Multiple tissue-specific expression of rice seed-shattering gene SH4 regulated by its promoter pSH4

Domestication, breeding, omics research, and important genes of Zizania latifolia and Zizania palustris

Wild rice (Zizania spp.), an aquatic grass belonging to the subfamily Gramineae, has a high economic value. Zizania provides food (such as grains and vegetables), a habitat for wild animals, and paper-making pulps, possesses certain medicinal values, and helps control water eutrophication. Zizania is an ideal resource for expanding and enriching a rice breeding gene bank to naturally preserve valuable characteristics lost during domestication. With the Z. latifolia and Z. palustris genomes completely sequenced, fundamental achievements have been made toward understanding the origin and domestication, as well as the genetic basis of important agronomic traits of this genus, substantially accelerating the domestication of this wild plant. The present review summarizes the research results on the edible history, economic value, domestication, breeding, omics research, and important genes of Z. latifolia and Z. palustris over the past decades. These findings broaden the collective understanding of Zizania domestication and breeding, furthering human domestication, improvement, and long-term sustainability of wild plant cultivation.

Reducing Seed Shattering in Weedy Rice by Editing SH4 and qSH1 Genes: Implications in Environmental Biosafety and Weed Control through Transgene Mitigation

Mitigating the function of acquired transgenes in crop wild/weedy relatives can provide an ideal strategy to reduce the possible undesired environmental impacts of pollen-mediated transgene flow from genetically engineered (GE) crops. To explore a transgene mitigation system in rice, we edited the seed-shattering genes, SH4 and qSH1, using a weedy rice line ("C9") that originally had strong seed shattering. We also analyzed seed size-related traits, the total genomic transcriptomic data, and RT-qPCR expression of the SH4 or qSH1 gene-edited and SH4/qSH1 gene-edited weedy rice lines. Substantially reduced seed shattering was observed in all gene-edited weedy rice lines. The single gene-edited weedy rice lines, either the SH4 or qSH1 gene, did not show a consistent reduction in their seed size-related traits. In addition, reduced seed shattering was closely linked with the weakness and absence of abscission layers and reduced abscisic acid (ABA). Additionally, the genes closely associated with ABA biosynthesis and signaling transduction, as well as cell-wall hydrolysis, were downregulated in all gene-edited weedy rice lines. These findings facilitate our deep insights into the underlying mechanisms of reduced seed shattering in plants in the rice genus Oryza. In addition, such a mitigating technology also has practical applications for reducing the potential adverse environmental impacts caused by transgene flow and for managing the infestation of weedy rice by acquiring the mitigator from GE rice cultivars through natural gene flow.

Systematic Analysis of BELL Family Genes in Zizania latifolia and Functional Identification of ZlqSH1a/b in Rice Seed Shattering

The loss of seed shattering is an important event in crop domestication, and elucidating the genetic mechanisms underlying seed shattering can help reduce yield loss during crop production. This study is the first to systematically identify and analyse the BELL family of transcription factor-encoding genes in Chinese wild rice (Zizania latifolia). ZlqSH1a (Zla04G033720) and ZlqSH1b (Zla02G027130) were identified as key candidate genes involved in seed shattering in Z. latifolia. These genes were involved in regulating the development of the abscission layer (AL) and were located in the nucleus of the cell. Over-expression of ZlqSH1a and ZlqSH1b resulted in a complete AL between the grain and pedicel and significantly enhanced seed shattering after grain maturation in rice. Transcriptome sequencing revealed that 172 genes were differentially expressed between the wild type (WT) and the two transgenic (ZlqSH1a and ZlqSH1b over-expressing) plants. Three of the differentially expressed genes related to seed shattering were validated using qRT-PCR analysis. These results indicate that ZlqSH1a and ZlqSH1b are involved in AL development in rice grains, thereby regulating seed shattering. Our results could facilitate the genetic improvement of seed-shattering behaviour in Z. latifolia and other cereal crops.

