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Inheritance of marsh spot disease resistance in cranberry common bean(Phaseolus vulgaris L.)

The Crop Journal 2022年第2期10卷 456-467页

作者： Bosen Jia Robert L.Conner Nadeem Khan Anfu Hou Xuhua Xia frank m.you Ottawa Research and Development Centre Agriculture and Agri-Food CanadaOttawaOntario K1A 0C6Canada Department of Biology University of OttawaOttawaOntario K1N 6N5Canada morden Research and Development Centre Agriculture and Agri-Food CanadaMordenManitoba R6M 1Y5Canada

Common bean(Phaseolus vulgaris) is an annual legume crop that is grown worldwide for its edible dry seeds and tender pods. marsh spot(mS) of the seeds is a physio-genic stress disease affecting seed quality in beans. Studies have suggested that this disease involves a nutritional disorder caused by manganese deficiency, but the inheritance of resistance to this disease has not been reported. A biparental genetic population composed of 138 recombinant inbred lines(RILs) was developed from a cross between an mS resistant cultivar ‘Cran09’ and an mS susceptible cultivar ‘messina’. The 138 RILs and their two parents were evaluated for mS resistance during five consecutive years from 2015 to 2019 in sandy and heavy clay soils in morden, manitoba, Canada. The mS incidence(mSI) and the mS resistance index(mSRI) representing disease severity were shown to be both highly correlated heritable traits that had high broad-sense heritability values(H;) of 86.5% and 83.2%, respectively. No significant differences for mSI and mSRI were observed between the two soil types in all five-(mSI) or four-year(mSRI) data collection, but significant correlations among years were observed despite mS resistance was moderately affected by year. The mSIs and mSRIs displayed a right-skewed distribution, indicating a mixed genetic model involving a few major genes and polygenes. Using the joint segregation analysis method, the same four major genes with additive-epistasis effects showed the best fit for both traits, explaining 84.4% and85.3% of the phenotypic variance for mSI and mSRI, respectively. For both traits, the m1, m2, m3 and m4 acted as the favorable(resistant) alleles for the four genes where m and m represent two alleles of each gene. However, due to epistatic effects, only the individuals of the m1 m2 m3 m4 haplotype appeared to be highly resistant, whereas those of the m1 m2 m3 m4 haplotype were the most susceptible. The m4 allele significantly suppressed the additive effects of m1 m2 m3 on resistance, but decreased susceptibility

关键词： Common bean Cranberry bean marsh spot Resistance Recombinant inbred line(RIL) Joint segregation analysis major gene Polygene

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Accuracy of genomic selection in biparental populations of flax(Linum usitatissimum L.)

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The Crop Journal 2016年第4期4卷 290-303页

作者： frank m.you Helen m.Booker Scott D.Duguid Gaofeng Jia Sylvie Cloutier morden Research and Development Centre Agriculture and Agri-Food Canada Crop Development Centre Department of Plant Sciences University of Saskatchewan Ottawa Research and Development Centre Agriculture and Agri-Food Canada

Flax is an important economic crop for seed oil and stem fiber. Phenotyping of traits such as seed yield, seed quality, stem fiber yield, and quality characteristics is expensive and time consuming. Genomic selection(GS) refers to a breeding approach aimed at selecting preferred individuals based on genomic estimated breeding values predicted by a statistical model based on the relationship between phenotypes and genome-wide genetic markers. We evaluated the prediction accuracy of GS(rmP) and the efficiency of GS relative to phenotypic selection(RE) for three GS models: ridge regression best linear unbiased prediction(RR-BLUP),Bayesian LASSO(BL), and Bayesian ridge regression(BRR), for seed yield, oil content, iodine value, linoleic, and linolenic acid content with a full and a common set of genome-wide simple sequence repeat markers in each of three biparental populations. The three GS models generated similar rmPand RE, while BRR displayed a higher coefficient of determination(R^2)of the fitted models than did RR-BLUP or BL. The mean rmPand RE varied for traits with different heritabilities and was affected by the genetic variation of the traits in the populations.GS for seed yield generated a mean RE of 1.52 across populations and marker sets, a value significantly superior to that for direct phenotypic selection. Our empirical results provide the first validation of GS in flax and demonstrate that GS could increase genetic gain per unit time for linseed breeding. Further studies for selection of training populations and markers are warranted.

