Projecting the effect of climate change on planting date and cultivar choice for South African dryland maize production

DATA AVAILABILITY : Data will be made available on request.The anticipated climate change in South Africa is of great concern as Southern Africa appears to be warming at twice that of the global average, limiting maize production in the country and threatening food security in the region. The formulation of effective adaptation measures calls for understanding how projected changes in temperature, precipitation, and climate extremes might become misaligned with the critical maize developmental stages, which are likely to impact crop development. We conducted an analysis of the climate change impacts for dryland maize phenology in Bloemfontein and Lichtenburg, which represent major maize growing regions of South Africa. The climate projections generated by six Global Climate Models under the Representative Concentration Pathways (RCP) 4.5 and 8.5 were used. Analyses were performed for four representative planting dates: November 15 (early), December 15 (optimal), January 15 (late), and February 5 (very late). Days to maturity decreased (by approx. 5-10 days) as years progressed from baseline period (1991-2020) to the far future period (2051-2080), at both locations with higher rates projected under RCP 8.5. The results suggest a longer summer season with receding freeze dates in these regions and might provide additional flexibility for adaptive strategies. At the optimal planting dates, future climate will likely affect both vegetative and reproductive stages of maize leading to the decrease in the days to maturity. A major factor affecting maize productivity is extreme temperature, with the number of days above 35 °C expected to increase 20–30% at the optimal planting date as climate changes progresses, which will likely limit grain filling and yield. Exploring maize phenology in the future at later planting dates revealed a decrease in days to maturity trending towards the optimal number of days required for each cultivar (100–110 days) in both regions. This coupled with the projected receding freeze date at these planting dates under future climates suggests there may be opportunities to shift planting to later dates in the region.https://www.elsevier.com/locate/agrformetForestry and Agricultural Biotechnology Institute (FABI)Plant Production and Soil Scienc

Navigating the transcriptional roadmap regulating plant secondary cell wall deposition

The current status of lignocellulosic biomass as an invaluable resource in industry, agriculture, and health has spurred increased interest in understanding the transcriptional regulation of secondary cell wall (SCW) biosynthesis. The last decade of research has revealed an extensive network of NAC, MYB and other families of transcription factors regulating Arabidopsis SCW biosynthesis, and numerous studies have explored SCW-related transcription factors in other dicots and monocots. Whilst the general structure of the Arabidopsis network has been a topic of several reviews, they have not comprehensively represented the detailed protein-DNA and protein-protein interactions described in the literature, and an understanding of network dynamics and functionality has not yet been achieved for SCW formation. Furthermore the methodologies employed in studies of SCW transcriptional regulation have not received much attention, especially in the case of non-model organisms. In this review, we have reconstructed the most exhaustive literature-based network representations to date of SCW transcriptional regulation in Arabidopsis. We include a manipulable Cytoscape representation of the Arabidopsis SCW transcriptional network to aid in future studies, along with a list of supporting literature for each documented interaction. Amongst other topics, we discuss the various components of the network, its evolutionary conservation in plants, putative modules and dynamic mechanisms that may influence network function, and the approaches that have been employed in network inference. Future research should aim to better understand network function and its response to dynamic perturbations, whilst the development and application of genome-wide approaches such as ChIP-seq and systems genetics are in progress for the study of SCW transcriptional regulation in non-model organisms.The Mandela Rhodes Foundation and National Research Foundation of South Africahttp://www.frontiersin.orgam201

Induced somatic sector analysis of cellulose synthase (CesA) promoter regions in woody stem tissues

The increasing focus on plantation forestry as a renewable source of cellulosic biomass has emphasized the need for tools to study the unique biology of woody genera such as Eucalyptus, Populus and Pinus. The domestication of these woody crops is hampered by long generation times, and breeders are now looking to molecular approaches such as marker-assisted breeding and genetic modification to accelerate tree improvement. Much of what is known about genes involved in the growth and development of plants has come from studies of herbaceous models such as Arabidopsis and rice. However, transferring this information to woody plants often proves difficult, especially for genes expressed in woody stems. Here we report the use of induced somatic sector analysis (ISSA) for characterization of promoter expression patterns directly in the stems of Populus and Eucalyptus trees. As a case study, we used previously characterized primary and secondary cell wall-related cellulose synthase (CesA) promoters cloned from Eucalyptus grandis. We show that ISSA can be used to elucidate the phloem and xylem expression patterns of the CesA genes in Eucalyptus and Populus stems and also show that the staining patterns differ in Eucalyptus and Populus stems. These findings show that ISSA is an efficient approach to investigate promoter function in the developmental context of woody plant tissues and raise questions about the suitability of heterologous promoters for genetic manipulation in plant species.This work was supported through funding provided by Mondi and Sappi to the Forest Molecular Genetics (FMG) Programme, the Technology and Human Resources for Industry Programme (THRIP) and the National Research Foundation (NRF) of South Africa as well as a Linkage Grant from the Australian Research Council (LP0776563) to GB, AAM and AVS.http://link.springer.com/journal/425hb201

