The Harbinger transposon-derived gene PANDA epigenetically coordinates panicle number and grain size in rice

OsHARBI1-1 enhances cadmium tolerance in yeast through YAP1 mediated modulation of cell wall integrity genes and catalase genes

Harbinger transposase-derived 1 proteins (HARBI1s) play important roles in plant growth, development, and response to abiotic stress. OsHARBI1-1 has been identified as a gene encoding HARBI1-1 protein in rice and has been shown to be responsive to Cadmium (Cd) stress. However, the function of OsHARBI1-1 protein under heavy metal stress remains unclear. In this study, the function of a novel rice Cd-responsive gene, OsHARBI1-1, under Cd stress was characterized by heterologous expression in yeast. The heterologous expression OsHARBI1-1 conferred yeast with increased tolerance to Cd. In addition, the yeast cells expressing OsHARBI1-1 exhibited enhanced tolerance to Congo red and exhibited an increase in cell wall thickness under Cd stress, suggesting a potential correlation between increased Cd tolerance and cell wall thickness in the transgenic yeast. When OsHARBI1-1 was expressed in ∆yap1 or ∆yap1∆ycf1 yeast mutants, there was no significant difference in the tolerance of transgenic yeast to Cd and Congo red, as well as in cell wall thickness compared to the control. Meanwhile, the expression of cell wall integrity (CWI) genes and catalase genes in transgenic yeast was up-regulated in a YAP1-dependent manner under Cd or Congo red stress. The above facts supported the inference that OsHARBI1-1 may counteract Cd toxicity by enhancing the expression of YAP1, thereby increasing the thickness of the cell wall and activating the expression of catalase genes.

Natural variation in TaERF-A1 confers semi-dwarf and lodging-resistant plant architecture in wheat

The introduction of Reduced height (Rht) genes into wheat varieties has been pivotal in developing semi-dwarf plant architectures, significantly improving lodging resistance and harvest indices. Therefore, identifying new Rht gene resources for breeding semi-dwarf wheat cultivars has been a key strategy for ensuring high and stable grain yields since the 1960s. In this study, we report the map-based cloning of TaERF-A1, which encodes an AP2/ERF (APETALA2/ethylene responsive factor) transcription factor that acts as a positive regulator of wheat stem elongation, as a novel gene that regulates plant height and spike length. The natural variant, TaERF-A1JD6, features a Phe (derived from 'Nongda3338') to Ser (derived from 'Jingdong6') substitution at position 178, which significantly reduces the stability of the TaERF-A1 protein. This substitution leads to partially attenuated transcriptional activation of downstream target genes, including TaPIF4 (Triticum aestivum Phytochrome Interacting Factor 4), thereby restricting stem and spike elongation. Importantly, the introgression of the semi-dwarfing allele TaERF-A1JD6 into wheat can significantly enhance lodging resistance, particularly in dense cropping systems. Therefore, our study identifies TaERF-A1JD6 as a new Rht gene resource for breeding semi-dwarf wheat varieties with increased yield stability.

Genome-wide identification and characterization of SLEEPER, a transposon-derived gene family and their expression pattern in Brassica napus L

BACKGROUND

The transposons of the hAT superfamily are the most widespread transposons ever known. SLEEPER genes encode domesticated transposases from the hAT superfamily, which may have lost their transposable functions during long-term evolution and transformed into host proteins that regulate plant growth and development.

RESULTS

This study identified 162 members of the SLEEPER gene family from Brassica napus. These members are widely distributed on 19 chromosomes, mainly in the Cn subgenome, and have promoters with various cis-acting elements related to hormone regulation, abiotic stress, and growth and development regulation. Most of the genes in this family contain similar conserved domains and motifs, and the closer the genes are distributed on evolutionary branches, the more similar their structures are. Transcriptome sequencing performed on tissues at different growth stages from B. napus line 3529 indicated that these genes had different expression patterns, and nearly half of the genes were not detectably expressed in all samples.

CONCLUSIONS

This study investigated the gene structure, expression patterns, evolutionary features, and gene localization of the SLEEPER family members to confirm the significance of these genes in the growth of B. napus, providing a reference for the study of transposon domestication and outstanding genetic resources for the genetic improvement of B. napus.