关键词： Genomic selection SSR Flax Linseed Seed yield Fatty acid composition

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Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

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The Crop Journal 2016年第2期4卷 107-118页

作者： frank m.you Qijian Song Gaofeng Jia Yanzhao Cheng Scott Duguid Helen Booker Sylvie Cloutier morden Research and Development Centre Agriculture and Agri-Food Canada Soybean Genomics and Improvement Laboratory USDA-ARS Crop Development Centre University of Saskatchewan Ottawa Research and Development Centre Agriculture and Agri-Food Canada

The type 2 modified augmented design(mAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in mAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters.Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed mAD data analysis pipeline(http://probes.***.usda.gov/bioinformatics_ tools/mADPipeline/index.html).

关键词： Broad-sense heritability Genetic correlation Sampling variance modified augmented design

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Sequencing a Juglans regia×J.microcarpa hybrid yields high-quality genome assemblies of parental species

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Horticulture Research 2019年第1期6卷 1271-1286页

作者： Tingting Zhu Le Wang frank m.you Juan C.Rodriguez Karin R.Deal Limin Chen Jie Li Sandeep Chakraborty Bipin Balan Cai-Zhong Jiang Patrick J.Brown Charles ALeslie mallikarjuna KAradhya Abhaya m.Dandekar Patrick E.mcGuire Daniel Kluepfel Jan Dvorak ming-Cheng Luo Department of Plant Sciences University of CaliforniaDavisCA 95616USA Ottawa Research and Development Centre Agriculture and Agri-Food CanadaOttawaON K1A 0C6Canada Genome Center University of CaliforniaDavisCA 95616USA Crops Pathology and Genetics Research Unit USDA-ARSDavisCA 95616USA National Clonal Germplasm Repository USDA-ARSDavisCA 95616USA

members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence assembly.The genomes of interspecific hybrids are usually comprised of haploid genomes of parental species.We exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa×J.regia using a novel combination of single-molecule sequencing and optical genome mapping technologies.The resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere regions.Chromosome termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb long.The centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes,many of them transcribed.Juglans genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes,which were fractionated by numerous short gene deletions evenly distributed along the length of the chromosomes.Fractionation was shown to be asymmetric with one subgenome exhibiting greater gene loss than the other.The asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the subgenomes.Given the importance of J.microcarpa×J.regia hybrids as potential walnut rootstocks,we catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution.We also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.

关键词： Juglans parental evenly

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The cloning of Rht23 revealed a point mutation in 5Dq leading to plant dwarfness and compact spike in common wheat

The cloning of Rht23 revealed a point mutation in 5Dq leadin...

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2017中国长三角遗传学大会

作者： Kaijun Zhao Jin Xiao Yu Liu Shulin Chen Chunxia Yuan Aizhong Cao frank m.you Donglei Yang An Shengmin Haiyan Wang Xiue Wang State Key Laboratory of Crop Genetics and Germplasm Enhancement Cytogenetics InstituteNanjing Agricultural University/JCIC-MCP morden Research and Development Centre Agriculture and Agri-Food Canada

The domesticated Q gene on wheat chromosome 5 A(5 AQ) encode an AP2 transcription factor,conferring characters of free-threshing and subcompact spike.The B and D homeoalleles of hexaploid bread wheat are thought to be either a pseudogene or expressed at a low level,respectively.The function of the low expressed allele on chromosome 5 D(5 Dq) was still unclear.We identified a compact spike and dwarf mutant of Sumai 3,NAUH164,by EmS mutagenesis,and the mutant gene was designated as Rht23.Rht23 was mapped to a physical interval of 8.5 mb on chromosome 5 DL,in which the 5 Dq was located.In present study,the 5 Dq/q’ were cloned from wild type Sumai 3 and its mutant.Sequence comparison showed that there occurred a SNP substitution(G3147 A) in the 5 Dq ORF-region,which has been proved as the binding site of miR172.The SNP resulted in an Ala416 Thr mutation and changed the structure of 5 Dq protein.No expression change was observed for 5 AQ in the wild type and the mutant.While the 5 Dq expression was significantly up-regulated in leaves,stems and spikes of NAUH164 than those in Sumai 3.Compared in the wild type Sumai 3,the Ta-miR172 expression was down regulated in leaf,stem and spike of the mutant.This may due to the induced mismatch to Ta-miR172.To further study the relationship of 5 Dq’ with Rht23,a SNP-based co-dominant marker,was developed.Linkage analysis using a(NAUH164×Alondra’s) RIL population showed that the marker allele was co-segregated with the Rht23 mutant traits.These results suggest that Rht23 was a 5 Dq point mutation,which led to plant dwarf and compact spike phenotype.Our results provided the evidence that the Q homolog on chromosome 5 D also has pleiotropic effect in regulation of plant architecture.

