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Molecular diversity of barley yellow dwarf virus-PAV from China and the Czech Republic

Journal of Integrative Agriculture 2020年第11期19卷 2736-2745页

作者： May Oo KHINE Brozenka MICHAELA LIU Yan Jiban Kumar KUNDU WANG Xi-feng State Key Laboratory for Biology of plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193P.R.China division of crop Protection and plant Health Crop Research InstitutePraha 16106Czech Republic

Wheat yellow dwarf disease(BYD),caused by different species of barley/cereal yellow dwarf viruses(B/CYDVs),is one of the most serious cereal diseases in China and the Czech Republic.Because genetic diversity of the virus directly influences disease epidemiology,the molecular diversity and population structure of 24 Chinese isolates and 16 the Czech Republic isolates of BYDV-PAV from different regions in two countries were analyzed by sequencing their coat protein(CP)and readthrough protein(RTP)domain(RTD)genes and comparing the sequences with six CP and 16 RTP sequences of BYDVPAV isolates from the NCBI database based on nucleotide identity position,phylogenetic analysis and nucleotide diversity.Nucleotide identities between the Chinese and the Czech Republic isolates for the CP were 76.6–99.4%,73.9–89.1%for RTD(ORF5),respectively.The Chinese and the other country isolates showed 74.7–99.2%nucleotide identity for RTP(ORF3+ORF5).Phylogenetic analysis of CP sequences showed that 20 Chinese isolates clustered in the same clade,but the other four Chinese isolates clustered in another clade with the isolates from the Czech Republic and other counties.The population of BYDV-PAV in China had greater nucleotide variability and was more divergent than that in the Czech Republic.Geographical and ecological factors but not hosts might contribute to the population differences in the two countries.

关键词： barley yellow dwarf virus-PAV coat protein(CP) readthrough protein(RTP) phylogeny genetic diversity China the Czech Republic

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Fertility,genome stability,and homozygosity in a diverse set of resynthesized rapeseed lines

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The crop Journal 2023年第2期11卷 468-477页

作者： Elizabeth Ihien Katche Antje Schierholt Heiko C.Becker Jacqueline Batley Annaliese S.Mason plant Breeding Department The University of Bonn53115 BonnGermany Department of plant Breeding Justus Liebig University35392 GiessenGermany Department of crop sciences Division of Plant Breeding MethodologyGeorg-August University Göttingen37073 GöttingenGermany School of Biological sciences The University of Western AustraliaPerthWA 6009Australia

Rapeseed(Brassica napus,AACC)was formed by hybridization between progenitor species Brassica rapa(AA)and Brassica oleracea(CC).As a result of a limited number of hybridization events between specific progenitor genotypes and strong breeding selection for oil quality traits,rapeseed has limited genetic diversity.The production of resynthesized B.napus lines via interspecific hybridization of the diploid progenitor species B.rapa and B.oleracea is one possible way to increase genetic variation in rapeseed.However,most resynthesized lines produced so far have been reported to be meiotically unstable and infertile,in contrast to established B.napus cultivars.This hinders both maintenance and use of this germplasm in breeding programs.We characterized a large set of 140 resynthesized lines produced by crosses between B.rapa and B.oleracea,as well as between B.rapa and wild C genome species(B.incana,B.hilarionis,B.montana,B.Bourgeaui,B.villosa and B.cretica)for purity(homozygosity),fertility,and genome stability.Self-pollinated seed set,seeds per ten pods as well as percentage pollen viability were used to estimate fertility.SNP genotyping was performed using the Illumina Infinium Brassica 60K array for 116 genotypes,with at least three individuals per line.Most of the material which had been advanced through multiple generations was no longer pure,with heterozygosity detected corresponding to unknown parental contributions via outcrossing.Fertility and genome stability were both genotypedependent.Most lines had high numbers of copy number variants(CNVs),indicative of meiotic instability,and high numbers of CNVs were significantly associated with reduced fertility.Eight putatively stable resynthesized B.napus lines were observed.Further investigation of these lines may reveal the mechanisms underlying this effect.Our results suggest that selection of stable resynthesized lines for breeding purposes is possible.