Transcription factor OsNF-YC1 regulates grain size by coordinating the transcriptional activation of OsMADS1 in Oryza sativa L

Grain weight, grain number per panicle, and the number of panicles are the three factors that determine rice (Oryza sativa L.) yield. Of these, grain weight, which not only directly determines rice yield but also influences appearance and quality, is often considered the most important for rice production. Here, we describe OsNF-YC1, a member of the NF-Y transcription factor family that regulates rice grain size. OsNF-YC1 knockout plants (osnf-yc1), obtained using CRISPR-Cas9 technology, showed reduced grain weight due to reduced width and thickness, with no change in grain length, leading to a slenderer grain shape. Downregulation of OsNF-YC1 using RNA interference resulted in similar grain phenotypes as osnf-yc1. OsNF-YC1 affects grain formation by regulating both cell proliferation and cell expansion. OsNF-YC1 localizes in both the nucleus and cytoplasm, has transcriptional activation activity at both the N-terminus and C-terminus, and is highly expressed in young panicles. OsNF-YC1 interacts with OsMADS1 both in vivo and in vitro. Further analysis showed that the histone-like structural CBFD-NFYB-HMF domain of OsNF-YC1 conserved in the OsNF-YC transcription factor family can directly interact with the MADS-box domain of OsMADS1 to enhance its transcriptional activation activity. This interaction positively regulates the expression of OsMADS55, the direct downstream target of OsMADS1. Therefore, this paper reveals a potential grain size regulation pathway controlled by an OsNF-YC1-OsMADS1-OsMADS55 module in rice.

A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB's relative expression activity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

GW9 determines grain size and floral organ identity in rice

Grain weight is an important determinant of grain yield. However, the underlying regulatory mechanisms for grain size remain to be fully elucidated. Here, we identify a rice mutant grain weight 9 (gw9), which exhibits larger and heavier grains due to excessive cell proliferation and expansion in spikelet hull. GW9 encodes a nucleus-localized protein containing both C2H2 zinc finger (C2H2-ZnF) and VRN2-EMF2-FIS2-SUZ12 (VEFS) domains, serving as a negative regulator of grain size and weight. Interestingly, the non-frameshift mutations in C2H2-ZnF domain result in increased plant height and larger grain size, whereas frameshift mutations in both C2H2-ZnF and VEFS domains lead to dwarf and malformed spikelet. These observations indicated the dual functions of GW9 in regulating grain size and floral organ identity through the C2H2-ZnF and VEFS domains, respectively. Further investigation revealed the interaction between GW9 and the E3 ubiquitin ligase protein GW2, with GW9 being the target of ubiquitination by GW2. Genetic analyses suggest that GW9 and GW2 function in a coordinated pathway controlling grain size and weight. Our findings provide a novel insight into the functional role of GW9 in the regulation of grain size and weight, offering potential molecular strategies for improving rice yield.

Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology

DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.

Identification and characterization of BES1 genes involved in grain size development of Oryza sativa L

BES1 (BRI1-EMS-SUPPRESSOR1) defines a unique class of plant-specific transcription factors that plays an essential role in response to Brassinosteroids (BRs) signal induction pathways. In our study, we conducted genome-wide scanning and comprehensive characterization of the BES1 gene family in rice and other eukaryotes, leading to valuable findings. Molecular docking experiments showed that all OsBES1 genes in rice could directly bind to BR small molecules. Among the identified genes, OsBES1-4 exhibited a remarkable response as it consistently showed induction upon exposure to various phytohormones after treatment. Further functional verification of OsBES1-4 revealed its impact on grain size. Overexpression of OsBES1-4 resulted in increased grain size, as confirmed by cytological observations showing an increase in cell length and cell number. Moreover, we identified that OsBES1-4 plays a role in rice grain size development by binding to the BR response element in the promoter region of the OsBZR1 gene. Evolutionary analysis indicated differentiation of OsBES1-4 between indica and japonica rice varieties, suggesting natural selection during the domestication process of cultivated rice. Therefore, we conclude that OsBES1-4 plays a crucial role in regulating rice grain size and has the potential to be an important target in rice breeding programs, and haplotype analysis found that all OsBES1 genes were associated with grain size development, either thousand-grain weight, grain length, or grain width. Overall, these findings suggest that the BES1 genes are involved in the regulation of grain size development in rice, and the utilization of SNPs in the OsBES1-4 gene promoter could be a favorable option for distinguishing indica and japonica.

A transposon-derived gene family regulates heading date in rice

As a consequence of transposon domestication, transposon-derived proteins often acquire important biological functions. However, there have been limited studies on transposon-derived proteins in rice, and a systematic analysis of transposon-derived genes is lacking. Here, for the first time, we conducted a comprehensive analysis of the DDE_Tnp_4 (DDE) gene family, which originated from transposons but lost their transpositional ability and acquired new gene functions in Oryza species. A total of 58 DDE family genes, categorized into six groups, were identified in Oryza species, including 13 OsDDE genes in Oryza sativa ssp. japonica. Our analysis indicates that gene duplication events were not the primary mechanism behind the expansion of OsDDE genes in rice. Promoter cis-element analysis combined with haplotype analysis confirmed that OsDDEs regulate the heading date in rice. Specifically, OsDDE9 is a nuclear-localized protein expressed ubiquitously, which promotes heading date by regulating the expression of Ghd7 and Ehd1 under both short-day and long-day conditions. Single-nucleotide polymorphism (SNP) variations in the OsDDE9 promoter leads to changes in promoter activity, resulting in variations in heading dates. This study provides valuable insights into the molecular function and mechanism of the OsDDE genes.

Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley

Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin-proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function.

Introduction of Plant Transposon Annotation for Beginners

Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate transposons, especially for beginners, as transposon prediction requires necessary expertise in both transposon biology and bioinformatics. Moreover, the complexity of plant genomes and the dynamic evolution of transposons also bring difficulties for genome-wide transposon discovery. This review summarizes the three major strategies for transposon detection including repeat-based, structure-based, and homology-based annotation, and introduces the transposon superfamilies identified in plants thus far, and some related bioinformatics resources for detecting plant transposons. Furthermore, it describes transposon classification and explains why the terms 'autonomous' and 'non-autonomous' cannot be used to classify the superfamilies of transposons. Lastly, this review also discusses how to identify misannotated transposons and improve the quality of the transposon database. This review provides helpful information about plant transposons and a beginner's guide on annotating these repetitive sequences.

Expression of OsHARBI1-1 enhances the tolerance of Arabidopsis thaliana to cadmium

BACKGROUND

As one of the major food crops in the world, rice is vulnerable to cadmium (Cd) pollution. Understanding of the molecular mechanisms of Cd uptake, transport and detoxification in rice is essential for the breeding of low-Cd rice. However, the molecular mechanisms underlying the response of rice to Cd stress remains to be further clarified.

RESULTS

In this study, a novel Cd-responsive gene OsHARBI1-1 was identified in the rice genome and its expression pattern and function were characterized. Bioinformatics analysis showed that the promoter region of OsHARBI1-1 had multiple cis-acting elements in response to phytohormones and stress, and the expression of OsHARBI1-1 was induced by phytohormones. OsHARBI1-1 protein was targeted to the nucleus. qRT-PCR analysis results showed that the expression of OsHARBI1-1 in the roots was repressed while the expression in the shoots was increased under Cd stress. Heterologous expression of OsHARBI1-1 in yeast conferred tolerance to Cd and reduced Cd content in the cells. Meanwhile, the expression of OsHARBI1-1 in Arabidopsis thaliana (A. thaliana) enhanced the tolerance of A. thaliana to Cd stress. In addition, compared with the wild type plants, the POD activity of transgenic plants was increased, while the SOD and CAT activities were decreased. Interestingly, the accumulation of Cd in the roots of A. thaliana expressing OsHARBI1-1 was significantly increased, whereas the Cd accumulation in the shoots was slightly decreased. Compared to the WT plants, the expression of genes related to Cd absorption and chelation was upregulated in transgenic A. thaliana under Cd stress, while the expression of genes responsible for the translocation of Cd from the roots to the shoots was downregulated. Moreover, the expression of phytohormone-related genes was significantly influenced by the expression of OsHARBI1-1 with and without Cd treatment.

CONCLUSIONS

Findings of this study suggest that OsHARBI1-1 might play a role in the response of plants to Cd response by affecting antioxidant enzyme activities, Cd chelation, absorption and transport, and phytohormone homeostasis and signaling.

Identification of transcriptionally active transposons in Barley

BACKGROUND

The genomes of many major crops including barley (Hordeum vulgare) consist of numerous transposons. Despite their important roles in crop genome evolution and morphological variations, most of these elements are silent or truncated and unable to be mobile in host genomes. Thus far, only a very limited number of active transposons were identified in plants.

RESULTS

We analyzed the barley full-length cDNA (FLcDNA) sequences and detected 71 unique FLcDNAs exhibiting significant sequence similarity to the extant transposase proteins. These FLcDNAs were then used to search against the genome of a malting barley cultivar 'Morex', seven new intact transposons were identified. Sequence alignments indicated that six intact transposons contained the entire FLcDNAs whereas another one served as 3' untranslated region (3' UTR) of a barley gene. Our reverse transcription-PCR (RT-PCR) experiment further confirmed the expression of these six transposons and revealed their differential expression. We conducted genome-wide transposon comparisons and detected polymorphisms of three transposon families between the genomes of 'Morex' and other three genotypes including the wild barley (Hordeum spontaneum, B1K-04-12) and two cultivated barley varieties, 'Golden Promise' and 'Lasa Goumang'. Lastly, we screened the transcripts of all annotated barley genes and found that some transposons may serve as the coding regions (CDSs) or UTRs of barley genes.