The circadian clock controls temporal and spatial patterns of floral development in sunflower

DATA AVAILABILITY : All source data have been uploaded to Dryad under the following accession codes: 10.25338/B8865X (timelapse scoring), 10.25338/B86358 (pollinator visits), 10.25338/B8963G (consensus scoring), 10.25338/B8CW5R (ovary measurements), and 10.25338/B8HP9F (organ growth kinetics).Biological rhythms are ubiquitous. They can be generated by circadian oscillators, which produce daily rhythms in physiology and behavior, as well as by developmental oscillators such as the segmentation clock, which periodically produces modular developmental units. Here, we show that the circadian clock controls the timing of late-stage floret development, or anthesis, in domesticated sunflowers. In these plants, up to thousands of individual florets are tightly packed onto a capitulum disk. While early floret development occurs continuously across capitula to generate iconic spiral phyllotaxy, during anthesis floret development occurs in discrete ring-like pseudowhorls with up to hundreds of florets undergoing simultaneous maturation. We demonstrate circadian regulation of floral organ growth and show that the effects of light on this process are time-of- day dependent. Delays in the phase of floral anthesis delay morning visits by pollinators, while disruption of circadian rhythms in floral organ development causes loss of pseudowhorl formation and large reductions in pollinator visits. We therefore show that the sunflower circadian clock acts in concert with environmental response pathways to tightly synchronize the anthesis of hundreds of florets each day, generating spatial patterns on the developing capitulum disk. This coordinated mass release of floral rewards at predictable times of day likely promotes pollinator visits and plant reproductive success.The National Science Foundation and the US Department of Agriculture-National Institute of Food and Agriculture.https://elifesciences.orgam2024Plant Production and Soil ScienceSDG-15:Life on lan

Diversity and cis-element architecture of the promoter regions of cellulose synthase genes in Eucalyptus

Lignocellulosic biomass from fast-growing plantation trees is composed of carbohydrate-rich materials deposited into plant cell walls in a coordinated manner during wood formation. The diversity and evolution of the transcriptional networks regulating this process have not been studied extensively.We investigated patterns of species-level nucleotide diversity in the promoters of cellulose synthase (CesA) genes from different Eucalyptus tree species and assessed the possible roles of DNA sequence polymorphism in the gain or loss of cis-elements harboured within the promoters. Promoter regions of three primary and three secondary cell wall-associated CesA genes were isolated from 13 Eucalyptus species and were analysed for nucleotide and cis-element diversity. Species-level nucleotide diversity (π) ranged from 0.014 to 0.068, and different CesA promoters exhibited distinct patterns of sequence conservation. A set of 22 putative cis-elements were mapped to the CesA promoters using in silico methods. Forty-two percent of the mapped cis-element occurrences contained singleton polymorphisms which resulted in either gain or loss of a ciselement in a particular Eucalyptus species. The promoters of Eucalyptus CesA genes contained regions that are highly conserved at the species (Eucalyptus) and genus (with Arabidopsis and Populus) level, suggesting the presence of regulatory modules imposing functional constraint on such regions. Nucleotide polymorphisms in the CesA promoters more frequently created new cis-element occurrences than disrupted existing cis-element occurrences, a process which may be important for the maintenance and evolution of cellulose gene regulation in plants.Mondi and Sappi, through the Forest Molecular Genetics (FMG) Programme, the Technology and Human Resources for Industry Programme (THRIP)and the National Research Foundation of South Africa (NRF).http://link.springer.com/journal/11295hb201

In-field climatic factors driving Sclerotinia head rot progression across different sunflower planting dates