关键词： Common wheat Q gene Rht23 mutagenesis Single nucleotide polymorphism（SNP）

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Solving traffic data occlusion problems in computer vision algorithms using DeepSORT and quantum computing

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Journal of Traffic and Transportation Engineering(English Edition) 2024年第1期11卷 1-15页

作者： frank Ngeni Judith mwakalonge Saidi Siuhi Department of Engineering South Carolina State UniversityOrangeburgSC 29117USA

Inaccuracies of traffic sensors during traffic counting and vehicle classification have persisted as transportation agencies have been prompted to calibrate sensors periodically.Detection of multiple objects,heavy occlusions,and similar appearances in congested places are some causes of computer vision model inaccuracies.This paper used the YOLOv5 model for detection and the DeepSORT model for tracking objects.Due to the nature of the reported problem caused by many misses and mismatches,the power of quantum computing with the alternating direction method of multipliers(ADmm)optimizer was leveraged.A basic Kalman filter and the Hungarian algorithm features were used in combination with a quantum optimizer to present robust multiple object tracking(mOT)algorithms.This hybrid combination of the classical and quantum model has fastened learning the occludes during frame matching of tracks and detections by generating minimum quantum cost function value.Comparisons with the existing models indicated a significant increase in the primary mOT metric multiple object tracking accuracy(mOTA)by 16%more than the regular YOLOv5-DeepSORT model when using a quantum optimizer.Also,a 6%multiple object tracking precision(mOTP)increases and a 6%identification metrics(F_(1))score increase were observed using the quantum optimizer with identity switching reduced from 6 to 4.This model is expected to assist transportation officials in improving the accuracy of traffic counts and vehicle classification and reduce the need for regular computer vision software calibration.

关键词： Traffic classification Traffic counting DeepSORT YOLOv5 Quantum computing

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Transferability of microsatellite markers from Brachypodium distachyon to miscanthus sinensis,a Potential Biomass Crop

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Journal of Integrative Plant Biology 2011年第3期53卷 232-245页

作者： Hua Zhao Jiangyan Yu frank m. you mingcheng Luo Junhua Peng Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden the Chinese Academy of Sciences Wuhan 430074 China Department of Plant Sciences University of California Davis CA 95616 USA Department of Soil and Crop Sciences Colorado State University Fort Collins CO 80523-1170 USA

miscanthus sinensis has high biomass yield and contributed two of the three genomes in m. x giganteus, a bioenergy crop widely studied in Europe and North America, and thus is a potential biomass crop and an important germplasm for miscanthus breeding. molecular markers are essential for germplasm evaluation, genetic analyses and new cultivar development in m. sinensis. In the present study, we reported transferability of simple sequence repeat （SSR） markers from Brachypodium distachyon to m. sinensis. A set of 57 SSR markers evenly distributed across the B. distachyon genome were deliberately designed. Out of these B. distachyon SSR markers, 86.0% are transferable to m. sinensis. The SSR loci amplified in m. sinensis were validated by re-sequencing the amplicons. The polymorphism information content （PIC） of the transferable SSR markers varied from 0.073 to 0.375 with a mean of 0.263, assessed based on 21 m. sinensis genotypes. Phylogenetic tree based on 162 alleles detected by 49 SSR markers could unambiguously distinguish B. distachyon from m. sinensis, and cluster 21 m. sinensis genotypes into three groups that are basically in coincidence with their geographical distribution and ecotype classifications. The markers developed by the comparative genomic approach could be useful for germplasm evaluation, genetic analysis, and marker-assisted breeding in miscanthus.

关键词： miscanthus Genomes Biomass Evaluation Genetics Viverridae Crops Oesophagus Germplasm Geographical distribution

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Piezo1 expression in chondrocytes controls endochondral ossification and osteoarthritis development

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Bone Research 2024年第1期12卷 199-214页

作者： Laura J.Brylka Assil-Ramin Alimy miriam E.A.Tschaffon-müller Shan Jiang Tobias malte Ballhause Anke Baranowsky Simon von Kroge Julian Delsmann Eva Pawlus Kian Eghbalian Klaus Püschel Astrid Schoppa melanie Haffner-Luntzer David J.Beech frank Timo Beil michael Amling Johannes Keller Anita Ignatius Timur A.Yorgan Tim Rolvien Thorsten Schinke Department of Osteology and Biomechanics University Medical Center Hamburg-Eppendorf20246 HamburgGermany Department of Trauma and Orthopedic Surgery University Medical Center Hamburg-Eppendorf20246 HamburgGermany Institute of Orthopedic Research and Biomechanics University Medical Center UlmBadenWürttemberg89081 UlmGermany Department Legal medicine University Medical Center Hamburg-Eppendorf20246 HamburgGermany Leeds Institute of Cardiovascular and metabolic medicine School of MedicineUniversity of LeedsLS29JT LeedsUK

