. As a result, S. viridis is used for genome editing research, such as CRISPR/Cas9 [74]. Additionally, various studies on C4 photosynthesis using S. viridis as a model plant were conducted [75,76]. Therefore, S. viridis is highly valuable for breeding research within the Poaceae family alongside B. distachyon.
In the Setaria genus, some species were applied as garden materials. S. italica, which is cultivated for food or forage in Korea, was planted and analyzed for composition and utilization in garden settings [77]. Also, according to Frey and Moretti [78], four species in the Setaria genus (S. italica, S. pumila, S. verticillata, and S. viridis) were discovered in urban gardens. Additionally, in the Panicoideae subfamily, the Paspalum genus and the Axonopus genus have been applied for lawns [79]. Apart from S. viridis, the reference genomes of S. italica and Paspalum notatum have been reported [80,81], but those of S. pumila, S. verticillata, and carpet grasses (Axonopus spp.) have not yet been reported. Also, S. viridis has a smaller genome than S. italica [72,82]. Therefore, S. viridis can be utilized as a model plant for annual C4 grass for garden materials.
Z. japonica is a widely used turfgrass that is distributed in East Asia, including in Korea, Japan, and China [83,84]. The genomes of Z. japonica were reported by Tanaka et al. [23] and Yang et al. [25]. However, there were large differences between the two genomes; therefore, further studies should be conducted to improve accuracy (Table 4). Also, considering the errors in Z. japonica, the estimated genome sizes of the other species, Z. matrella and Z. pacifica, could be uncertain as well. Therefore, genome assemblies of both Z. matrella and Z. pacifica using other accessions would be required to estimate more accurate genome sizes of both species. Additionally, utilizing Z. matrella and Z. pacifica as garden materials in Korea will inevitably require significant cost and effort, as these species are not native but cultivated in the country.
B. distachyon, B. sylvaticum, and S. viridis were reported as model plants for annual C3 grasses, perennial C3 grasses, and annual C4 grasses, respectively, whereas a model plant for perennial C4 grasses has not been reported. The Zoysia genus, which consists of 11 species, is a perennial C4 grass in the Chloridoideae subfamily and is native to the western Pacific Rim and Indian Ocean [84,85]. Z. japonica, Z. matrella, and Z. pacifica have been utilized as turf and ornate grasses [83]. Also, their genome sizes were relatively small [23], so one species in the Zoysia genus, which are perennial C4 grasses, can be utilized as a model plant for perennial C4 grasses. However, compared to B. sylvaticum and S. viridis, plants in the Zoysia genus were less studied, probably because they are not native to Europe or America. Additionally, plants in the Zoysia genus were allotetraploids, but Flavell [86] presented diploid genetics as one of the characteristics of model plants. Therefore, Zoysia species are suitable as garden materials but can be unsuitable as model plants. For the appearance of a model plant for perennial C4 grasses, the discovery of a diploid perennial C4 species with a small genome size is necessary.

5. Conclusions

In summary, three candidate plants were selected as model plants for breeding garden materials in Korean native Poaceae plants. Brachypodium sylvaticum and Setaria viridis were used as model plants for perennial C3 grasses and annual C4 grasses, respectively; thus, they could also be utilized in breeding research for garden materials. Zoysia japonica cannot be a model plant for perennial C4 grasses, but it has been studied and applied for various horticultural purposes. The application of these newly selected candidate plants in breeding research can build a foundation for the breeding of native Poaceae plants in Korea and contribute to the garden industry in Korea. Also, further research is required for the breeding and utilization of native plants in preparation for the new climate regime.

Supplementary Materials

The following supporting information can be downloaded at https://www.mdpi.com/article/10.3390/horticulturae10111158/s1. Table S1: The list of 352 species registered as ‘species’ of the 494 Poaceae plants listed in the Korean Plant Names Index (KPNI); Table S2: The list of Poaceae plant species with assembled reference genomes based on the flowering plant cladogram from the Published Plant Genomes database.

