Sequencing and comparative analyses of the genomes of zoysiagrasses

Whole-genome sequencing of allotetraploid bermudagrass reveals the origin of Cynodon and candidate genes for salt tolerance

Bermudagrass (Cynodon dactylon) is a globally distributed, extensively used warm-season turf and forage grass with high tolerance to salinity and drought stress in alkaline environments. However, the origin of the species and genetic mechanisms for salinity tolerance in the species are basically unknown. Accordingly, we set out to study evolution divergence events in the Cynodon genome and to identify genes for salinity tolerance. We developed a 604.0 Mb chromosome-level polyploid genome sequence for bermudagrass 'A12359' (n = 18). The C. dactylon genome comprises 2 complete sets of homoeologous chromosomes, each with approximately 30 000 genes, and most genes are conserved as syntenic pairs. Phylogenetic study showed that the initial Cynodon species diverged from Oropetium thomaeum approximately 19.7-25.4 million years ago (Mya), the A and B subgenomes of C. dactylon diverged approximately 6.3-9.1 Mya, and the bermudagrass polyploidization event occurred 1.5 Mya on the African continent. Moreover, we identified 82 candidate genes associated with seven agronomic traits using a genome-wide association study, and three single-nucleotide polymorphisms were strongly associated with three salt resistance genes: RAP2-2, CNG channels, and F14D7.1. These genes may be associated with enhanced bermudagrass salt tolerance. These bermudagrass genomic resources, when integrated, may provide fundamental insights into evolution of diploid and tetraploid genomes and enhance the efficacy of comparative genomics in studying salt tolerance in Cynodon.

Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages

Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.

Genome-Wide Identification and Expression Analysis of the PUB Gene Family in Zoysia japonica under Salt Stress

The U-box protein family of ubiquitin ligases is important in the biological processes of plant growth, development, and biotic and abiotic stress responses. Plants in the genus Zoysia are recognized as excellent warm-season turfgrass species with drought, wear and salt tolerance. In this study, we conducted the genome-wide identification of plant U-box (PUB) genes in Zoysia japonica based on U-box domain searching. In total, 71 ZjPUB genes were identified, and a protein tree was constructed of AtPUBs, OsPUBs, and ZjPUBs, clustered into five groups. The gene structures, characteristics, cis-elements and protein interaction prediction network were analyzed. There were mainly ABRE, ERE, MYB and MYC cis-elements distributed in the promoter regions of ZjPUBs. ZjPUBs were predicted to interact with PDR1 and EXO70B1, related to the abscisic acid signaling pathway. To better understand the roles of ZjPUBs under salt stress, the expression levels of 18 ZjPUBs under salt stress were detected using transcriptome data and qRT-PCR analysis, revealing that 16 ZjPUBs were upregulated in the roots under salt treatment. This indicates that ZjPUBs might participate in the Z. japonica salt stress response. This research provides insight into the Z. japonica PUB gene family and may support the genetic improvement in the molecular breeding of salt-tolerant zoysiagrass varieties.

Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high-quality reference transcript dataset

Inadequate reference databases in RNA-seq analysis can hinder data utilization and interpretation. In this study, we have successfully constructed a high-quality reference transcript dataset, ZjRTD1.0, for Zoysia japonica, a widely-used turfgrass with exceptional tolerance to various abiotic stress, including low temperatures and salinity. This dataset comprises 113,089 transcripts from 57,143 genes. BUSCO analysis demonstrates exceptional completeness (92.4%) in ZjRTD1.0, with reduced proportions of fragmented (3.3%) and missing (4.3%) orthologs compared to prior datasets. ZjRTD1.0 enables more precise analyses, including transcript quantification and alternative splicing assessments using public datasets, which identified a substantial number of differentially expressed transcripts (DETs) and differential alternative splicing (DAS) events, leading to several novel findings on Z. japonica's responses to abiotic stresses. First, spliceosome gene expression influenced alternative splicing significantly under abiotic stress, with a greater impact observed during low-temperature stress. Then, a significant positive correlation was found between the number of differentially expressed genes (DEGs) encoding protein kinases and the frequency of DAS events, suggesting the role of protein phosphorylation in regulating alternative splicing. Additionally, our results suggest possible involvement of serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in generating inclusion/exclusion isoforms under low-temperature stress. Furthermore, our investigation revealed a significantly enhanced overlap between DEGs and differentially alternatively spliced genes (DASGs) in response to low-temperature stress, suggesting a unique co-regulatory mechanism governing transcription and splicing in the context of low-temperature response. In conclusion, we have proven that ZjRTD1.0 will serve as a reliable and useful resource for future transcriptomic analyses in Z. japonica.

CRISPR/Cas9-mediated knockout of NYC1 gene enhances chlorophyll retention and reduces tillering in Zoysia matrella (L.) Merrill

KEY MESSAGE

Genome editing by CRISPR/Cas9 can be applied to Z. matrella 'Wakaba', and knockout mutants of ZmNYC1 gene exhibited stay-green phenotype and reduced tillering. Zoysia matrella is a widely used C4 warm-season turfgrass for landscaping, golf courses, and sports fields. Here, we used the CRISPR/Cas9 system to target the Non-Yellow Coloring1 (ZmNYC1) gene in the highly heterozygous allotetraploid Z. matrella 'Wakaba', aiming to generate a novel stay-green variety. Of 441 Agrobacterium-infected calli, 22 (5.0%) were transformed, and 14 of these (63.6%) showed targeted mutations through cleaved amplified polymorphic sequences analysis. Sequencing analysis revealed mutations mostly consisting of 1 or 2 bp indels, occurring 2 to 4 bp upstream of the PAM sequence. Regenerated plants exhibited five ZmNYC1 target locus genotypes, including homozygous mutants with a complete knockout of all four alleles in the T0 generation. Under dark treatment, ZmNYC1-mutated plants displayed suppressed chlorophyll b (Chl b) degradation, leading to higher chlorophyll content and Chl b, with a lower chlorophyll a/chlorophyll b ratio compared to the wild type (WT). However, the ZmNYC1 mutation also inhibited plant growth in homozygous mutant genotypes, exhibiting reduced tillering compared to WT. Additionally, during winter simulation, mutant with a complete knockout retained greenness longer than the WT. This is the first successful use of CRISPR/Cas9 genome editing in zoysiagrass. The mutants of the ZmNYC1 gene would serve as valuable breeding material for developing improved zoysiagrass varieties that can maintain their green color for longer periods, even during winter dormancy.