Isolation and characterization of drought and ABA responsive promoter of a transcription factor encoding gene from rice

Water deficit is a significant impediment to enhancing rice yield. Genetic engineering tools have enabled agriculture researchers to develop drought-tolerant cultivars of rice. A common strategy to achieve this involves expressing drought-tolerant genes driven by constitutive promoters such as CaMV35S. However, the use of constitutive promoters is often limited by the adverse effects it has on the growth and development of the plant. Additionally, it has been observed that monocot-derived promoters are more successful in driving gene expression in monocots than in dicots. Substitution of constitutive promoters with stress-inducible promoters is the currently used strategy to overcome this limitation. In the present study, a 1514 bp AP2/ERF promoter that drives the expression of a transcription factor was cloned and characterized from drought-tolerant Indian rice genotype N22. The AP2/ERF promoter was fused to the GUS gene (uidA) and transformed in Arabidopsis and rice plants. Histochemical GUS staining of transgenic Arabidopsis plants showed AP2/ERF promoter activity in roots, stems, and leaves. Water deficit stress and ABA upregulate promoter activity in transformed Arabidopsis and rice. Quantitative PCR for uidA expression confirmed induced GUS activity in Arabidopsis and rice. This study showed that water deficit inducible Os-AP2/ERF-N22 promoter can be used to overcome the limitations of constitutive promoters. Transformants overexpressing Os-AP2/ERF-N22 showed higher relative water content, membrane stability index, total chlorophyll content, chlorophyll stability index, wax content, osmotic potential, stomatal conductance, transpiration rate, photosynthetic rate and radical scavenging activity. Drought tolerant (N22) showed higher expression of Os-AP2/ERF-N22 than the susceptible (MTU1010) cultivar.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01246-9.

Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples

In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.

Functional characterization of wheat myo-inositol oxygenase promoter under different abiotic stress conditions in Arabidopsis thaliana

The production of wheat is severely affected by abiotic stresses such as cold, drought, salinity, and high temperature. Although constitutive promoters are frequently used to regulate the expression of alien genes, these may lead to undesirable side-effects in transgenic plants. Therefore, identification and characterization of an inducible promoter that can express transgene only when exposed to stresses are of great importance in the genetic engineering of crop plants. Previous studies have indicated the abiotic stress-responsive behavior of myo-inositol oxygenase (MIOX) gene in different plants. Here, we isolated the MIOX gene promoter from wheat (TaMIOX). The in-silico analysis revealed the presence of various abiotic stress-responsive cis-elements in the promoter region. The TaMIOX promoter was fused with the UidA reporter gene and transformed into Arabidopsis thaliana. The T₃ single-copy homozygous lines were analyzed for GUS activity using histochemical and fluorometric assays. Transcript expression of TaMIOX::UidA was significantly up-regulated by heat (five fold), cold (seven fold), and drought (five fold) stresses as compared to transgenic plants grown without stress-induced conditions. The CaMV35S::UidA plants showed very high GUS activity even in normal conditions. In contrast, the TaMIOX::UidA plants showed prominent GUS activity only in stress treatments (cold, heat, and drought), which suggests the inducible behavior of the TaMIOX promoter. The substrate myo-inositol feeding assay of TaMIOX::UidA plants showed lesser GUS activity as compared to plants treated in abiotic stress conditions. Results support that the TaMIOX promoter could be used as a potential candidate for conditional expression of the transgene in abiotic stress conditions.

Identification and expression of genes associated with the abscission layer controlling seed shattering in Lolium perenne

Perennial ryegrass (Lolium perenne) is one of the most important pasture grasses in the world. However, seed production is negatively impacted by the seed shattering (shedding) nature of this species. Recently, genes involved in the seed shattering process have been isolated and functionally characterized in several crop species. The aim of this study was to identify the genes playing critical roles in the seed shattering process in perennial ryegrass. DNA sequences of genes involved in seed shattering in the Poaceae were used to identify and isolate target genes in perennial ryegrass using a comparative genomics strategy. The candidate seed shattering genes were identified using an 'in-house' perennial ryegrass transcriptome database. The relative expression levels of the candidate ryegrass shattering genes were determined using RT-qPCR during different floret and seed developmental stages. Histological analysis of the abscission layer was also conducted. Homologues of seed shattering genes were identified and isolated from perennial ryegrass, and the relative gene expression results suggested that several genes, including LpqSH1 and LpSH1, might have a role in abscission layer formation during seed development. In addition, lignification of the abscission layer may play an important role in the abscission process. A genetic model for seed shattering in perennial ryegrass is suggested and may be useful for directing gene editing towards the production of a reduced-shattering ryegrass.

