Review
Biochemistry & Molecular Biology
Lei Liu, Penelope L. Lindsay, David Jackson
Summary: This review discusses the knowledge of inflorescence yield-related traits in cereal crops, introduces recent advances in breeding optimization using genome-editing technologies, and anticipates a new era of breeding practice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Rabiya Parveen, Mankesh Kumar, Digvijay Swapnil, Digvijay Singh, Monika Shahani, Zafar Imam, Jyoti Prakash Sahoo
Summary: Although modern breeding techniques have resulted in long-term genetic gain, the pace of genetic gain needs to be accelerated to meet global agricultural demand. Marker-assisted selection has proven effective for improving qualitative traits regulated by few genes, while genomic selection (GS) is the most promising method for enhancing complex traits regulated by multiple genes. GS uses all marker data to accurately predict breeding potential, speeding up the breeding cycle and improving genotype selection. Developing optimal GS models considering non-additive effects, genotype-by-environment interaction, and cost-effectiveness will enable widespread implementation in plants.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Biochemistry & Molecular Biology
Krishna Kumar Rai
Summary: Breeding crops with improved productivity and adaptability is crucial in the face of climate change, and artificial intelligence can help accelerate the breeding cycle and understand plant responses to environmental perturbations.
MOLECULAR BIOLOGY REPORTS
(2022)
Review
Plant Sciences
Bhavna Hurgobin, Muluneh Tamiru-Oli, Matthew T. Welling, Monika S. Doblin, Antony Bacic, James Whelan, Mathew G. Lewsey
Summary: With legislation on cannabis cultivation being relaxed in certain jurisdictions, there is now potential for accelerating cultivar development of this plant species using modern genomics technologies.
Article
Agronomy
Tony Fischer, Karim Ammar, Ivan Ortiz Monasterio, Marta Monjardino, Ravi Singh, Nele Verhulst
Summary: Continued global wheat yield increase is crucial for world food security. The average farm yield of irrigated spring wheat in the Yaqui Valley of Mexico has significantly increased from 1960 to 2019, largely due to the research and efforts of the International Maize and Wheat Improvement Centre. Factors such as agronomic progress, breeding improvements, and government support have contributed to the increase in yield. It is expected that breeding progress will slow down in the future, while new agronomy practices have limited potential. Developing countries have the opportunity to close yield gaps and play a key role in global wheat food security.
FIELD CROPS RESEARCH
(2022)
Article
Agronomy
K. Ann Bybee-Finley, Uriel D. Menalled, Christopher J. Pelzer, Lindsey Ruhl, Natalie P. Lounsbury, Nicholas D. Warren, Jerome H. Cherney, Heather M. Darby, Richard G. Smith, Matthew R. Ryan
Summary: Increases in extreme weather events from climate change may hinder forage crop production. Cropping system diversification can improve productivity and yield stability, but farmers often face constraints in adopting these strategies. The specific diversity needed and potential tradeoffs are largely unknown.
FIELD CROPS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Muhammad Hafeez Ullah Khan, Shoudong Wang, Jun Wang, Sunny Ahmar, Sumbul Saeed, Shahid Ullah Khan, Xiaogang Xu, Hongyang Chen, Javaid Akhter Bhat, Xianzhong Feng
Summary: Artificial intelligence has provided great opportunities for modern crop breeding, helping to solve problems in high-throughput phenotyping and gene functional analysis, and bringing new possibilities for future breeding. Integrating AI with omics tools can accelerate gene identification and expedite crop improvement programs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Genetics & Heredity
Nur Shuhadah Mohd Saad, Anita A. Severn-Ellis, Aneeta Pradhan, David Edwards, Jacqueline Batley
Summary: Breeders face the challenge of meeting the demands of a growing world population amidst imminent climate change. Utilizing genetic diversity and genomic tools is crucial for developing resilient Brassica crops, while genomic advancements provide insights into crop evolution, breeding histories, and desired agronomic traits. The multidisciplinary approach of plant breeding, incorporating genotype-environment-management interactions, ensures the selection of Brassica varieties ready for climate change.