Comprehensive transcriptomic analysis of age-, dark-, and salt-induced senescence reveals underlying mechanisms and key regulators of leaf senescence in Zoysia japonica

The lawn grass Zoysia japonica is widely cultivated for its ornamental and recreational value. However, its green period is subject to shortening, which significantly decreases the economic value of Z. japonica, especially for large cultivations. Leaf senescence is a crucial biological and developmental process that significantly influences the lifespan of plants. Moreover, manipulation of this process can improve the economic value of Z. japonica by extending its greening period. In this study, we conducted a comparative transcriptomic analysis using high-throughput RNA sequencing (RNA-seq) to investigate early senescence responses triggered by age, dark, and salt. Gene set enrichment analysis results indicated that while distinct biological processes were involved in each type of senescence response, common processes were also enriched across all senescence responses. The identification and validation of differentially expressed genes (DEGs) via RNA-seq and quantitative real-time PCR provided up- and down-regulated senescence markers for each senescence and putative senescence regulators that trigger common senescence pathways. Our findings revealed that the NAC, WRKY, bHLH, and ARF transcription factor (TF) groups are major senescence-associated TF families that may be required for the transcriptional regulation of DEGs during leaf senescence. In addition, we experimentally validated the senescence regulatory function of seven TFs including ZjNAP, ZjWRKY75, ZjARF2, ZjNAC1, ZjNAC083, ZjARF1, and ZjPIL5 using a protoplast-based senescence assay. This study provides new insight into the molecular mechanisms underlying Z. japonica leaf senescence and identifies potential genetic resources for enhancing its economic value by prolonging its green period.

Genome-wide identification, expression analysis, and transcriptome analysis of the IAA gene family in Zoysia japonica

BACKGROUND

AUX/IAA is an essential signaling molecule and has great physiological importance in various plants, but its function in Zoysia japonica remains unknown.

METHODS AND RESULTS

Genome-wide identification and analysis of AUX/IAA genes used bioinformatics methods to investigate the ZjIAA genes' expression of exogenous IAA hydroponics treatment for 2 h by qRT-PCR, control and exogenous IAA treated zoysia were subjected to transcriptome sequencing. ZjIAAs were distributed across the 13 subfamilies by phylogenetic analysis with Oryza sativa and Arabidopsis thaliana. Multiple sequence alignment revealed that the majority of genes were non-canonical ZjIAAs with incomplete domain. The optimal growth concentration of the IAA hormone was 0.05 mM, and the qRT-PCR analysis revealed that eight ZjIAAs were differentially expressed, with seven genes considerably upregulating and one gene significantly downregulating. The result of transcriptome sequencing revealed that 515 differentially expressed genes (DEGs) were identified, with 344 upregulated genes and 171 downregulated genes. A total of 18 genes were annotated as involved in the plant hormone signal transduction pathway. And 8 ZjIAAs exhibited distinct expressions, 7 upregulated, and only one downregulated, according to the qRT-PCR study.

CONCLUSIONS

Genome-wide identification and analysis increased the understanding of the evolution and function of the IAA family in zoysia. DEGs of control and treatment with 0.05 mM exogenous IAA hormone were investigated by transcriptome sequencing. ZjIAAs had substantial variations in the expression of associated genes, with the majority of genes upregulated and 18 genes implicated in plant hormone signal transduction.

GGDB: A Grameneae genome alignment database of homologous genes hierarchically related to evolutionary events

The genomes of Gramineae plants have been preferentially sequenced owing to their economic value. These genomes are often quite complex, for example harboring many duplicated genes, and are the main source of genetic innovation and often the result of recurrent polyploidization. Deciphering these complex genome structures and linking duplicated genes to specific polyploidization events are important for understanding the biology and evolution of plants. However, efforts have been hampered by the complexity of analyzing these genomes. Here, we analyzed 29 well-assembled and up-to-date Gramineae genome sequences by hierarchically relating duplicated genes in collinear regions to specific polyploidization or speciation events. We separated duplicated genes produced by each event, established lists of paralogous and orthologous genes, and ultimately constructed an online database, GGDB (http://www.grassgenome.com/). Homologous gene lists from each plant and between plants can be displayed, searched, and downloaded from the database. Interactive comparison tools are deployed to demonstrate homology among user-selected plants and to draw genome-scale or local alignment figures and gene-based phylogenetic trees corrected by exploiting gene collinearity. Using these tools and figures, users can easily detect structural changes in genomes and explore the effects of paleo-polyploidy on crop genome structure and function. The GGDB will provide a useful platform for improving our understanding of genome changes and functional innovation in Gramineae plants.

The combination of RNA-seq transcriptomics and data-independent acquisition proteomics reveals the mechanisms underlying enhanced salt tolerance by the ZmPDI gene in Zoysia matrella [L.] Merr

Zoysia matrella [L.] Merr. is one of the three most economically important Zoysia species due to its strong salt tolerance and wide application. However, the molecular mechanisms regulating salt tolerance in Z. matrella remain unknown. The protein disulfide isomerase ZmPDI of Z. matrella was obtained by salt stress screening with yeast cells, and its expression was significantly upregulated after salt stress. Based on the obtained ZmPDI overexpression transgenic Z. matrella plants, we carried out salt tolerance identification and found that ZmPDI can significantly enhance the salt tolerance of Z. matrella. Root samples of OX-ZmPDI transgenic and wild-type plants were collected at 0 and 24 h after salt treatments for RNA-seq and data-independent acquisition (DIA) proteome sequencing. Combined analysis of the transcriptome and proteome revealed that ZmPDI may enhance the salt tolerance of Z. matrella by regulating TUBB2, PXG4, PLDα2, PFK4, and 4CL1. This research presents the molecular regulatory mechanism of the ZmPDI gene in Z. matrella for resistance to salt stress and facilitates the use of molecular breeding to improve the salt tolerance of grasses.

Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses

BACKGROUND

Zoysiagrass (Zoysia spp.) is a warm-season turfgrass. It is widely used as turfgrasses throughout the world, offers good turf qualities, including salt tolerance, resistance to drought and heat. However, the underlying genetic mechanism of zoysiagrass responsive to salt stress remains largely unexplored.

RESULTS

In present study, we performed a whole-genome comparative analysis for ten plant genomes. Evolutionary analysis revealed that Chloridoideae diverged from Panicoideae approximately 33.7 million years ago (Mya), and the phylogenetic relationship among three zoysiagrasses species suggested that Zoysia matrella may represent an interspecific hybrid between Zoysia japonica and Zoysia pacifica. Genomic synteny indicated that Zoysia underwent a genus-specific whole-genome duplication (WGD) event approximately 20.8 Mya. The expression bais of homologous genes between the two subgenomes suggested that the B subgenome of Z. japonica contributes to salt tolerance. In additon, comparative genomic analyses revealed that the salt adaptation of Zoysia is likely attributable to the expanded cytochrome P450 and ABA biosynthetic gene families. Furthermore, we further found that many duplicated genes from the extra WGD event exhibited distinct functional divergence in response to salt stress using transcriptomic analysis, suggesting that this WGD event contributed to strong resistance to salt stress.

CONCLUSIONS

Here, our results revealed that expanded cytochrome P450 and ABA biosynthetic gene families, and many of those duplicated genes from recent zoysia-specific WGD event contributed to salt adaptation of zoysiagrass, which provided insight into the genetic underpinning of salt adaptation and valuable information for further studies on salt stress-related traits in Zoysia.

Progress and Challenges in China Turfgrass Abiotic Stress Resistance Research

Turfgrasses are an important vehicle for urban ecology and one of the most important indicators of economy and civilization. The biological characteristics of different turfgrass species affect the productivity and quality of the turf and its potential use in landscapes, slopes, and sports fields. Cultivation and management techniques can assist turfgrasses to meet the challenges of climate change, while the development of molecular breeding will provide a broader platform for the application of turfgrasses. The turfgrass industry of China has developed considerably in the last three decades; however, there is still an objective gap with developed countries. This manuscript reviewed the research progress of turfgrass resistance breeding, analyzed the bottlenecks in the development of turfgrass resistance breeding, and put forward the strategies to cope with the bottlenecks. Our review aims to promote research and utilization of turfgrasses.

Genomic insights into the origin, adaptive evolution, and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields

Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. The L. chinensis genome is derived from two diploid progenitors that diverged ∼10.9 million years ago, and its two subgenomes display neither fractionation bias nor overall gene expression dominance. Comparative genomic analyses reveal substantial genome rearrangements in L. chinensis after its divergence from the common ancestor of Chloridoideae and, together with transcriptome profiling, demonstrate the important contribution of tetraploidization to the gene sources for the herbicide resistance of L. chinensis. Population genomic analyses of 89 accessions from China reveal that L. chinensis accessions collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting that L. chinensis spread in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis developed significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. Taken together, our study generated valuable genomic resources for future fundamental research and agricultural management of L. chinensis, and provides significant new insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.

Expression of a Chlorophyll b Reductase Gene from Zoysia japonica Causes Changes in Leaf Color and Chlorophyll Morphology in Agrostis stolonifera

The NYC-like (NOL) enzyme is considered as an essential enzyme for chlorophyll b degradation, which catalyzes the formation of 7-hydroxymethyl chlorophyll a from chlorophyll b. The ZjNOL gene was cloned from Zoysia japonica with a completed coding sequence of 981-bp in length, encoding 326 amino acids. ZjNOL was localized on the stroma side of the thylakoid membrane, and co-localized with ZjNYC in the chloroplasts. Multiple photoregulatory elements and hormone regulatory elements were identified in the promoter region of the ZjNOL gene, and the expression level of the ZjNOL gene was dramatically up-regulated in senescence leaves, which were regulated by a variety of plant hormones. ZjNOL's ectopic expression in creeping bentgrass produced yellow leaves, thicker cortex, and smaller vascular column cells. Additionally, transgenic plants exhibited morphological alterations in their chloroplast structure, and the number of grana and thylakoids per grana stack reduced dramatically. Transgenic plants also had a lower photosynthetic rate and Fm/Fv than the control. The transgenic plants displayed a decreased chlorophyll content and a greater rate of ion leakage. The properties and activities of ZjNOL will serve as a foundation for future research into gene functions and regulatory processes.

Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica

BACKGROUND

Zoysia japonica is an important warm-season turfgrass used worldwide. Although the draft genome sequence and a vast amount of next-generation sequencing data have been published, the current genome annotation and complete mRNA structure remain incomplete. Therefore, to analyze the full-length transcriptome of Z. japonica, we used the PacBio single-molecule long-read sequencing method in this study.

RESULTS

First, we generated 37,056 high-confidence non-redundant transcripts from 16,005 gene loci. Next, 32,948 novel transcripts, 913 novel gene loci, 8035 transcription factors, 89 long non-coding RNAs, and 254 fusion transcripts were identified. Furthermore, 15,675 alternative splicing events and 5325 alternative polyadenylation sites were detected. In addition, using bioinformatics analysis, the underlying transcriptional mechanism of senescence was explored based on the revised reference transcriptome.