CONCLUSION

We identified six newly expressed transposons in the barley genome and revealed the recent mobility of three transposon families. Our efforts provide a valuable resource for understanding the effects of transposons on barley genome evolution and for developing novel molecular tools for barley genetic improvement and other research.

Molecular basis of genetic improvement for key rice quality traits in Southern China

Grain qualities including milling quality, appearance quality, eating and cooking quality, and nutritional quality are important indicators in rice breeding. Significant achievements in genetic improvement of rice quality have been made. In this study, we analyzed the variation patterns of 16 traits in 1570 rice varieties and found significant improvements in appearance quality and eating and cooking quality, particularly in hybrid rice. Through genome-wide association study and allelic functional nucleotide polymorphisms analysis of quality trait genes, we found that ALK, FGR1, FLO7, GL7/GW7, GLW7, GS2, GS3, ONAC129, OsGRF8, POW1, WCR1, and Wx were associated with the genetic improvement of rice quality traits in Southern China. Allelic functional nucleotide polymorphisms analysis of 13 important rice quality genes, including fragrance gene fgr, were performed using the polymerase chain reaction amplification refractory mutation system technology. The results showed that Gui516, Gui569, Gui721, Ryousi, Rsimiao, Rbasi, and Yuehui9802 possessed multiple superior alleles. This study elucidates the phenotypic changes and molecular basis of key quality traits of varieties in Southern China. The findings will provide guidance for genetic improvement of rice quality and the development of new varieties.

TaSPL17s act redundantly with TaSPL14s to control spike development and their elite haplotypes may improve wheat grain yield

Wheat is a staple crop for the world's population, and there is constant pressure to improve grain yield, which is largely determined by plant architecture. SQUAMOSA promotor-binding protein-like (SPL) genes have been widely studied in rice, including their effects on plant architecture, grain development, and grain yield. However, the function of SPL homologous genes in wheat has not been well investigated. In this study, TaSPL14s and TaSPL17s, wheat's closest orthologous of OsSPL14, were functionally investigated using gene-editing assays, revealing that these genes redundantly influence plant height, tiller number, spike length, and thousand-grain weight (TGW). Bract outgrowth was frequently observed in the hexa-mutant, occasionally in the quintuple mutant but never in the wild type. Transcriptome analysis revealed that the expression of many spike development-associated genes was altered in taspl14taspl17 hexa-mutants compared to that in the wild type. In addition, we analyzed the sequence polymorphisms of TaSPL14s and TaSPL17s among wheat germplasm and found superior haplotypes of TaSPL17-A and TaSPL17-D with significantly higher TGW, which had been positively selected during wheat breeding. Accordingly, dCAPS and KASP markers were developed for TaSPL17-A and TaSPL17-D, respectively, providing a novel insight for molecular marker-assisted breeding in wheat. Overall, our results highlight the role of TaSPLs in regulating plant architecture and their potential application for wheat grain yield improvement through molecular breeding.

Advances in Plant Epigenome Editing Research and Its Application in Plants

Plant epistatic regulation is the DNA methylation, non-coding RNA regulation, and histone modification of gene sequences without altering the genome sequence, thus regulating gene expression patterns and the growth process of plants to produce heritable changes. Epistatic regulation in plants can regulate plant responses to different environmental stresses, regulate fruit growth and development, etc. Genome editing can effectively improve plant genetic efficiency by targeting the design and efficient editing of genome-specific loci with specific nucleases, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9). As research progresses, the CRISPR/Cas9 system has been widely used in crop breeding, gene expression, and epistatic modification due to its high editing efficiency and rapid translation of results. In this review, we summarize the recent progress of CRISPR/Cas9 in epigenome editing and look forward to the future development direction of this system in plant epigenetic modification to provide a reference for the application of CRISPR/Cas9 in genome editing.

Co-Overexpression of Two Key Source Genes, OsBMY4 and OsISA3, Improves Multiple Key Traits of Rice Seeds

Optimized source-sink interactions are determinants of both rice yield and quality. However, most source genes have not been well studied in rice, a major grain crop. In this study, OsBMY4 and OsISA3, the key β-amylase and debranching enzymes that control transient starch degradation in rice leaves, were co-overexpressed in rice in order to accelerate starch degradation efficiency and increase the sugar supply for sink organs. Systematic analyses of the transgenic rice indicated that co-overexpression of OsBMY4 and OsISA3 not only promoted rice yield and quality, but also improved seed germination and stress tolerance. Moreover, since the OsBMY4 gene has not been characterized, we generated osbmy4 mutants using CRIPSR/Cas9 gene editing, which helped to reveal the roles of β-amylase in rice yield and quality. This study demonstrated that specific modulation of the expression of some key source genes improves the source-sink balance and leads to improvements in multiple key traits of rice seeds.