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Ground-Based LiDAR Improves Phenotypic Repeatability of Above-Ground Biomass and Crop Growth Rate in Wheat

Plant Phenomics 2020年第1期2卷 138-148页

作者： David M.Deery Greg J.Rebetzke Jose A.Jimenez-Berni Anthony G.Condon David J.Smith Kathryn M.Bechaz William D.Bovill csiro agriculture and food CanberraACTAustralia csiro agriculture and food YancoNSWAustralia NSW Department of Primary Industries YancoNSWAustralia

Highly repeatable,nondestructive,and high-throughput measures of above-ground biomass(AGB)and crop growth rate(CGR)are important for wheat improvement programs.This study evaluates the repeatability of destructive AGB and CGR measurements in comparison to two previously described methods for the estimation of AGB from LiDAR:3D voxel index(3DVI)and 3D profile index(3DPI).Across three field experiments,contrasting in available water supply and comprising up to 98 wheat genotypes varying for canopy architecture,several concurrent measurements of LiDAR and AGB were made from jointing to anthesis.Phenotypic correlations at discrete events between AGB and the LiDAR-derived biomass indices were significant,ranging from 0.31(P<0:05)to 0.86(P<0:0001),providing confidence in the LiDAR indices as effective surrogates for AGB.The repeatability of the LiDAR biomass indices at discrete events was at least similar to and often higher than AGB,particularly under water limitation.The correlations between calculated CGR for AGB and the LiDAR indices were moderate to high and varied between experiments.However,across all experiments,the repeatabilities of the CGR derived from the LiDAR indices were appreciably greater than those for AGB,except for the 3DPI in the water-limited environment.In our experiments,the repeatability of either LiDAR index was consistently higher than that of AGB,both at discrete time points and when CGR was calculated.These findings provide promising support for the reliable use of ground-based LiDAR,as a surrogate measure of AGB and CGR,for screening germplasm in research and wheat breeding.

关键词： Wheat Biomass LiDAR

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Harnessing genetic variation at regulatory regions to fine-tune traits for climate-resilient crops

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Molecular Plant 2022年第2期15卷 222-224页

作者： Diep R.Ganguly Lee T.Hickey Peter A.Crisp Australian Research Council Centre of Excellence in Plant Energy Biology Research School of BiologyThe Australian National UniversityActonCanberraACT 2601Australia csiro Synthetic Biology Future Science Platform CanberraACTAustralia Queensland Alliance for agriculture and food Innovation The University of QueenslandBrisbaneQLD 4072Australia School of agriculture and food Sciences The University of QueenslandBrisbaneQLD 4072Australia

Climate change is making it more challenging to meet the food demands of a growing global population.Increased food produc-tion relies on continual crop improvements to generate higher and more stable yields,especially with increasingly unpredictable environments and less arable land.The improvement of traits that promote climate resilience and resource utilization,for example,greater photosynthetic capacity,increased nitrogen use efficiency,and optimized root and shoot architecture,repre-sents a promising avenue for engineering crops to yield more with less(Evans and Lawson,2020).A key challenge for crop engineering is optimizing performance in specific environments.

关键词： crops traits environments

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Unsupervised Plot-Scale LAI Phenotyping via UAV-Based Imaging, Modelling, and Machine Learning

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Plant Phenomics 2022年第1期4卷 196-214页

作者： Qiaomin Chen Bangyou Zheng Karine Chenu Pengcheng Hu Scott C.Chapman School of agriculture and food Sciences The University of QueenslandSt LuciaQLDAustralia agriculture and food CSIROQueensland Bioscience PrecinctSt LuciaQLDAustralia The University of Queensland Queensland Alliance for Agriculture and Food InnovationToowoombaQLDAustralia

High-throughput phenotyping has become the frontier to accelerate breeding through linking genetics to crop growth estimation,which requires accurate estimation of leaf area index(LAI).This study developed a hybrid method to train the random forest regression(RFR)models with synthetic datasets generated by a radiative transfer model to estimate LAI from UAV-based multispectral images.