CONCLUSION

This study provides a full-length reference transcriptome of Z. japonica using PacBio single-molecule long-read sequencing for the first time. These results contribute to our knowledge of the transcriptome and improve the knowledge of the reference genome of Z. japonica. This will also facilitate genetic engineering projects using Z. japonica.

Tissue Culture and Somatic Embryogenesis in Warm-Season Grasses—Current Status and Its Applications: A Review

Warm-season grasses are C4 plants and have a high capacity for biomass productivity. These grasses are utilized in many agricultural production systems with their greatest value as feeds for livestock, bioethanol, and turf. However, many important warm-season perennial grasses multiply either by vegetative propagation or form their seeds by an asexual mode of reproduction called apomixis. Therefore, the improvement of these grasses by conventional breeding is difficult and is dependent on the availability of natural genetic variation and its manipulation through breeding and selection. Recent studies have indicated that plant tissue culture system through somatic embryogenesis complements and could further develop conventional breeding programs by micropropagation, somaclonal variation, somatic hybridization, genetic transformation, and genome editing. This review summarizes the tissue culture and somatic embryogenesis in warm-season grasses and focus on current status and above applications including the author’s progress.

High-quality chromosome-scale de novo assembly of the Paspalum notatum 'Flugge' genome

BACKGROUND

Paspalum notatum 'Flugge' is a diploid with 20 chromosomes (2n = 20) multi-purpose subtropical herb native to South America and has a high ecological significance. It is currently widely planted in tropical and subtropical regions. Despite the gene pool of P. notatum 'Flugge' being unearthed to a large extent in the past decade, no details about the genomic information of relevant species in Paspalum have been reported. In this study, the complete genome information of P. notatum was established and annotated through sequencing and de novo assembly of its genome.

RESULTS

The latest PacBio third-generation HiFi assembly and sequencing revealed that the genome size of P. notatum 'Flugge' is 541 M. The assembly result is the higher index among the genomes of the gramineous family published so far, with a contig N50 = 52Mbp, scaffold N50 = 49Mbp, and BUSCOs = 98.1%, accounting for 98.5% of the estimated genome. Genome annotation revealed 36,511 high-confidence gene models, thus providing an important resource for future molecular breeding and evolutionary research. A comparison of the genome annotation results of P. notatum 'Flugge' with other closely related species revealed that it had a close relationship with Zea mays but not close compared to Brachypodium distachyon, Setaria viridis, Oryza sativa, Puccinellia tenuiflora, Echinochloa crusgalli. An analysis of the expansion and contraction of gene families suggested that P. notatum 'Flugge' contains gene families associated with environmental resistance, increased reproductive ability, and molecular evolution, which explained its excellent agronomic traits.

CONCLUSION

This study is the first to report the high-quality chromosome-scale-based genome of P. notatum 'Flugge' assembled using the latest PacBio third-generation HiFi sequencing reads. The study provides an excellent genetic resource bank for gramineous crops and invaluable perspectives regarding the evolution of gramineous plants.

Expression of ZjPSY, a Phytoene Synthase Gene from Zoysia japonica Affects Plant Height and Photosynthetic Pigment Contents

Phytoene synthase (PSY) is a key limiting enzyme in the carotenoid biosynthesis pathway for regulating phytoene synthesis. In this study, ZjPSY was isolated and identified from Zoysia japonica, an important lawn grass species. ZjPSY cDNA was 1230 bp in length, corresponding to 409 amino acids. ZjPSY showed higher expression in young leaves and was downregulated after GA₃, ABA, SA, and MeJA treatments, exhibiting a sensitivity to plant hormones. Regulatory elements of light and plant hormone were found in the upstream of ZjPSY CDS. Expression of ZjPSY in Arabidopsis thaliana protein led to carotenoid accumulation and altered expression of genes involved in the carotenoid pathway. Under no-treatment condition, salt treatment, and drought treatment, transgenic plants exhibited yellowing, dwarfing phenotypes. The carotenoid content of transgenic plants was significantly higher than that of wild-type under salt stress and no-treatment condition. Yeast two-hybrid screening identified a novel interacting partner ZjJ2 (DNAJ homologue 2), which encodes heat-shock protein 40 (HSP40). Taken together, this study suggested that ZjPSY may affect plant height and play an important role in carotenoid synthesis. These results broadened the understanding of carotenoid synthesis pathways and laid a foundation for the exploration and utilization of the PSY gene.

A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth

Common bermudagrass (Cynodon dactylon L.) is an important perennial warm-season turfgrass species with great economic value. However, the reference genome is still deficient in C. dactylon, which severely impedes basic studies and breeding studies. In this study, a high-quality haplotype-resolved genome of C. dactylon cultivar Yangjiang was successfully assembled using a combination of multiple sequencing strategies. The assembled genome is approximately 1.01 Gb in size and is comprised of 36 pseudo chromosomes belonging to four haplotypes. In total, 76,879 protein-coding genes and 529,092 repeat sequences were annotated in the assembled genome. Evolution analysis indicated that C. dactylon underwent two rounds of whole-genome duplication events, whereas syntenic and transcriptome analysis revealed that global subgenome dominance was absent among the four haplotypes. Genome-wide gene family analyses further indicated that homologous recombination-regulating genes and tiller-angle-regulating genes all showed an adaptive evolution in C. dactylon, providing insights into genome-scale regulation of polyploid genome stability and prostrate growth. These results not only facilitate a better understanding of the complex genome composition and unique plant architectural characteristics of common bermudagrass, but also offer a valuable resource for comparative genome analyses of turfgrasses and other plant species.