关键词： Fertility Genome stability Copy number variants SNP genotyping Resynthesized lines

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crop phenotyping in a context of global change:What to measure and how to do it

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Journal of Integrative plant Biology 2022年第2期64卷 592-618页

作者： Jose Luis Araus Shawn Carlisle Kefauver Omar Vergara-Díaz Adrian Gracia-Romero Fatima Zahra Rezzouk Joel Segarra Maria Luisa Buchaillot Melissa Chang-Espino Thomas Vatter Rut Sanchez-Bragado JoséArmando Fernandez-Gallego Maria Dolores Serret Jordi Bort Integrative crop Ecophysiology Group Plant Physiology SectionFaculty of BiologyUniversity of BarcelonaBarcelonaSpain AGROTECNIO Center LleidaSpain plant Ecophysiology and Metabolism Lab ITQB NovaPlant Sciences DivisionOeirasPortugal Programa de Ingeniería Electrónica Facultad de IngenieríaUniversidad de IbaguéIbaguéColombia

High-throughput crop phenotyping,particularly under field conditions,is nowadays perceived as a key factor limiting crop genetic advance.Phenotyping not only facilitates conventional breeding,but it is necessary to fully exploit the capabilities of molecular breeding,and it can be exploited to predict breeding targets for the years ahead at the regional level through more advanced simulation models and decision support systems.In terms of phenotyping,it is necessary to determined which selection traits are relevant in each situation,and which phenotyping tools/methods are available to assess such traits.Remote sensing methodologies are currently the most popular approaches,even when lab-based analyses are still relevant in many circumstances.On top of that,data processing and automation,together with machine learning/deep learning are contributing to the wide range of applications for phenotyping.This review addresses spectral and red-green-blue sensing as the most popular remote sensing approaches,alongside stable isotope composition as an example of a lab-based tool,and root phenotyping,which represents one of the frontiers for field phenotyping.Further,we consider the two most promising forms of aerial platforms(unmanned aerial vehicle and satellites)and some of the emerging data-processing techniques.The review includes three Boxes that examine specific case studies.

关键词： crop phenotyping deep learning models photosynthesis platforms remote sensing roots satellites sensors stable isotopes

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Genetic Dissection of Grain Size Traits Through Genome-Wide Association Study Based on Genic Markers in Rice

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Rice science 2022年第5期29卷 462-472,I0032-I0034页

作者： Amrit Kumar NAYAK Anilkumar C Sasmita BEHERA Rameswar Prasad SAH Gera Roopa LAVANYA Awadhesh KUMAR Lambodar BEHERA Muhammed Azharudheen TP division of crop Improvement Indian Council of Agricultural Research-National Rice Research InstituteCuttack 753006India division of crop Physiology and Biochemistry ICAR-National Rice Research InstituteCuttack 753006India Department of Genetics and plant Breeding Sam Higginbottom University of AgricultureTechnology and SciencesPrayagraj 211007India

Grain size plays a significant role in rice,starting from affecting yield to consumer preference,which is the driving force for deep investigation and improvement of grain size characters.Quantitative inheritance makes these traits complex to breed on account of several alleles contributing to the complete trait expression.We employed genome-wide association study in an association panel of 88 rice genotypes using 142 new candidate gene based SSR(cgSSR)markers,derived from yield-related candidate genes,with the efficient mixed-model association coupled mixed linear model for dissecting complete genetic control of grain size traits.A total of 10 significant associations were identified for four grain size-related characters(grain weight,grain length,grain width,and length-width ratio).Among the identified associations,seven marker trait associations explain more than 10%of the phenotypic variation,indicating major putative QTLs for respective traits.The allelic variations at genes OsBC1L4,SHO1 and OsD2 showed association between 1000-grain weight and grain width,1000-grain weight and grain length,and grain width and length-width ratio,respectively.The cgSSR markers,associated with corresponding traits,can be utilized for direct allelic selection,while other significantly associated cgSSRs may be utilized for allelic accumulation in the breeding programs or grain size improvement.The new cgSSR markers associated with grain size related characters have a significant impact on practical plant breeding to increase the number of causative alleles for these traits through marker aided rice breeding programs.

关键词： best linear unbiased predictor estimate candidate gene based SSR efficient mixed-model association approach genome-wide association study VanRaden kinship

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Genetic diversity for mycorrhizal symbiosis and phosphate transporters in rice

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Journal of Integrative plant Biology 2015年第11期57卷 969-979页

作者： Kwanho Jeong Nicolas Mattes Sheryl Catausan Joong Hyoun Chin Uta Paszkowski Sigrid Heuer Southern Cross plant Science Southern Cross University International Rice Research Institute(IRRI) Crop and Environmental Sciences Division Seoul National University College of Agriculture and Life SciencesPlant Genomics and Breeding Institute University of Cambridge Department of Plant Sciences Australian Center For plant Functional Genomics(ACPFG)