关键词： breeding forest estimation

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PlantcircBase 7.0:Full-length transcripts and conservation of plant circRNAs

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Plant Communications 2022年第4期3卷 64-71页

作者： Xiaoxu Xu Tianyu Du Weihua Mao Xiaohan Li Chu-Yu Ye Qian-Hao Zhu Longjiang Fan Qinjie Chu Institute of Crop Science&Institute of Bioinformatics Zhejiang UniversityHangzhou 310058China Shandong(Linyi)Institute of Modern agriculture of Zhejiang University Linyi 310014China Analysis Center of Agrobiology and Environmental Science Zhejiang UniversityHangzhou 310058China csiro agriculture and food Black Mountain LaboratoriesCanberraACT 2601Australia

Circular RNA(circRNA)is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants.Five years ago,we developed a comprehensive plant circRNA database(PlantcircBase),which has attracted much attention from the plant circRNA community.Here,we report an updated PlantcircBase(v.7.0),which contains 171,118 circRNAs from 21 plant species.Over 31,000 of the circRNAs have full-length sequences constructed based on analysis of 749 bulk RNA sequencing(RNAseq)datasets downloaded from the public domain and Nanopore long-read sequencing results of rice RNAs newly generated in this study.A plant multiple conservation score(PMCS),based on the conservation of both sequence and expression profiles,was calculated for each circRNA to quantify and compare the conservation of all circRNAs.A new parameter,plant circRNA confidence level(PCCL),is introduced to measure the identity reliability of each circRNA based on experimental validation results and the number of references that support the circRNA.All this information and other details of circRNAs can be browsed,searched,and downloaded from PlantcircBase 7.0,which also provides online bioinformatics tools for visualization and sequence alignment.PlantcircBase 7.0 is publicly and freely accessible at http://***/plantcircbase/.

关键词： plant circRNA PlantcircBase conservation full-length transcripts long-read sequencing

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Construction of an integrated map and location of a bruchid resistance gene in mung bean

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The Crop Journal 2016年第5期4卷 360-366页

作者： Lixia Wang Chuanshu Wu Min Zhong Dan Zhao Li Mei Honglin Chen Suhua Wang Chunji Liu Xuzhen Cheng Institute of Crop Science Chinese Academy of Agricultural Sciences csiro agriculture and food

Bruchid beetle(Callosobruchus chinensis) poses a serious threat to the production and storage of mung bean(Vigna radiata). Mapping bruchid resistance(Br) will provide an important basis for cloning the responsible gene(s) and elucidating its functional mechanism, and will also facilitate marker-assisted selection in mung bean breeding. Here, we report the construction of the genetic linkage groups of mung bean and mapping of the Br1 locus using an RIL population derived from a cross between Berken, a bruchid-susceptible line, and ACC41, a bruchid-resistant line. A total of 560 markers were mapped onto 11 linkage groups,with 38.0% of the markers showing distorted segregation. The lengths of the linkage groups ranged from 45.2 to 117.0 c M with a total coverage of 732.9 c M and an average interval of1.3 c M between loci. Br1 was located on LG9 between BM202(0.7 c M) and Vr2-627(1.7 c M).Based on 270 shared SSR markers, most of the linkage groups were assigned to specific chromosomes. These results should further accelerate the genetic study of this crop.

关键词： Vigna radiata Callosobruchus chinensis Linkage map Resistance Gene mapping

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Field Phenomics:Will It Enable Crop Improvement?

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Plant Phenomics 2021年第1期3卷 310-325页

作者： David M.Deery Hamlyn G.Jones csiro agriculture and food CanberraACTAustralia Division of Plant Sciences University of DundeeUK School of agriculture and Environment University of Western AustraliaAustralia

Field phenomics has been identified as a promising enabling technology to assist plant breeders with the development of improved cultivars for farmers.Yet,despite much investment,there are few examples demonstrating the application of phenomics within a plant breeding program.We review recent progress in field phenomics and highlight the importance of targeting breeders’needs,rather than perceived technology needs,through developing and enhancing partnerships between phenomics researchers and plant breeders.

关键词： breeding cultivar Crop

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Polysaccharide composition during cotton seed fibre development:temporal differences between species and in different seasons

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Journal of Cotton Research 2022年第4期5卷 12-24页

作者： PETTOLINO Filomena A. YULIA Dina BACIC Antony LLEWELLYN Danny J. Commonwealth Scientific and Industrial Research Organisation(csiro) Agri-culture and FoodCanberraACT 2601Australia Department of Animal Plant&Soil SciencesLa Trobe Institute for Agriculture and FoodLa Trobe UniversityAgriBio BuildingBundooraVIC 3083Australia