A high-quality chromosome-scale assembly of the centipedegrass [Eremochloa ophiuroides (Munro) Hack.] genome provides insights into chromosomal structural evolution and prostrate growth habit

Centipedegrass [Eremochloa ophiuroides (Munro) Hack.], a member of the Panicoideae subfamily, is one of the most important warm-season turfgrasses originating from China. This grass has an extremely developed prostrate growth habit and has been widely used in transitional and warm climatic regions. To better understand the genetic basis of important biological characteristics, such as prostrate growth and seed yield, in warm-season turfgrasses, we present a high-quality reference genome for centipedegrass and use PacBio, BioNano, and Hi-C technologies to anchor the 867.43 Mb genome assembly into nine pseudochromosomes, with a scaffold N50 of 86.05 Mb and 36,572 annotated genes. Centipedegrass was most closely related to sorghum and diverged from their common ancestor ~16.8 Mya. We detected a novel chromosome reshuffling event in centipedegrass, namely, the nest chromosome fusion event in which fusion of chromosomes 8 and 10 of sorghum into chromosome 3 of centipedegrass likely occurred after the divergence of centipedegrass from sorghum. The typical prostrate growth trait in centipedegrass may be linked to the expansion of candidate PROSTRATE GROWTH 1 (PROG1) genes on chromosome 2. Two orthologous genes of OsPROG1, EoPROG1, and EoPROG2, were confirmed to increase the stem number and decrease the stem angle in Arabidopsis. Collectively, our assembled reference genome of centipedegrass offers new knowledge and resources to dissect the genome evolution of Panicoideae and accelerate genome-assisted breeding and improvement of plant architecture in turf plants.

Genetic Diversity and Population Structure of a Rhodes Grass (Chloris gayana) Collection

Rhodes grass (Chloris gayana Kunth) is one of the most important forage grasses used throughout the tropical and subtropical regions of the world. Enhancing the conservation and use of genetic resources requires the development of knowledge and understanding about the existing global diversity of the species. In this study, 104 Rhodes grass accessions, held in trust in the ILRI forage genebank, were characterized using DArTSeq markers to evaluate the genetic diversity and population structure, and to develop representative subsets, of the collection. The genotyping produced 193,988 SNP and 142,522 SilicoDArT markers with an average polymorphic information content of 0.18 and 0.26, respectively. Hierarchical clustering using selected informative markers showed the presence of two and three main clusters using SNP and SilicoDArT markers, respectively, with a cophenetic correction coefficient of 82%. Bayesian population structure analysis also showed the presence of two main subpopulations using both marker types indicating the existence of significant genetic variation in the collection. A representative subset, containing 21 accessions from diverse origins, was developed using the SNP markers. In general, the results revealed substantial genetic diversity in the Rhodes grass collection, and the generated molecular information, together with the developed subset, should help enhance the management, use and improvement of Rhodes grass germplasm in the future.

The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

Widespread lateral gene transfer among grasses

Lateral gene transfer (LGT) occurs in a broad range of prokaryotes and eukaryotes, occasionally promoting adaptation. LGT of functional nuclear genes has been reported among some plants, but systematic studies are needed to assess the frequency and facilitators of LGT. We scanned the genomes of a diverse set of 17 grass species that span more than 50 Ma of divergence and include major crops to identify grass-to-grass protein-coding LGT. We identified LGTs in 13 species, with significant variation in the amount each received. Rhizomatous species acquired statistically more genes, probably because this growth habit boosts opportunities for transfer into the germline. In addition, the amount of LGT increases with phylogenetic relatedness, which might reflect genomic compatibility among close relatives facilitating successful transfers. However, genetic exchanges among highly divergent species indicates that transfers can occur across almost the entire family. Overall, we showed that LGT is a widespread phenomenon in grasses that has moved functional genes across the grass family into domesticated and wild species alike. Successful LGTs appear to increase with both opportunity and compatibility.

The genome of the warm-season turfgrass African bermudagrass (Cynodon transvaalensis)

Cynodon species can be used for multiple purposes and have high economic and ecological significance. However, the genetic basis of the favorable agronomic traits of Cynodon species is poorly understood, partially due to the limited availability of genomic resources. In this study, we report a chromosome-scale genome assembly of a diploid Cynodon species, C. transvaalensis, obtained by combining Illumina and Nanopore sequencing, BioNano, and Hi-C. The assembly contains 282 scaffolds (~423.42 Mb, N50 = 5.37 Mb), which cover ~93.2% of the estimated genome of C. transvaalensis (~454.4 Mb). Furthermore, 90.48% of the scaffolds (~383.08 Mb) were anchored to nine pseudomolecules, of which the largest was 60.78 Mb in length. Evolutionary analysis along with transcriptome comparison provided a preliminary genomic basis for the adaptation of this species to tropical and/or subtropical climates, typically with dry summers. The genomic resources generated in this study will not only facilitate evolutionary studies of the Chloridoideae subfamily, in particular, the Cynodonteae tribe, but also facilitate functional genomic research and genetic breeding in Cynodon species for new leading turfgrass cultivars in the future.

Research advances in and prospects of ornamental plant genomics

The term 'ornamental plant' refers to all plants with ornamental value, which generally have beautiful flowers or special plant architectures. China is rich in ornamental plant resources and known as the "mother of gardens". Genomics is the science of studying genomes and is useful for carrying out research on genome evolution, genomic variations, gene regulation, and important biological mechanisms based on detailed genome sequence information. Due to the diversity of ornamental plants and high sequencing costs, the progress of genome research on ornamental plants has been slow for a long time. With the emergence of new sequencing technologies and a reduction in costs since the whole-genome sequencing of the first ornamental plant (Prunus mume) was completed in 2012, whole-genome sequencing of more than 69 ornamental plants has been completed in <10 years. In this review, whole-genome sequencing and resequencing of ornamental plants will be discussed. We provide analysis with regard to basic data from whole-genome studies of important ornamental plants, the regulation of important ornamental traits, and application prospects.