FRONTIERS IN GENETICS
(2021)
Article
Agronomy
Ye-Geon Kim, Hyun-Hwa Park, Hyo-Jin Lee, Hee-Kwon Kim, Yong-In Kuk
Summary: Climate change has resulted in disruptions to food systems, with a particularly alarming impact on global nutrition due to decreased grain production and reduced protein content and quality. This study examines the effects of temperature on barley growth and yield at different stages in four different climate areas. The research findings highlight variations in growth parameters, yield levels, soil composition, and mineral content between the group areas. The study concludes that certain areas are still not suitable for barley cultivation despite climate change.
Article
Environmental Sciences
Stephen Whitfield, Sarah Chapman, Marcelin Tonye Mahop, Chetan Deva, Kennedy Masamba, Andekelile Mwamahonje
Summary: Crop breeding for resilience to changing climates is a key investment area in African agricultural development, but actively breeding for uncertain future climates presents challenges. This paper examines efforts to breed new varieties of crops for climate resilience in southern Africa and assesses the influence of climate model projections on current breeding activities. Despite some limitations, utilizing climate model projections can help inform breeding priorities and agenda setting in agricultural development.
Article
Meteorology & Atmospheric Sciences
Ali Mokhtar, Hongming He, Karam Alsafadi, Safwan Mohammed, Olusola O. Ayantobo, Ahmed Elbeltagi, Ossama M. M. Abdelwahab, Hongfei Zhao, Ye Quan, Hazem Ghassan Abdo, Yeboah Gyasi-Agyei, Yu Li
Summary: This study investigated the drought vulnerability of wheat, rice, maize, and sugarcane cultivated in southwest China. The results showed that the southern part of the study area, especially Yunnan Province, experienced the highest drought duration. Among the crops studied, winter wheat suffered the highest annual crop yield losses, particularly in 2010.
INTERNATIONAL JOURNAL OF CLIMATOLOGY
(2022)
Article
Plant Sciences
Clive T. Darwell, Samart Wanchana, Vinitchan Ruanjaichon, Meechai Siangliw, Burin Thunnom, Wanchana Aesomnuk, Theerayut Toojinda
Summary: Agricultural crop breeding programs should pay attention to the potential contributions of landraces and secondary accessions, as well as avoid accumulating deleterious alleles in elite cultivars. Additionally, it is important to consider global database findings, rather than solely relying on SNP-based methods. The fully automated bioinformatics pipeline, riceExplorer, allows integration of local breeding program sequence data with international database resources, facilitating the identification of functional haplotypes associated with extreme phenotypic variation at a global level.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Beatriz E. Garcia-Gomez, Juan A. Salazar, Maria Nicolas-Almansa, Mitra Razi, Manuel Rubio, David Ruiz, Pedro Martinez-Gomez
Summary: Fruit ripening in plants involves complex processes that require the coordinated change in expression of hundreds to thousands of genes and various biochemical and physiological signal cascades. In Prunus species, ripening includes carbohydrate conversion, fruit firmness reduction, color changes, acidity decrease, and aroma increase, all of which are regulated at molecular levels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Agronomy
Oliver Schliebs, Chon-Kit Kenneth Chan, Philipp E. Bayer, Jakob Petereit, Ajit Singh, Keywan Hassani-Pak, Jacqueline Batley, David Edwards
Summary: Daisychain is an interactive graph visualization and search tool for custom-built gene homology databases, aiming to help researchers identify homologs of specific genes in other annotation releases. It supports genome sequences and annotation files, with minimum user interaction required for building the homology database. The software includes a web viewer for data analysis and publishing, based on JavaScript.
Article
Chemistry, Multidisciplinary
Heinrich M. du Plessis, John G. Annandale, Nico Benade
Summary: This paper describes a newly developed software-based Decision Support System that assesses the fitness for use of water for irrigation. It considers site-specific factors, several non-traditional water constituents, and the risk of negative effects.
APPLIED SCIENCES-BASEL
(2023)
Article
Plant Sciences
Lily Chen, Diep R. Ganguly, Sarah H. Shafik, Maria Ermakova, Barry J. Pogson, Christopher P. L. Grof, Robert E. Sharwood, Robert T. Furbank
Summary: This study investigates the role of SWEET13 homologues in the apoplastic phloem loading of C-4 grasses. The research shows abundant expression levels of SWEET13 homologues in C-4 species, indicating their potential role in high-capacity sugar transport and providing evidence for an apoplastic phloem loading pathway. Immuno-localization results and transport kinetics studies further support the hypothesis, demonstrating the importance of SWEETs in the efficient transport of glucose and sucrose in Setaria and possibly other C-4 species.