Background:Cotton seed fibres are long single-celled epidermal trichomes that first appear on the surface of the ovule at anthesis and then elongate rapidly over a period of 15-25 days until a secondary cell wall(SCW)begins to develop through a rapid increase in the deposition of microfibrillar cellulose between the plasma membrane and the primary cell wall that eventually terminates elongation.Quantitative measurements of the different polysaccharide components in both wall types over time and how they influence fibre quality can direct studies involved in enhanc-ing fibre properties for yarn quality through cell wall manipulation or molecular breeding.Results:A detailed chemical analysis of cell wall composition by differential solvent fractionation was used to identify the range of polysaccharides present in mature cotton fibres and used to validate a simpler total cell wall monosaccharide linkage analysis protocol for wall compositional analysis.Analysis of fibres from 5 days post-anthesis through maturity for three cultivated species,Gossypium hirsutum,G.barbadense,and G.arboreum,showed the dynamic nature of cell wall polysaccharide composition through fibre development and that it progressed differently for each species.Plants grown in the glasshouse during either autumn to winter or spring to summer and within each species had fibre qualities and temporal aspects of cell wall development that were different for each season.Notably,the timing of the deposition of the SCW was delayed in winter grown plants and appeared to influence key fibre qual-ity properties.Conclusions:These results suggest that the temporal aspects of cell wall polysaccharide biogenesis during fibre development influence final fibre quality,and this timing is determined by both genetic and environmental factors.The onset of SCW synthesis appears to be a critical factor coinciding with termination of fibre elongation and specify-ing the duration of wall thickening that then affects fibre length and other wall-associated quality parameter

关键词： Fibre development Gossypium hirsutum Gossypium barbadense Gossypium arboreum

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Using a systems modeling approach to improve soil management and soil quality

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Frontiers of Agricultural Science and Engineering 2020年第3期7卷 289-295页

作者： Enli WANG Di HE Zhigan ZHAO Chris J.SMITH Ben C.T.MACDONALD csiro agriculture and food CanberraACT 2601Australia

Soils provide the structural support, water andnutrients for plants in nature and are considered to be thefoundation of agriculture production. Improving soilquality and soil health has been advocated as the goal ofsoil management toward sustainable agricultural intensifi-cation. There have been renewed efforts to define andquantify soil quality and soil health but establishing aconsensus on the key indicators remains difficult. It isargued that such difficulties are due to the former ways ofthinking in soil management which largely focus on soilproperties alone. A systems approach that treats soils as akey component of agricultural production systems ispromoted. It is argued that soil quality must be quantifiedin terms of crop productivity and impacts on ecosystemsservices that are also strongly driven by climate andmanagement interventions. A systems modeling approachcaptures the interactions among climate, soil, crops andmanagement, and their impacts on system performance,thus helping to quantify the value and quality of soils.Here, three examples are presented to demonstrate this. Inthis systems context, soil management must be an integralpart of systems management practices that also includemanaging the crops and cropping systems under specificclimatic conditions, with cognizance of future climatechange.

关键词： APSIM available water capacity nitrogen management soil functional properties soil health soil-plant modeling

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When domestication bottleneck meets weed

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Molecular Plant 2022年第9期15卷 1405-1408页

作者： Yanqing Sun Longbiao Guo Qian-Hao Zhu Longjiang Fan State Key Lab for Rice Biology China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou 311401China Institute of Crop Science&Institute of Bioinformatics Zhejiang UniversityHangzhou 310058China csiro agriculture and food CanberraACT 2601Australia

DOMESTICATION OF CROPS BY TWO DIFFERENT SCENARIOS Crop domestication is a unique pattern of plant evolution,commonly referred to as the process of generation of cultivated crops from wild specles due to morphological and gen-etic transformation as a result of human intervention and selec-tion.Studies on the relationship between weeds and crops in archaeology,evolutionary biology,and genetics have revolution-ized our understanding of the role of weeds in the agroecosystem and of the intricacy of crop domestication.Weeds,generally be-ing effective competitors of crops,are not the targets of human cultivation;however,like crops,they can adapt to human-made habitats and thereby are under unintentional human selection.The peculiar environment of the agricultural system alows some arable weeds to develop domestication syndrome,Le.,to mimic crop characteristics,such as plant architecture and seed size,to escape being detected and eradicated.

关键词： crops weed cultivated

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Does Global agriculture Need Another Green Revolution？

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Engineering 2018年第4期4卷 449-451页

作者： Danny Llewellyn Chief Research Scientist of csiro agriculture and food Fellow of the Australian Academy of Technology and Engineering Australia

1.引言科学和技术是社会变革的历史驱动力,这些变革大多是有益的,但有时会产生意想不到的(通常是环境方面的)后果,其中一些后果我们目前仍在努力应对。18世纪和19世纪的工业革命,带来的以化石燃料为动力的采矿和制造业机械化发展,以及... 详细信息

1.引言科学和技术是社会变革的历史驱动力,这些变革大多是有益的,但有时会产生意想不到的(通常是环境方面的)后果,其中一些后果我们目前仍在努力应对。18世纪和19世纪的工业革命,带来的以化石燃料为动力的采矿和制造业机械化发展,以及航运和陆路运输的快速发展,导致城市化和人口不断增长。即使在18世纪,人口增长率也显然不能保持稳定。随着城市人口的增多和耕地的减少,除非农业生产率能够跟上发展的步伐。

关键词：科学技术发展现状现代农业技术创新

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