ARC Centre of Excellence for Plant Success in Nature and Agriculture

Interested in joining the Centre of Excellence for Plant Success? Have a look at the range of #PhD #Postdoc and other #jobs we have available here https://lnkd.in/gSHHK6Zr

📢 New publication 'Plant SABATH Methyltransferases: Diverse Functions, Unusual Reaction Mechanisms and Complex #Evolution' by Weijiao Wang, Hong Guo, John Bowman and Feng Chen in Critical Reviews in Plant Sciences. Abstract It has been a quarter century since salicylic acid methyltransferase, the founding member of the plant SABATH enzyme family, was discovered. From making methyl benzoate to synthesizing caffeine, from modulating auxins and gibberellins to participating in strigolactone biosynthesis, new biochemical functions of SABATH methyltransferases have continuously been revealed, with more than 20 substrates of diverse structures identified. Three-dimensional structures for several members of the SABATH family have been solved, rendering explanations of reaction mechanism and structural basis of substrate specificity. The biological functions of several SABATH genes from diverse plants were elucidated by analyzing transgenic plants with overexpression, reduced expression or knock-out mutants of respective SABATH genes. In the majority of sequenced plants examined, SABATH genes constitute a medium-sized family. Diverse catalytic functions of SABATHs have evolved largely via gene duplication followed by functional divergence. Some SABATH family members have a deep evolutionary origin; some others, while catalyzing an identical reaction, evolved more than once. Equally important, many members acquired lineage-specific functions. All these are indicative of the important contributions of the SABATH family to land plant evolution and adaptation. https://lnkd.in/gC4fZyA5

📢 New publication 'Modeling gene content across a #phylogeny to determine when genes become associated' by JIAHAO DIAO, Malgorzata O'Reilly and Barbara Holland in Stochastic Models. Abstract We consider a #model for inferring functional links between genes. We begin with the simple case of two genes whose presence or absence evolves stochastically along a phylogenetic tree. We develop a hidden Markov model where the hidden states of the model correspond to whether or not the genes perform a joint function. In the case that two genes do perform a joint function, the rates of gain or loss of each gene depend on the presence or absence of the other gene. Otherwise, those two genes are assumed to be gained and lost independently. Using simulation, we investigate the conditions under which the package corHMM can infer the hidden state correctly, and we also investigate when the Akaike information criterion (AIC) has the power to reject the simpler model when it is incorrect. We find that we can more accurately determine the dependent and independent rate class regimes when the trees have more tips and when the differences in the two rate classes are larger. We find the accuracy of corHMM is not overly affected by whether or not there are multiple transitions between the rate classes or just a single transition. We show how the two-gene case can be extended to a more general n-gene model with a level-dependent quasi-birth-and-death (LD-QBD) framework. We assume that the level n of the QBD corresponds to the number of genes that are required for some beneficial function, and the phases within each level record the presence/absence of particular genes. https://lnkd.in/gH-nfmR5

📢 New publication 'Application of #Genomics in Supporting Efficient #Conservation and Utilization of Plant Genetic Resources' by Peterson Wambugu, Marie-Noelle Ndjiondjop, Parimalan Rangan and Robert Henry. Abstract Many gene banks have adopted various genomic tools and have integrated them into their routine genebank operations. In this chapter, we review the actual and potential applications of genomics in advancing seed bank-based ex situ conservation and utilization of plant genetic resources. Genomic tools are supporting germplasm acquisition efforts through conservation gap analysis and enabling the identification of rare, threatened, and novel genetic resources that need to be prioritized for conservation. Analysis of germplasm from different environments using transcriptomic approaches assists in identifying the candidate genes associated with desirable traits and biologically important pathways. Identification of genetic redundancy is enabling collection rationalization thus enhancing cost efficiency in plant genetic resources conservation. Genomics is providing greater capacity on developing core collections and trait-specific subsets thus promoting utilization of plant genetic resource collections. Emerging genomic technologies are providing capacity to support in situ conservation and biodiversity restoration using ex situ conserved diversity. Analysis of genome environment associations is enabling the identification of germplasm that potentially possesses the necessary adaptive capacity and desired traits. The lack of a standardized approach on documenting and sharing big genomic data being generated from ex situ collections however remains a major challenge in enhancing genomics-assisted conservation. https://lnkd.in/gXCDDhtm