Author Contributions

Conceptualization, S.H.K. and W.C.; methodology, S.H.K.; software, S.H.K.; validation, S.H.K. and W.C.; formal analysis, S.H.K.; investigation, S.H.K.; resources, S.H.K.; data curation, S.H.K.; writing—original draft preparation, S.H.K.; writing—review and editing, S.H.K.; visualization, S.H.K.; supervision, S.H.K.; project administration, W.C.; funding acquisition, W.C. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Korea National Arboretum of the Korea Forest Service (Development of Breeding Models for Native Garden Plants in the New Climate Regime, KNA 1-5-1-24-1).

Data Availability Statement

Data are contained within the article.

Conflicts of Interest

The authors declare no conflicts of interest.

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Horticulturae 10 01158 g001
Figure 1. Geographic distributions of B. distachyon (A) and B. sylvaticum (B). Bright gray indicates native regions, and dark gray indicates introduced regions.
Figure 1. Geographic distributions of B. distachyon (A) and B. sylvaticum (B). Bright gray indicates native regions, and dark gray indicates introduced regions.
Horticulturae 10 01158 g001
Table 1. Characteristics of 38 plant species in the Poaceae family selected from the KPNI.
Table 1. Characteristics of 38 plant species in the Poaceae family selected from the KPNI.
Plant CategorySubfamilyScientific NameGenome Size (Mbps)Life Cycle zPhotosynthetic Type
NativeArundinoideaePhragmites australis1200PC3 [25]
NativeChloridoideaeLeptochloa chinensis460AC4 [26]
NativeChloridoideaeEleusine indica590AC4 [27]
NativeChloridoideaeCynodon dactylon1020PC4 [28]
NativeChloridoideaeZoysia japonica390PC4 [28]
NativeOryzoideaeZizania latifolia1800PC3 [26]
NativePanicoideaeSetaria viridis400AC4 [29]
NativePanicoideaeEchinochloa oryzoides1000AC4 [30]
NativePanicoideaeMicrostegium vimineum1300AC4 [31]
NativePanicoideaeEchinochloa crus-galli1400AC4 [30]
NativePanicoideaeThemeda triandra840PC4 [32]
NativePanicoideaeMiscanthus sinensis2500PC4 [26]
NativePooideaePoa annua1800AC3 [29]
NativePooideaeBrachypodium sylvaticum360PC3 [33]
CultivatedBambusoideaePhyllostachys edulis2080PC3 [34]
CultivatedChloridoideaeZoysia matrella380PC4 [35]
CultivatedChloridoideaeZoysia pacifica370PC4 [35]
CultivatedOryzoideaeOryza sativa430AC3 [29]
CultivatedPanicoideaePanicum miliaceum920AC4 [29]
CultivatedPanicoideaeSorghum bicolor820AC4 [29]
CultivatedPanicoideaeCoix lacryma-jobi1560AC4 [29]
CultivatedPanicoideaeZea mays2300AC4 [29]
CultivatedPanicoideaeSetaria italica490AC4 [29]
CultivatedPooideaeAvena sativa4000AC3 [29]
CultivatedPooideaeTriticum aestivum17,000AC3 [29]
CultivatedPooideaeHordeum vulgare5100AC3 [29]
ExoticChloridoideaeEragrostis curvula660PC4 [36]
ExoticPanicoideaeSaccharum spontaneum3360PC4 [29]
ExoticPanicoideaePaspalum notatum550PC4 [29]
ExoticPanicoideaeEremochloa ophiuroides800PC4 [29]
ExoticPanicoideaePanicum virgatum1200PC4 [29]
ExoticPooideaeLolium rigidum2400AC3 [29]
ExoticPooideaePoa pratensis3500PC3 [29]
ExoticPooideaeAlopecurus myosuroides3500AC3 [37]
ExoticPooideaeLolium multiflorum600AC3 [29]
ExoticPooideaePoa trivialis1350PC3 [29]
ExoticPooideaeBromus tectorum2500AC3 [29]
ExoticPooideaeLolium perenne2000PC3 [29]
z P: perennial; A: annual.
Table 2. Basic information about the 2 representative model plants and the 3 candidate model plants.
Table 2. Basic information about the 2 representative model plants and the 3 candidate model plants.