DATA AVAILABILITY STATEMENT : The data are available upon request from the corresponding author.Sclerotinia head rot, caused by Sclerotinia sclerotiorum, is a major disease limiting sunflower production in tropical and subtropical agroecological zones. Sporadic outbreaks across South Africa have resulted in major losses, yet little is known about the in-field climatic factors driving this infection. Short-interval, staggered plantings have been proposed as a control method for Sclerotinia head rot, which help to limit the number of plants in a susceptible developmental stage during conducive environmental conditions. However, this complicates field management practices, especially if working at the fringes of a planting window due to delayed rains. This study aimed to investigate the effect of planting date on Sclerotinia head rot progression in monthly plantings across the summer period. Artificial mycelial plug inoculations were performed at the R5.9 flowering stage in an open field. Disease establishment, progression and severity were monitored at 3-day intervals for 30 days. We show that disease establishment was delayed by low relative humidity or extreme low temperatures in the January and March planting dates where the first lesions were only observed 6 days post-inoculation. Consistently high temperatures above 27°C also suppressed disease progression and produced low area under the disease progress curve (AUDPC) scores of 75.15 and 29.4 for the October and November planting dates, respectively. These findings suggest that regardless of season or location, selecting a planting date that ensures the sunflower bloom period aligns with the hottest, driest part of the season will probably suppress Sclerotinia head rot in regions with average summer highs above 27°C.Oil and Protein Seed Development Trust / Oilseed Advisory committee.http://www.wileyonlinelibrary.com/journal/ppahj2024BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsGeography, Geoinformatics and MeteorologyMicrobiology and Plant PathologyPlant Production and Soil ScienceSDG-02:Zero HungerSDG-13:Climate actionSDG-15:Life on lan

Flower orientation influences floral temperature, pollinator visits and plant fitness

Effective insect pollination requires appropriate responses to internal and external environmental cues in both the plant and the pollinator. Helianthus annuus, a highly outcrossing species, is marked for its uniform eastward orientation of mature pseudanthia, or capitula. Here we investigate how this orientation affects floral microclimate and the consequent effects on plant and pollinator interactions and reproductive fitness. We artificially manipulated sunflower capitulum orientation and temperature in both field and controlled conditions and assessed flower physiology, pollinator visits, seed traits and siring success. East-facing capitula were found to have earlier style elongation, pollen presentation and pollinator visits compared with capitula manipulated to face west. East-facing capitula also sired more offspring than west-facing capitula and under some conditions produced heavier and better-filled seeds. Local ambient temperature change on the capitulum was found to be a key factor regulating the timing of style elongation, pollen emergence and pollinator visits. These results indicate that eastward capitulum orientation helps to control daily rhythms in floral temperature, with direct consequences on the timing of style elongation and pollen emergence, pollinator visitation, and plant fitness.University of Virginia; Division of Integrative Organismal Systems; University of California Berkeley; US Department of Agriculture-National Institute of Food and Agriculture.http://www.newphytologist.comhj2022Plant Production and Soil Scienc

In silico and functional characterization of the cellulose synthase 8 gene promoter of Eucalyptus trees

Cellulose is a highly abundant biopolymer which forms the basis of several industrial applications including paper and textile products. Cellulose is deposited into the plant cell wall by a large membrane bound protein complex which is comprised of different cellulose synthase (CesA) subunits. Plants maintain several different CesA genes which have specific expression patterns depending on the cell wall type, tissue type, developmental stage and environment of the cell. While CesA genes and proteins have been the focus of many studies, the upstream regulatory regions which govern their complex expression patterns have remained largely unexplored. The aim of this study was to use the previously identified CesA promoter regulatory modules and putative cis-elements to identify conserved cis-element clusters in the Eucalyptus CesA and the transcription factors which interact with the regulatory regions of the EgrCesA8 promoter. The promoters of six cellulose synthase genes (CesA1, CesA3, CesA6, CesA4, CesA7 and CesA8) were isolated from 13 Eucalyptus species of different sections in the Symphyomyrtus subgenus of Eucalyptus. Species-level nucleotide diversity was calculated for the promoters of each gene. The promoters each contained a highly conserved region at the transcriptional start site (TSS), possibly marking the core promoter. The Eucalyptus promoters appeared to be TATA-less and cis-elements which resembled alternate core plant promoter elements were found clustered close to the TSS. Other localised regions of low species-level nucleotide diversity were identified upstream of the TSS in each promoter set and could indicate the location of cis-regulatory modules (CRMs). The conserved promoter regions and cis-element maps of the SCW-associated EgrCesA8 promoter were used to direct promoter truncation for reporter gene analysis in Arabidopsis, Eucalyptus and Populus. Comparative analysis of the cis-element maps and GUS expression data revealed that two main conserved regions of the CesA8 promoter harboured clusters of cis-elements and modulated GUS expression. The CT(11)-microsatellite in the conserved TSS-associated cis-element cluster produced strong non-specific GUS expression in Eucalyptus and Arabidopsis when appended to the 5’UTR which suggests a role in the EgrCesA8 core promoter. Further upstream in the promoter a second conserved promoter region coincided with a cluster of SCW-associated cis-elements and caused a loss of expression in leaf vasculature, suggesting a role for this CRM in modulating tissue-specific expression of EgrCesA8. The conserved EgrCesA8 promoter regions which coincided with cis-element clusters and GUS regulatory modules were used as baits in a yeast-1-hybrid screen against the a panel of 14 Eucalyptus SCW transcription factors. EgrMYB31 (AtMYB46) and EgrZincFinger-A were found to interact with the EgrCesA8 5’UTR. The interaction of these transcription factors with the 5’UTR were blocked by the presence of the CT(11)-microsatellite and could explain the loss of tissue-specific expression. EgrNAC170 (AtSND2) directly interacted with the CRM containing a cluster of SCW-related cis-elements. A dual Y1H assay revealed that EgrKNAT7 in the presence of EgrMYB80 (AtMYB52) or EgrMYB87 (AtMYB54) could also interact with the ErgCesA8 CRM. Together the results of the dissertation indicate that EgrCesA8 regulation is modulated by different protein-DNA and protein-protein interactions acting at highly conserved regions of the promoter.Thesis (PhD)--University of Pretoria, 2013.GeneticsPhDUnrestricte