Phosphorus （P） is a major plant nutrient and developing crops with higher P-use efficiency is an important breeding goal. In this context we have conducted a comparative study of irrigated and rainfed rice varieties to assess genotypic differences in colonization with arbuscular mycorrhizal （AM） fungi and expression of different P trans- porter genes. plants were grown in three different soil samples from a rice farm in the Philippines. The data show that AM symbiosis in all varieties was established after 4 weeks of growth under aerobic conditions and that, in soil derived from a rice paddy, natural AM populations recovered within 6 weeks. The analysis of AM marker genes （AM1, AM3, AM14） and P transporter genes for the direct Pi uptake （PT2, PT6） and AM-mediated pathway （PTll, PT13） were largely in agreement with the observed root AM colonization providing a useful tool for diversity studies. Interestingly, delayed AM colonization was observed in the aus-type rice varieties which might be due to their different root structure and might confer an advantage for weed competition in the field. The data further showed that P-starvation induced root growth and expression of the high-affinity P transporter PT6 was highest in the irrigated variety IR66 which a]so maintained grain yield under P-deficient field conditions.

关键词： Mycorrhiza P deficiency tolerance phosphatetransporters rice roots

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Quantifying relationships between rooting traits and water uptake under drought in Mediterranean barley and durum wheat

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Journal of Integrative plant Biology 2014年第5期56卷 455-469页

作者： Pedro Carvalho Sayed Azam-Ali M.John Foulkes Division of Plant and Crop Sciences University of Nottingham Sutton Bonington Campus The University of Nottingham Malaysia Campus Jalan Broga Semenyih Selangor Darul

In Mediterranean regions drought is the major factor limiting spring barley and durum wheat grain yields. This study aimed to compare spring barley and durum wheat root and shoot responses to drought and quantify relationships between root traits and water uptake under terminal drought.One spring barley（Hordeum vulgare L. cv. Rum） and two durum wheat Mediterranean cultivars（Triticum turgidum L. var durum cvs Hourani and Karim） were examined in soil‐column experiments under well watered and drought conditions. Root system architecture traits, water uptake, and plant growth were measured. Barley aerial biomass and grain yields were higher than for durum wheat cultivars in well watered conditions. Drought decreased grain yield more for barley（47%） than durum wheat（30%, Hourani）. Root‐to‐shoot dry matter ratio increased for durum wheat under drought but not for barley, and root weight increased for wheat in response todrought but decreased for barley. The critical root length density（RLD） and root volume density（RVD） for 90% available water capture for wheat were similar to（cv. Hourani） or lower than（cv. Karim） for barley depending on wheat cultivar. For both species, RVD accounted for a slightly higher proportion of phenotypic variation in water uptake under drought than RLD.

关键词： Barley Mediterranean root architecture root length density root traits root volume density water wheat

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Applying plant-based irrigation scheduling to assess water use efficiency of cotton following a high-biomass rye cover crop

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Journal of Cotton Research 2020年第2期3卷 134-145页

作者： MEEKS Calvin D SNIDER John L CULPEPPER Stanley HAWKINS Gary division of plant sciences University of MissouriPortagevilleMO 63873USA Department of crop and Soil sciences University of GeorgiaTiftonGA 31793USA Department of crop and Soil sciences University of GeorgiaWatkinsvilleGA 30677USA.

Background:This study addressed the potential of combining a high biomass rye winter cover crop with predawn leaf water potential(ΨPD)irrigation thresholds to increase agricultural water use efficiency(WUE)in cotton.To this end,a study was conducted near Tifton,Georgia under a manually-controlled,variable-rate lateral irrigation system using a Scholander pressure chamber approach to measure leaf water potential and impose varying irrigation scheduling treatments during the growing season.ΨPDthresholds were-0.4 MPa(T1),-0.5 MPa(T2),and-0.7 MPa(T3).A winter rye cover crop or conventional tillage were utilized for T1-T3 as well.Results:Reductions in irrigation of up to 10%were noted in this study for the driest threshold(-0.7 MPa)with no reduction in lint yield relative to the-0.4 MPa and-0.5 MPa thresholds.Drier conditions during flowering(2014)limited plant growth and node production,hastened cutout,and decreased yield and WUE relative to 2015.Conclusions:We conclude thatΨPDirrigation thresholds between-0.5 MPa and-0.7 MPa appear to be viable for use in aΨPDscheduling system with adequate yield and WUE for cotton production in the southeastern U.S.Rye cover positively impacted water potential at certain points throughout the growing season but not yield or WUE indicating the potential for rye cover crops to improve water use efficiency should be tested under longer-term production scenarios.