Arabidopsis thalianaBrachypodium distachyonBrachypodium sylvaticumSetaria viridisZoysia japonica
Common namemouseear
cress		purple false bromeslender false bromegreen bristlegrassKorean lawngrass
CotyledonEudicotsMonocotsMonocotsMonocotsMonocots
OrderBrassicalesPoalesPoalesPoalesPoales
FamilyBrassicaceaePoaceaePoaceaePoaceaePoaceae
TribeCamelineaeBrachypodieaeBrachypodieaePaniceaeZoysieae
GenusArabidopsisBrachypodiumBrachypodiumSetariaZoysia
Life cycleAnnualAnnualPerennialAnnualPerennial
Photosynthetic typeC3C3C3C4C4
Chromosome number2n = 2x = 102n = 2x = 102n = 2x = 182n = 2x = 182n = 4x = 40
Native in KoreaYNYYY
Table 3. Comparison of the reference genome data of the 4 model plants from Phytozome 13.
Table 3. Comparison of the reference genome data of the 4 model plants from Phytozome 13.
Arabidopsis thalianaBrachypodium distachyonBrachypodium sylvaticumSetaria viridis
Genome
version		TAIR10Araport11v2.1v3.2v1.1v2.1v2.1v4.1
SourceTAIRTAIRJGIJGIJGIJGIJGIJGI
Accession‘Col-0’‘Col-0’‘Bd21’‘Bd21’‘Ain-1’‘Ain-1’‘A10.1’‘A10’
Assembled genome size119,667,750119,667,750271,997,306271,163,419358,283,154360,731,464395,731,502397,277,387
No. of
contigs		169169485341117147539
Protein-coding
transcripts		35,38648,45642,86856,84750,26354,42352,45950,526
Protein-coding genes27,41627,65531,69432,43936,92731,64338,33429,807
Reference publicationLamesch et al. [39]Cheng et al. [40] Lei et al. [41] Mamidi et al. [42]
Table 4. Comparison of the reference genome data of Zoysia species.
Table 4. Comparison of the reference genome data of Zoysia species.
Zoysia japonicaZoysia matrellaZoysia pacifica
Accession‘Yaji’‘Nagirizaki’‘Wakaba’‘Zanpa’
Estimated genome size421 Mbps390 Mbps380 Mbps370 Mbps
Genome versionunknownZJN_r1.1ZMW_r1.0ZPZ_r1.0
SourceunreleasedZoysia Genome DatabaseZoysia Genome DatabaseZoysia Genome Database
Number of sequences135011,78613,60911,428
Total length373,429,196334,384,427563,438,595397,009,957
Average length276,61428,37141,40234,740
Max. length17,601,8608,501,8951,041,5061,506,652
Min. lengthunknown500500500
N50 length3,962,5542,370,062108,897111,449
Number of predicted genes50,14059,27195,07965,252
Reference publicationYang et al. [38]Tanaka et al. [23]Tanaka et al. [23]Tanaka et al. [23]
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Kim, S.H.; Cho, W. An Exploration of Candidate Korean Native Poaceae Plants for Breeding New Varieties as Garden Materials in the New Climate Regime Based on Existing Data. Horticulturae 2024, 10, 1158. https://doi.org/10.3390/horticulturae10111158

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Kim SH, Cho W. An Exploration of Candidate Korean Native Poaceae Plants for Breeding New Varieties as Garden Materials in the New Climate Regime Based on Existing Data. Horticulturae. 2024; 10(11):1158. https://doi.org/10.3390/horticulturae10111158

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Kim, Sang Heon, and Wonwoo Cho. 2024. "An Exploration of Candidate Korean Native Poaceae Plants for Breeding New Varieties as Garden Materials in the New Climate Regime Based on Existing Data" Horticulturae 10, no. 11: 1158. https://doi.org/10.3390/horticulturae10111158

APA Style

Kim, S. H., & Cho, W. (2024). An Exploration of Candidate Korean Native Poaceae Plants for Breeding New Varieties as Garden Materials in the New Climate Regime Based on Existing Data. Horticulturae, 10(11), 1158. https://doi.org/10.3390/horticulturae10111158

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