Article
Biochemical Research Methods
N. Dhami, B. J. Pogson, D. T. Tissue, C. Cazzonelli
Summary: The study established a foliar pigment-based bioassay using Arabidopsis rosette leaves and found that environmental treatments and chemical inhibition of carotenoid biosynthesis reduce chlorophyll levels in young leaves. Disruption of CAROTENOID ISOMERASE (CRTISO) activity, but not ZETA-CAROTENE ISOMERASE (Z-ISO) activity, also reduces chlorophyll levels in young leaves. These findings suggest that carotenoid isomerase activity and NFZ-induced inhibition of PDS activity elicit different signaling pathways to control chlorophyll homeostasis in young leaves of Arabidopsis.
Article
Ecology
Firouzeh Taghikhah, Justin Borevitz, Robert Costanza, Alexey Voinov
Summary: Threats to sustainable food production are increasing due to various factors, and understanding and managing agro-ecosystems is crucial for future wellbeing. The Dynamic Agro-Ecosystem Simulation (DAESim) model can simulate and assess the dynamics of soil health and analyze management options.
ECOLOGICAL MODELLING
(2022)
Article
Biochemistry & Molecular Biology
Jason G. Bragg, Marlien van der Merwe, Jia-Yee Samantha Yap, Justin Borevitz, Maurizio Rossetto
Summary: Plant collections are crucial for conservation and ecological restoration. There is a tradeoff between promoting genetic diversity and selecting for specific traits, which varies between species.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Lei Li, Owen Duncan, Diep R. Ganguly, Chun Pong Lee, Peter A. Crisp, Akila Wijerathna-Yapa, Karzan Salih, Josua Trosch, Barry J. Pogson, A. Harvey Millar
Summary: This study reveals that high light stress in Arabidopsis leads to increases in markers of protein degradation and transcriptional up-regulation of proteases and proteolytic machinery. However, proteostasis is largely maintained through a light-induced transcriptional program for nuclear-encoded genes. Plastid-encoded proteins with enhanced degradation rates showed decreased transcript abundances and must maintain protein abundance by other processes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Scott Ferguson, Ashley Jones, Kevin Murra, Benjamin Schwessinger, Justin O. Borevitz
Summary: Synteny loss, primarily caused by unequal homologous recombination, is commonly observed when comparing closely related species. In this study, the genomes of three closely related Eucalyptus species were analyzed, revealing that approximately 48% of the genomes remained syntenic while approximately 36% underwent rearrangements. It was found that rearrangements highly fragmented microsynteny and potentially altered the phenotypes of the Eucalyptus species. This study highlights the importance of using an unbiased framework in genomic variation studies and emphasizes the potential impact of rearrangements on species differentiation and adaptation.
Article
Plant Sciences
Marja M. Mostert-O'Neill, Hannah Tate, S. Melissa Reynolds, Makobatjatji M. Mphahlele, Gert van den Berg, Steve D. Verryn, Juan J. Acosta, Justin O. Borevitz, Alexander A. Myburg
Summary: This study analyzed the genomic consequences of artificial selection in Eucalyptus grandis, a wood crop. Results showed significant genetic differentiation between breeding and wild populations, indicating the importance of intra- and interspecific hybridization during early domestication.
Article
Multidisciplinary Sciences
Aaron L. Phillips, Scott Ferguson, Nathan S. Watson-Haigh, Ashley W. Jones, Justin O. Borevitz, Rachel A. Burton, Brian J. Atwell
Summary: This study provides an important resource for the discovery of critical genes involved in development and stress tolerance through the assembly of a high-quality genome for O. australiensis.
SCIENTIFIC REPORTS
(2022)
Review
Plant Sciences
Andres Garcia, Oorbessy Gaju, Andrew F. Bowerman, Sally A. Buck, John R. Evans, Robert T. Furbank, Matthew Gilliham, A. Harvey Millar, Barry J. Pogson, Matthew P. Reynolds, Yong-Ling Ruan, Nicolas L. Taylor, Stephen D. Tyerman, Owen K. Atkin
Summary: This review explores the potential to increase crop yield potential by optimizing the efficiency of converting light energy into biomass, respiratory ATP production, and ATP use. By targeting factors such as photoprotective machinery, enzymatic kinetics, and metabolic pathways, it is possible to significantly enhance the yield potential of globally important crops.