Analysis of a radiation-induced dwarf mutant of a warm-season turf grass reveals potential mechanisms involved in the dwarfing mutant

Zoysia matrella [L.] Merr. is a widely cultivated warm-season turf grass in subtropical and tropical areas. Dwarf varieties of Z. matrella are attractive to growers because they often reduce lawn mowing frequencies. In this study, we describe a dwarf mutant of Z. matrella induced from the 60Co-γ-irradiated calluses. We conducted morphological test and physiological, biochemical and transcriptional analyses to reveal the dwarfing mechanism in the mutant. Phenotypically, the dwarf mutant showed shorter stems, wider leaves, lower canopy height, and a darker green color than the wild type (WT) control under the greenhouse conditions. Physiologically, we found that the phenotypic changes of the dwarf mutant were associated with the physiological responses in catalase, guaiacol peroxidase, superoxide dismutase, soluble protein, lignin, chlorophyll, and electric conductivity. Of the four endogenous hormones measured in leaves, both indole-3-acetic acid and abscisic acid contents were decreased in the mutant, whereas the contents of gibberellin and brassinosteroid showed no difference between the mutant and the WT control. A transcriptomic comparison between the dwarf mutant and the WT leaves revealed 360 differentially-expressed genes (DEGs), including 62 up-regulated and 298 down-regulated unigenes. The major DEGs related to auxin transportation (e.g., PIN-FORMED1) and cell wall development (i.e., CELLULOSE SYNTHASE1) and expansin homologous genes were all down-regulated, indicating their potential contribution to the phenotypic changes observed in the dwarf mutant. Overall, the results provide information to facilitate a better understanding of the dwarfing mechanism in grasses at physiological and transcript levels. In addition, the results suggest that manipulation of auxin biosynthetic pathway genes can be an effective approach for dwarfing breeding of turf grasses.

Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations

Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome.

Sequence-based genetic mapping of Cynodon dactylon Pers. reveals new insights into genome evolution in Poaceae

Bermudagrass (Cynodon dactylon Pers.) is an important warm-season perennial used extensively for turf, forage, soil conservation and remediation worldwide. However, limited genomic information has hindered the application of molecular tools towards understanding genome evolution and in breeding new cultivars. We genotype a first-generation selfed population derived from the tetraploid (4x = 36) ‘A12359’ using genotyping-by-sequencing. A high-density genetic map of 18 linkage groups (LGs) is constructed with 3,544 markers. Comparative genomic analyses reveal that each of nine homeologous LG pairs of C. dactylon corresponds to one of the first nine chromosomes of Oropetium thomaeum. Two nested paleo-ancestor chromosome fusions (ρ6-ρ9-ρ6, ρ2-ρ10-ρ2) may have resulted in a 12-to-10 chromosome reduction. A segmental dissemination of the paleo-chromosome ρ12 (ρ1-ρ12-ρ1, ρ6-ρ12-ρ6) leads to the 10-to-9 chromosome reduction in C. dactylon genome. The genetic map will assist in an ongoing whole genome sequence assembly and facilitate marker-assisted selection (MAS) in developing new cultivars.

Tilin Fang et al. study the genome of Bermudagrass (Cynodon dactylon Pers.). They use genotyping-by-sequencing and provide a genetic map with a 10-fold increase in genetic marker density. Comparative genomics analyses reveal chromosome rearrangements. Their work will contribute to whole genome assembly efforts which will be beneficial for developing new cultivars.

Physiological and transcriptomic analyses reveal the mechanisms underlying the salt tolerance of Zoysia japonica Steud

BACKGROUND

Areas with saline soils are sparsely populated and have fragile ecosystems, which severely restricts the sustainable development of local economies. Zoysia grasses are recognized as excellent warm-season turfgrasses worldwide, with high salt tolerance and superior growth in saline-alkali soils. However, the mechanism underlying the salt tolerance of Zoysia species remains unknown.

RESULTS

The phenotypic and physiological responses of two contrasting materials, Zoysia japonica Steud. Z004 (salt sensitive) and Z011 (salt tolerant) in response to salt stress were studied. The results show that Z011 was more salt tolerant than was Z004, with the former presenting greater K+/Na+ ratios in both its leaves and roots. To study the molecular mechanisms underlying salt tolerance further, we compared the transcriptomes of the two materials at different time points (0 h, 1 h, 24 h, and 72 h) and from different tissues (leaves and roots) under salt treatment. The 24-h time point and the roots might make significant contributions to the salt tolerance. Moreover, GO and KEGG analyses of different comparisons revealed that the key DEGs participating in the salt-stress response belonged to the hormone pathway, various TF families and the DUF family.

CONCLUSIONS

Zoysia salt treatment transcriptome shows the 24-h and roots may make significant contributions to the salt tolerance. The auxin signal transduction family, ABA signal transduction family, WRKY TF family and bHLH TF family may be the most important families in Zoysia salt-stress regulation.

Suppression of Leaf Blade Development by BLADE-ON-PETIOLE Orthologs Is a Common Strategy for Underground Rhizome Growth

Rhizomes are modified stems that grow horizontally underground in various perennial species, a growth habit that is advantageous for vigorous asexual proliferation. In Oryza longistaminata, a rhizomatous wild relative of cultivated rice (Oryza sativa), leaves in the aerial shoots consist of a distal leaf blade and a proximal leaf sheath [1]. Leaf blade formation is, however, suppressed in rhizome leaves. In O. sativa, BLADE-ON-PETIOLE (BOP) genes are the main regulators of proximal-distal leaf patterning [2]. During the juvenile phase of O. sativa, BOP expression is maintained at high levels by the small regulatory RNA microRNA156 (miR156), leading to formation of leaves consisting predominantly of the sheath. Here, we show that in O. longistaminata, high expression of BOPs caused by miR156 was responsible for suppression of the blade in rhizomes and that bop loss-of-function mutants produced leaves consisting of the leaf blade only. Rhizome growth in soil was also hampered in the mutants due to a severe reduction in rhizome tip stiffness. Leaf blade formation is also suppressed in the stolons of Zoysia matrella, a monocot species, and in the rhizomes of Houttuynia cordata, a dicot species, indicating that leaf blade suppression is widely conserved. We also show that strong expression of BOP homologs in both rhizome and stolon leaves rather than in aerial leaves is another conserved feature. We propose that suppression of the leaf blade by BOP is an evolutionary strategy that has been commonly recruited by both rhizomatous and stoloniferous species to establish their unique growth habit.