You are invited to join us at the ARC Centre of Excellence for Plant Success Symposium. Hear from invited speakers and Centre members on their research and discuss opportunities for collaboration. Topics will include genomic prediction for varied environments, phylogenetic comparative analysis, advanced water status measurements for field and lab, and how the Nagoya protocol impacts plant research in Australia. 🗓️ Monday 17 June 🕙 9am-4pm (AEST) 📍 In person at The University of Queensland or online via Zoom, more information and register here: https://lnkd.in/g-DYHX75

📢 New publication 'Reflections on the ABC model of flower development' by John Bowman and Edwige Moyroud in The Plant Cell. Abstract The formulation of the ABC model by a handful of pioneer plant developmental geneticists was a seminal event in the quest to answer a seemingly simple question: how are #flowers formed? Fast forward 30 years and this elegant model has generated a vibrant and diverse community, capturing the imagination of developmental and evolutionary biologists, structuralists, biochemists and molecular biologists alike. Together they have managed to solve many floral mysteries, uncovering the regulatory processes that generate the characteristic spatio-temporal expression patterns of floral homeotic genes, elucidating some of the mechanisms allowing ABC genes to specify distinct organ identities, revealing how evolution tinkers with the ABC to generate morphological diversity, and even shining a light on the origins of the floral gene regulatory network itself. Here we retrace the history of the ABC model, from its genesis to its current form, highlighting specific milestones along the way before drawing attention to some of the unsolved riddles still hidden in the floral alphabet. https://lnkd.in/dFUjQba6

🌱 We're thrilled to share that EIT Food RisingFoodStar, Computomics, has embarked on a groundbreaking collaboration with the ARC Centre of Excellence for Plant Success ARC Centre of Excellence for Plant Success in Nature and Agriculture to advance plant science research. 🔬 This partnership aims to leverage Computomics' cutting-edge machine learning technologies to unlock deeper insights into plant genetics. The goal? To enhance crop resilience and productivity in the face of climate change, supporting sustainable agriculture initiatives worldwide. This is a significant milestone for Computomics and the potential impact of their work with ARC CoE on the future of farming. – Congratulations! #RisingFoodStars #Computomics #ARCCoE #PlantScience #Sustainability #Agriculture #Innovation #ClimateChange #FoodSecurity

📢 New publication 'Crop domestication in the Asia Pacific Region: A review' by Pauline Okemo, Upendra Wijesundra, Upuli Nakandala, Natalie Dillon, Rahul Chandora, Bradley Campbell, Millicent Smith, Craig Hardner, Charles Cadorna, Guillaume Martin, Nabila Yahiaoui, Olivier Garsmeur, Nicolas Pompidor, Angelique D'Hont and Robert Henry in Agriculture Communications. Abstract Understanding crop domestication provides a basis for ongoing genetic improvement of crops, especially in the utilization of wild crop relatives as a source of new variation and may guide the domestication of new crops. The Asia Pacific region is home to most of the world's human population and is a region in which many important crops were domesticated. Here we review the domestication of banana, citrus, coconut, macadamia, mango, millet, mungbean, rice, sugarcane and taro in the Asia Pacific region. These examples illustrate the importance of this region in the development of agriculture. The challenges of conservation of the genetic resources for these crops are exacerbated by the large human population and rapid economic development in the region. Advances in genetic technologies provide an opportunity for accelerated genetic improvement of these crops and the domestication of new crops. https://lnkd.in/gsdKEbNk

#PlantSuccess April 2024 #newsletter is out now! 👀 Read it here: https://lnkd.in/giWcEbdT 📨 Subscribe here: https://lnkd.in/dJaAbXWj

📢 New publication 'Linking nematodes and ecosystem function: a trait-based framework' by Chongzhe Zhang, Ian Wright, Uffe Nielsen, Stefan Geisen and Manqiang Liu in Trends in Ecology and Evolution. Abstract Trait-based approaches are being increasingly adopted to understand species’ ecological strategies and how organisms influence ecosystem function. Trait-based research on soil organisms, however, remains poorly developed compared with that for plants. The abundant and diverse soil nematodes are prime candidates to advance trait-based approaches belowground, but a unified trait framework to describe nematode ecological strategies and assess their linkages with ecosystem function is lacking. We categorized nematode traits as morphological, physiological, life history, and community clusters, and proposed the nematode economics spectrum (NES) to better understand nematode ecological strategies and their association with ecosystem function. We argue that bridging the NES and the plant economics spectrum will facilitate a more holistic understanding of ecosystem carbon and nutrient cycling under global change. https://lnkd.in/gFt9Ri_t