Global analysis of DNA methylation in young (J1) and senescent (J2) Gossypium hirsutum L. cotyledons by MeDIP-Seq

DNA methylation is an important epigenetic modification regulating gene expression, genomic imprinting, transposon silencing and chromatin structure in plants and plays an important role in leaf senescence. However, the DNA methylation pattern during Gossypium hirsutum L. cotyledon senescence is poorly understood. In this study, global DNA methylation patterns were compared between two cotyledon development stages, young (J1) and senescence (J2), using methylated DNA immunoprecipitation (MeDIP-Seq). Methylated cytosine occurred mostly in repeat elements, especially LTR/Gypsy in both J1 and J2. When comparing J1 against J2, there were 1222 down-methylated genes and 623 up-methylated genes. Methylated genes were significantly enriched in carbohydrate metabolism, biosynthesis of other secondary metabolites and amino acid metabolism pathways. The global DNA methylation level decreased from J1 to J2, especially in gene promoters, transcriptional termination regions and regions around CpG islands. We further investigated the expression patterns of 9 DNA methyltransferase-associated genes and 2 DNA demethyltransferase-associated genes from young to senescent cotyledons, which were down-regulated during cotyledon development. In this paper, we first reported that senescent cotton cotyledons exhibited lower DNA methylation levels, primarily due to decreased DNA methyltransferase activity and which also play important role in regulating secondary metabolite process.

Reduced weed seed shattering by silencing a cultivated rice gene: strategic mitigation for escaped transgenes

Transgene flow form a genetically engineered (GE) crop to its wild relatives may result in unwanted environmental consequences. Mitigating transgenes via introducing a gene that is disadvantageous to wild relatives but beneficial to crops, and is tightly-linked with the target transgenes, may provide a promising solution to limit the spread of transgenes in wild/weedy populations. Here we demonstrate a novel system with significantly reduced seed shattering in crop-weed hybrid descendants by partially silenced expression of the seed-shattering gene SH4 in cultivated rice, using artificial microRNA and antisense RNA techniques. Accordingly, fewer seeds were found in the soil of the field plots where transgenic hybrid lineages were grown. However, no differences in productivity-related traits were detected between GE and non-GE cultivated rice. To silence seed-shattering genes provides a useful strategy to reduce the potential environmental impacts caused by transgene flow from commercial GE rice to weedy rice, in addition to the control of weedy rice.

Isolation and characterization of a promoter responsive to salt, osmotic and dehydration stresses in soybean

Drought stress is the main limiting factor of soybean yield. Currently, genetic engineering has been one important tool in the development of drought-tolerant cultivars. A widely used strategy is the fusion of genes that confer tolerance under the control of the CaMV35S constitutive promoter; however, stress-responsive promoters would constitute the best alternative to the generation of drought-tolerant crops. We characterized the promoter of α-galactosidase soybean (GlymaGAL) gene that was previously identified as highly up-regulated by drought stress. The β-glucuronidase (GUS) activity of Arabidopsis transgenic plants bearing 1000- and 2000-bp fragments of the GlymaGAL promoter fused to the uidA gene was evaluated under air-dried, polyethylene glycol (PEG) and salt stress treatments. After 24 h of air-dried and PEG treatments, the pGAL-2kb led to an increase in GUS expression in leaf and root samples when compared to the control samples. These results were corroborated by qPCR expression analysis of the uidA gene. The pGAL-1kb showed no difference in GUS activity between control and treated samples. The pGAL-2kb promoter was evaluated in transgenic soybean roots, leading to an increase in EGFP expression under air-dried treatment. Our data indicates that pGAL-2kb could be a useful tool in developing drought-tolerant cultivars by driving gene expression.

Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana

The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plant's sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.

To Have and to Hold: Selection for Seed and Fruit Retention During Crop Domestication

Crop domestication provides a useful model system to characterize the molecular and developmental bases of morphological variation in plants. Among the most universal changes resulting from selection during crop domestication is the loss of seed and fruit dispersal mechanisms, which greatly facilitates harvesting efficiency. In this review, we consider the molecular genetic and developmental bases of the loss of seed shattering and fruit dispersal in six major crop plant families, three of which are primarily associated with seed crops (Poaceae, Brassicaceae, Fabaceae) and three of which are associated with fleshy-fruited crops (Solanaceae, Rosaceae, Rutaceae). We find that the developmental basis of the loss of seed/fruit dispersal is conserved in a number of independently domesticated crops, indicating the widespread occurrence of developmentally convergent evolution in response to human selection. With regard to the molecular genetic approaches used to characterize the basis of this trait, traditional biparental quantitative trait loci mapping remains the most commonly used strategy; however, recent advances in next-generation sequencing technologies are now providing new avenues to map and characterize loss of shattering/dispersal alleles. We anticipate that continued application of these approaches, together with candidate gene analyses informed by known shattering candidate genes from other crops, will lead to a rapid expansion of our understanding of this critical domestication trait.