Genetic diversity in centipedegrass [Eremochloa ophiuroides (Munro) Hack.]

Genetic diversity is the heritable variation within and among populations, and in the context of this paper describes the heritable variation among the germplasm resources of centipedegrass. Centipedegrass is an important warm-season perennial C4 grass belonging to the Poaceae family in the subfamily Panicoideae and genus Eremochloa. It is the only species cultivated for turf among the eight species in Eremochloa. The center of origin for this species is southern to central China. Although centipedegrass is an excellent lawn grass and is most widely used in the southeastern United States, China has the largest reserve of centipedegrass germplasm in the world. Presently, the gene bank in China holds ~200 centipedegrass accessions collected from geographical regions that are diverse in terms of climate and elevation. This collection appears to have broad variability with regard to morphological and physiological characteristics. To efficiently develop new centipedegrass varieties and improve cultivated species by fully utilizing this variability, multiple approaches have been implemented in recent years to detect the extent of variation and to unravel the patterns of genetic diversity among centipedegrass collections. In this review, we briefly summarize research progress in investigating the diversity of centipedegrass using morphological, physiological, cytological, and molecular biological approaches, and present the current status of genomic studies in centipedegrass. Perspectives on future research on genetics and genomics and modern breeding of centipedegrass are also discussed.

Molecular Dissection of Quantitative Variation in Bermudagrass Hybrids (Cynodon dactylon x transvaalensis): Morphological Traits

Bermudagrass (Cynodon (L.)) is the most important warm-season grass grown for forage or turf. It shows extensive variation in morphological characteristics and growth attributes, but the genetic basis of this variation is little understood. Detection and tagging of quantitative trait loci (QTL) affecting above-ground morphology with diagnostic DNA markers would provide a foundation for genetic and molecular breeding applications in bermudagrass. Here, we report early findings regarding genetic architecture of foliage (canopy height, HT), stolon (stolon internode length, ILEN and length of the longest stolon LLS), and leaf traits (leaf blade length, LLEN and leaf blade width, LW) in 110 F1 individuals derived from a cross between Cynodon dactylon (T89) and C. transvaalensis (T574). Separate and joint environment analyses were performed on trait data collected across two to five environments (locations, and/or years, or time), finding significant differences (P < 0.001) among the hybrid progeny for all traits. Analysis of marker-trait associations detected 74 QTL and 135 epistatic interactions. Composite interval mapping (CIM) and mixed-model CIM (MCIM) identified 32 main effect QTL (M-QTL) and 13 interacting QTL (int-QTL). Colocalization of QTL for plant morphology partially explained significant correlations among traits. M-QTL qILEN-3-2 (for ILEN; R2 = 11-19%), qLLS-7-1 (for LLS; R2 = 13-27%), qLEN-1-1 (for LLEN; R2 = 10-11%), and qLW-3-2 (for LW; R2 = 10-12%) were 'stable' across multiple environments, representing candidates for fine mapping and applied breeding applications. QTL correspondence between bermudagrass and divergent grass lineages suggests opportunities to accelerate progress by predictive breeding of bermudagrass.

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants

BACKGROUND

The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention.

RESULTS

We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events-transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database.

CONCLUSIONS

We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.

A DREB1 gene from zoysiagrass enhances Arabidopsis tolerance to temperature stresses without growth inhibition

The DREB (dehydration-responsive element binding) protein family comprises transcription factors that can increase the survivability of a plant under abiotic stresses by regulating expression of multiple genes and altering downstream metabolism at the cost of growth retardation and developmental delay. In this study, a gene for the DREB1-type transcription factor, designated ZjDREB1.4, was isolated from zoysiagrass (Zoysia japonica Steud.), a popular warm-season turfgrass. This gene contains a conserved AP2/ERF DNA-binding domain flanking the signature sequence of DREB1 and belongs to a DREB1 branch in the grass family that expands in the warm-season species. The expression of ZjDREB1.4 was significantly induced by chilling stress (4-15 °C), moderately induced by salt stress, and only slightly induced by drought stress. The product of ZjDREB1.4 was targeted to the nucleus and showed strong transactivation activity but weak binding to the DRE with ACCGAC as the core sequence. The ZjDREB1.4 protein bound to GCCGAC more preferentially than to ACCGAC. Overexpression of ZjDREB1.4 in Arabidopsis induced the expression of multiple genes including a part of the CBF-regulon, and moderately increased the levels of proline and soluble sugars under normal growth conditions. The transgenic Arabidopsis plants showed an increase in tolerance to high and freezing temperature stresses without obvious growth inhibition and with only a few days delay in bolting. ZjDREB1.4 is potentially useful for producing transgenic plants that are tolerant to high temperature and/or cold stresses with few negative effects.

Current Strategies of Polyploid Plant Genome Sequence Assembly

Polyploidy or duplication of an entire genome occurs in the majority of angiosperms. The understanding of polyploid genomes is important for the improvement of those crops, which humans rely on for sustenance and basic nutrition. As climate change continues to pose a potential threat to agricultural production, there will increasingly be a demand for plant cultivars that can resist biotic and abiotic stresses and also provide needed and improved nutrition. In the past decade, Next Generation Sequencing (NGS) has fundamentally changed the genomics landscape by providing tools for the exploration of polyploid genomes. Here, we review the challenges of the assembly of polyploid plant genomes, and also present recent advances in genomic resources and functional tools in molecular genetics and breeding. As genomes of diploid and less heterozygous progenitor species are increasingly available, we discuss the lack of complexity of these currently available reference genomes as they relate to polyploid crops. Finally, we review recent approaches of haplotyping by phasing and the impact of third generation technologies on polyploid plant genome assembly.