Review
Biochemistry & Molecular Biology
Andrew F. Bowerman, Caitlin S. Byrt, Stuart John Roy, Spencer M. Whitney, Jenny C. Mortimer, Rachel A. Ankeny, Matthew Gilliham, Dabing Zhang, Anthony A. Millar, Greg J. Rebetzke, Barry J. Pogson
Summary: This article reviews the impact of climate change on farming systems and discusses the traits and technologies needed to develop climate-resilient crops. It emphasizes the importance of public engagement and highlights the challenges of feeding a growing population under harsh and unpredictable climate conditions. It also emphasizes the need to prepare for floods, droughts, frosts, and heat waves, and advocates for modifying current practices and innovative breeding methods.
Article
Plant Sciences
Ryan P. McQuinn, Julie Leroux, Julio Sierra, Lina Escobar-Tovar, Sarah Frusciante, E. Jean Finnegan, Gianfranco Diretto, Giovanni Giuliano, James J. Giovannoni, Patricia Leon, Barry J. Pogson
Summary: The redundancy and interplay among transcriptional regulators of floral development play a crucial role in ensuring plant reproductive success and crop production. This study reveals an additional layer of complexity in the regulation of floral meristem identity and flower development, linking carotenoid biosynthesis and metabolism to the determinate flowering regulation. The accumulation and cleavage of various ?-carotenes in the clb5 mutant of Arabidopsis leads to the reprogramming of gene regulatory networks, establishing floral meristem identity similar to the master regulator APETALA1 (AP1). The findings also suggest that this link between carotenoid metabolism and floral development is conserved in tomato, involving AP1 and SEPALLATA3 (SEP3) as redundant regulators of floral meristem identity.
Article
Plant Sciences
Scott N. Johnson, Rebecca K. Vandegeer, Justin O. Borevitz, Susan E. Hartley, David T. Tissue, Casey R. Hall
Summary: A common garden experiment using 57 accessions of Brachypodium distachyon from different Mediterranean locations showed a negative correlation between silicon accumulation and temperature variables, as well as precipitation seasonality. However, these relationships were only observed in low-silicon soils and not in silicon-supplemented soils. These findings suggest that geographical origin and prevailing climatic conditions may influence patterns of silicon accumulation in grasses.
Article
Plant Sciences
Xin Hou, Yagiz Alagoz, Ralf Welsch, Matthew D. Mortimer, Barry J. Pogson, Christopher Cazzonelli
Summary: PHYTOENE SYNTHASE (PSY) is an important enzyme in carotenoid biosynthesis, and changes in its gene expression and activity can affect carotenoid composition and plastid differentiation in plants. In this study, four genetic variants of PSY were identified, and they were found to regulate leaf virescence phenotypes and plastid abnormalities in mutant plants. These variants influenced alternative splicing, enzyme-substrate interactions, and protein binding, thereby fine-tuning the levels and activity of PSY. Additionally, they also affected the accumulation of specific substances and the regulation of plastid development.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Environmental Sciences
Wolfram Buss, Christian Wurzer, David A. C. Manning, Eelco J. Rohling, Justin Borevitz, Ondrej Masek
Summary: Mineral doping of biomass before pyrolysis can reduce carbon loss, lower the cost of carbon dioxide removal, and improve the nutrient value of biochar and the availability of phosphorus. This method not only offers a ready-to-implement carbon dioxide removal technology, but also addresses global phosphorus and potassium shortages.
COMMUNICATIONS EARTH & ENVIRONMENT
(2022)
Article
Plant Sciences
Xiangxiang Meng, Lu Li, Jesus Pascual, Moona Rahikainen, Changyu Yi, Ricarda Jost, Cunman He, Alexandre Fournier-Level, Justin Borevitz, Saijaliisa Kangasjarvi, James Whelan, Oliver Berkowitz
Summary: The mitochondrial ACONITASE3 (ACO3) plays a crucial role in the acclimation to submergence stress by regulating carbon and nitrogen metabolism and stress signaling pathways in plants.