关键词： Cotton Irrigation management Water use efficiency Cover crops Cotton sustainability

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Molecular and morphological characterization of stunt nematodes of wheat, maize, and rice in the savannahs of northern Nigeria

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Journal of Integrative Agriculture 2022年第2期21卷 586-595页

作者： Sulaiman ABDULSALAM PENG Huan LIU Shi-ming HUANG Wen-kun KONG Ling-an PENG De-liang State Key Laboratory for Biology of plant Diseases and Insect Pests/Institute of plant Protection Chinese Academy of Agricultural SciencesBeijing 100193P.R.China division of Agricultural Colleges Department of Crop ProtectionAhmadu Bello UniversityZaria 810107Nigeria

Stunt nematodes(Tylenchorhynchus spp.)are obligate migratory root ecto-parasitic nematodes found in the fields of many cultivated crops.These nematodes,with phyto-sanitary potential,are frequently ignored or misdiagnosed as pests,and this may pose a threat to food security.The accuracy of its identification based on a morphological approach has been challenged recently,due to the overlapping of the morphological and morphometric characters of the species.Consequently,the objective of this study is to identify and characterize stunt nematodes present in 54 fields cultivated with cereal crops(wheat,maize and rice)in the savannahs of northern Nigeria,using integrative taxonomy and molecular approaches.The molecular and morphological studies identified and confirmed the presence of T.annulatus as the occurring specie in the savannahs of northern Nigeria.The phylogenetic analysis was carried out using the internal transcribed spacer(ITS)and 28S genes of ribosomal DNA further confirmed the presence of T.annulatus.The first molecular characterization and sequences of the ITS and 28S rDNA gene for T.annulatus from Nigeria were provided by this research.Also,according to our literature search,this is the first report on T.annulatus in wheat,maize and rice in the savannahs of northern Nigeria.Further study to test the pathogenicity of the parasitic nematode species found in this survey is recommended for the prioritization and development of efficient management strategies.

关键词： plant-parasitic nematodes food security Tylenchorhynchus annulatus ITS phylogeny

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Morpho-Physiological Changes in Roots of Rice Seedling upon Submergence

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Rice science 2019年第3期26卷 167-177页

作者： Liem T.BUI Evangelina S.ELLA Maribel L.DIONISIO-SESE Abdelbagi M.ISMAIL Department of plant Biotechnology Cuu Long Delta Rice Research Institute crop and Environmental sciences division International Rice Research Institute Institute of Biological sciences University of the Philippines Los Ba?os College

Submergence is a serious environmental condition that causes large loss in rice production in rain fed lowland and flood affected area. This study evaluated morphological and physiological responses of rice roots to submergence using two tolerant rice genotypes FR13A and Swarna-Sub 1 and two sensitive ones Swarna and IR42. The tolerant genotypes had higher survival rate and less shoot elongation but greater root elongation during submergence than the sensitive ones. After submergence,the tolerant genotypes also had higher root dry weight and more active roots than the sensitive ones.Tolerant genotypes exhibited less root injury, with less malondialdehyde production and slower electrolyte leakage after submergence. Tolerant genotypes also maintained higher concentrations of soluble sugar and starch in roots and shoots and higher chlorophyll retention after submergence than the sensitive ones.Our data showed that root traits such as root activity and root growth are associated with survival rate after submergence. This is probably accomplished through higher energy supply, and membrane integrity is necessary to preserve root function and reduce injury during submergence. These root traits are important for submergence tolerance in rice.

关键词： peroxidase root activity submergence rice seedling Sub1a gene

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Evaluation of high yielding soybean germplasm under water limitation

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Journal of Integrative plant Biology 2016年第5期58卷 475-491页

作者： Silvas J.Prince Mackensie Murphy Raymond N.Mutava Zhengzhi Zhang Na Nguyen Yoon Ha Kim Safiullah M.Pathan Grover J.Shannon Babu Valliyodan Henry T.Nguyen National Center for Soybean Biotechnology and division of plant sciences University of Missouri

Limited information is available for soybean root traits and their plasticity under drought stress. To date, no studies have focused on examining diverse soybean germ- plasm for regulation of shoot and root response under water limited conditions across varying soil types. In this study, 17 genetically diverse soybean germplasm lines were selected to study root response to water limited conditions in clay （trial 1） and sandy soil （trial 2） in two target environments. Physiological data on shoot traits was measured at multiple crop stages ranging from early vegetative to pod filling. The phenotypic root traits, and biomass accumulation data are collected at pod filling stage. In trial 1, the number of lateral roots and forks were positively correlated with plot yield under water limitation and in trial 2, lateral root thickness was positively correlated with the hill plot yield. plant Introduction （PI） 578477A and 088444 were found to have higher later root number and forks in clay soil with higher yield under water limitation, in sandy soil, P1458o2o was found to have a thicker lateral root system and higher yield under water limitation. The genotypes identified in this study could be used to enhance drought tolerance of elite soybean cultivars through improved root traits specific to target environments.

关键词： Fibrous root root angle root plasticity root systemarchitecture （RSA） root thickness spectral indices soybean spectralindices total root length water limitation

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