Isolation and characterization of the cellulose synthase promoters of Eucalyptus trees

Cellulose is one of the most abundant biopolymers on earth and is an important commodity for industries such as the pulp and paper industry. Cellulose is deposited into the plant cell walls by a complex of membrane bound enzymes known as cellulose synthases. A number of cellulose synthase (CesA) genes, which encode for different cellulose synthase proteins, have been identified from plant species such as Eucalyptus, Populus and Arabidopsis. Mutant and expression profile analysis of the CesA genes indicated that a set of three CesA genes are associated with secondary cell wall formation, while a different set of CesA genes are associated with primary cell wall formation. The aim of this study was to investigate the transcriptional regulation of the different members of the CesA gene family in Eucalyptus. The promoter regions were comparatively analysed with the orthologous regions in Arabidopsis and Populus using bioinformatics tools to identify putative regulatory motifs that playa role in CesA genes regulation. Six Eucalyptus CesA gene promoters were isolated using genome walking. The Eucalyptus promoter regions and the orthologous promoter regions from Populus and Arabidopsis were analysed using TSSP (Transcriptional start site plant promoter prediction) and NNPP (Neural network promoter prediction) software packages. The software packages predicted the transcriptional start sites of the genes and the core regulatory elements such as the TATA-box and initiator elements. The in silico results were compared among species and it was found that the predicted transcriptional start sites and the core elements of the CesA gene promoters showed substantial structural conservation. The promoter regions were used in a comparative in silico analysis with the orthologous promoter regions from Arabidopsis and Populus to identify putative regulatory motifs. This is the first study in which the promoters of the CesA gene family are characterized in Arabidopsis, Populus and Eucalyptus. Three software packages (Weeder, POCO and MotifSampler) were used to analyse the promoter regions and identify over-represented motif sequences. A number of key stem-specific and xylem-specific motifs such as the AC-motif and G-box motif were identified as well as a number of novel motifs. Although all of the predicted motifs identified here will have to be functionally tested, the results of this study provide a good map for directed deletion studies and functional testing of the CesA promoters.Dissertation (MSc (Genetics))--University of Pretoria, 2009.Geneticsunrestricte

Comparative analysis of orthologous cellulose synthase promoters from Arabidopsis, Populus and Eucalyptus : evidence of conserved regulatory elements in angiosperms

The cellulose synthase (CesA) gene family encodes the catalytic subunits of a large protein complex responsible for the deposition of cellulose into plant cell walls. Early in vascular plant evolution, the gene family diverged into distinct members with conserved structures and functions (e.g. primary or secondary cell wall biosynthesis). Although the functions and expression domains of CesA genes have been extensively studied in plants, little is known about transcriptional regulation and promoter evolution in this gene family. Here, comparative sequence analysis of orthologous CesA promoters from three angiosperm genera, Arabidopsis, Populus and Eucalyptus, was performed to identify putative cis-regulatory sequences. The promoter sequences of groups of Arabidopsis genes that are co-expressed with the primary or secondary cell wall-related CesA genes were also analyzed. Reporter gene analysis of newly isolated promoter regions of six E. grandis CesA genes in Arabidopsis revealed the conserved functionality of the promoter sequences. Comparative sequence analysis identified 71 conserved sequence motifs, of which 66 were significantly over-represented in either primary or secondary wall-associated promoters. The presence of conserved cis-regulatory elements in the evolutionary distant CesA promoters of Arabidopsis, Populus and Eucalyptus suggests an ancient transcriptional network regulating cellulose biosynthesis in vascular plants