SSR-enriched genetic linkage maps of bermudagrass (Cynodon dactylon × transvaalensis), and their comparison with allied plant genomes

We report SSR-enriched genetic maps of bermudagrass that: (1) reveal partial residual polysomic inheritance in the tetraploid species, and (2) provide insights into the evolution of chloridoid genomes. This study describes genetic linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), that integrate heterologous microsatellite markers from sugarcane into frameworks built with single-dose restriction fragments (SDRFs). A maximum likelihood approach was used to construct two separate parental maps from a population of 110 F₁ progeny of a cross between the two parents. The T89 map is based on 291 loci on 34 cosegregating groups (CGs), with an average marker spacing of 12.5 cM. The T574 map is based on 125 loci on 14 CGs, with an average marker spacing of 10.7 cM. Six T89 and one T574 CG(s) deviated from disomic inheritance. Furthermore, marker segregation data and linkage phase analysis revealed partial residual polysomic inheritance in T89, suggesting that common bermudagrass is undergoing diploidization following whole genome duplication (WGD). Twenty-six T89 CGs were coalesced into 9 homo(eo)logous linkage groups (LGs), while 12 T574 CGs were assembled into 9 LGs, both putatively representing the basic chromosome complement (x = 9) of the species. Eight T89 and two T574 CGs remain unassigned. The marker composition of bermudagrass ancestral chromosomes was inferred by aligning T89 and T574 homologs, and used in comparisons to sorghum and rice genome sequences based on 108 and 91 significant blast hits, respectively. Two nested chromosome fusions (NCFs) shared by two other chloridoids (i.e., zoysiagrass and finger millet) and at least three independent translocation events were evident during chromosome number reduction from 14 in the polyploid common ancestor of Poaceae to 9 in Cynodon.

Making Plants Break a Sweat: the Structure, Function, and Evolution of Plant Salt Glands

Salt stress is a complex trait that poses a grand challenge in developing new crops better adapted to saline environments. Some plants, called recretohalophytes, that have naturally evolved to secrete excess salts through salt glands, offer an underexplored genetic resource for examining how plant development, anatomy, and physiology integrate to prevent excess salt from building up to toxic levels in plant tissue. In this review we examine the structure and evolution of salt glands, salt gland-specific gene expression, and the possibility that all salt glands have originated via evolutionary modifications of trichomes. Salt secretion via salt glands is found in more than 50 species in 14 angiosperm families distributed in caryophyllales, asterids, rosids, and grasses. The salt glands of these distantly related clades can be grouped into four structural classes. Although salt glands appear to have originated independently at least 12 times, they share convergently evolved features that facilitate salt compartmentalization and excretion. We review the structural diversity and evolution of salt glands, major transporters and proteins associated with salt transport and secretion in halophytes, salt gland relevant gene expression regulation, and the prospect for using new genomic and transcriptomic tools in combination with information from model organisms to better understand how salt glands contribute to salt tolerance. Finally, we consider the prospects for using this knowledge to engineer salt glands to increase salt tolerance in model species, and ultimately in crops.

Heterologous expression of a novel Zoysia japonica salt-induced glycine-rich RNA-binding protein gene, ZjGRP, caused salt sensitivity in Arabidopsis

A novel Zoysia japonica salt-induced glycine-rich RNA-binding protein gene was cloned in this study and its overexpression caused salt sensitivity in transgenic Arabidopsis. Glycine-rich RNA-binding proteins (GRPs) play crucial roles in diverse plant developmental processes. However, the mechanisms and functions of GRPs in salinity stress responses remain largely unknown. In this study, rapid amplification of cDNA end (RACE) PCR methods was adopted to isolate ZjGRP from Zosyia japonica, a salt-tolerant grass species. ZjGRP cDNA was 456 bp in length, corresponding to 151 amino acids. ZjGRP was localized in the nucleus and cytoplasm, and was found particularly abundantly in stomatal guard cells. Quantitative real-time PCR showed that ZjGRP was expressed in the roots, stems, and leaves of Zoysia japonica, with the greatest expression seen in the fast-growing leaves. Furthermore, expression of ZjGRP was strongly induced by treatment with NaCl, ABA, MeJA, and SA. Overexpression of ZjGRP in Arabidopsis reduced the rate of germination and retarded seedling growth. ZjGRP-overexpressing Arabidopsis thaliana exhibited weakened salinity tolerance, likely as a result of effects on ion transportation, osmosis, and antioxidation. This study indicates that ZjGRP plays an essential role in inducing salt sensitivity in transgenic plants.

Functional and RNA-Sequencing Analysis Revealed Expression of a Novel Stay-Green Gene from Zoysia japonica (ZjSGR) Caused Chlorophyll Degradation and Accelerated Senescence in Arabidopsis

Senescence is not only an important developmental process, but also a responsive regulation to abiotic and biotic stress for plants. Stay-green protein plays crucial roles in plant senescence and chlorophyll degradation. However, the underlying mechanisms were not well-studied, particularly in non-model plants. In this study, a novel stay-green gene, ZjSGR, was isolated from Zoysia japonica. Subcellular localization result demonstrated that ZjSGR was localized in the chloroplasts. Quantitative real-time PCR results together with promoter activity determination using transgenic Arabidopsis confirmed that ZjSGR could be induced by darkness, ABA and MeJA. Its expression levels could also be up-regulated by natural senescence, but suppressed by SA treatments. Overexpression of ZjSGR in Arabidopsis resulted in a rapid yellowing phenotype; complementary experiments proved that ZjSGR was a functional homolog of AtNYE1 from Arabidopsis thaliana. Over expression of ZjSGR accelerated chlorophyll degradation and impaired photosynthesis in Arabidopsis. Transmission electron microscopy observation revealed that overexpression of ZjSGR decomposed the chloroplasts structure. RNA sequencing analysis showed that ZjSGR could play multiple roles in senescence and chlorophyll degradation by regulating hormone signal transduction and the expression of a large number of senescence and environmental stress related genes. Our study provides a better understanding of the roles of SGRs, and new insight into the senescence and chlorophyll degradation mechanisms in plants.