Piezo proteins are mechanically activated ion channels,which are required for mechanosensing functions in a variety of cell types.While we and others have previously demonstrated that the expression of Piezo1 in osteoblast lineage cells is essential for boneanabolic processes,there was only suggestive evidence indicating a role of Piezo1 and/or Piezo2 in cartilage.Here we addressed the question if and how chondrocyte expression of the mechanosensitive proteins Piezo1 or Piezo2 controls physiological endochondral ossification and pathological osteoarthritis(OA)development.mice with chondrocyte-specific inactivation of Piezo1(Piezo1^(Col2a1Cre)),but not of Piezo2,developed a near absence of trabecular bone below the chondrogenic growth plate postnatally.moreover,all Piezo1^(Col2a1Cre) animals displayed multiple fractures of rib bones at 7 days of age,which were located close to the growth plates.While skeletal growth was only mildly affected in these mice,OA pathologies were markedly less pronounced compared to littermate controls at 60 weeks of age.Likewise,when OA was induced by anterior cruciate ligament transection,only the chondrocyte inactivation of Piezo1,not of Piezo2,resulted in attenuated articular cartilage degeneration.Importantly,osteophyte formation and maturation were also reduced in Piezo1^(Col2a1Cre) mice.We further observed increased Piezo1 protein abundance in cartilaginous zones of human osteophytes.Finally,we identified Ptgs2 and Ccn2 as potentially relevant Piezo1 downstream genes in chondrocytes.Collectively,our data do not only demonstrate that Piezo1 is a critical regulator of physiological and pathological endochondral ossification processes,but also suggest that Piezo1 antagonists may be established as a novel approach to limit osteophyte formation in OA.

关键词： Piezo1 markedly ossification

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Impact on Soil Organic C and Total Soil N from Cool- and Warm-Season Legumes Used in a Green manure-Forage Cropping System

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Agricultural Sciences 2024年第3期15卷 333-357页

作者： Clark B. Neely Francis m. Rouquette Jr. Cristine L.S. morgan frank m. Hons William L. Rooney Gerald R. Smith Department of Soil and Crop Science Washington State University Pullman WA USA Texas A&m AgriLife Research Overton TX USA Chief Scientific Officer Soil Health Institute Morrisville NC USA Department of Soil and Crop Science Texas A&M University College Station TX USA

Annual forage legumes are important components of livestock production systems in East Texas and the southeastern US. Forage legumes contribute nitrogen (N) to cropping systems through biological N fixation, and their seasonal biomass production can be managed to complement forage grasses. Our research objectives were to evaluate both warm- and cool-season annual forage legumes as green manure for biomass, N content, ability to enhance soil organic carbon (SOC) and soil N, and impact on post season forage grass crops. Nine warm-season forage legumes (WSL) were spring planted and incorporated as green manure in the fall. Forage rye (Secale cereale L.) was planted following the incorporation of WSL treatments. Eight cool-season forage legumes (CSL) were fall planted in previously fallow plots and incorporated as green manure in late spring. Sorghum-sudangrass (Sorghum bicolor x Sorghum bicolor var. sudanense) was planted over all treatments in early summer after forage rye harvest and incorporation of CSL treatments. Sorghum-sudangrass was harvested in June, August and September, and treatments were evaluated for dry matter and N concentration. Soil cores were taken from each plot, split into depths of 0 to 15, 15 to 30 and 30 to 60 cm, and soil C and N were measured using combustion analysis. Nylon mesh bags containing plant samples were buried at 15 cm and used to evaluate decomposition rate of above ground legume biomass, including change in C and N concentrations. mungbean (Vigna radiata L. [Wilczek]) had the highest shoot biomass yield (6.24 t Dm ha-1) and contributed the most total N (167 kg∙ha-1) and total C (3043 kg∙ha-1) of the WSL tested. Decomposition rate of WSL biomass was rapid in the first 10 weeks and very slow afterward. Winter pea (Pisum sativum L. spp. sativum), arrow leaf clover (Trifolium vesiculosum Savi.), and crimson clover (Trifolium incarnatum L.) were the most productive CSL in this trial. Austrian winter pea produced 8.41 t Dm ha-1 with a total

关键词： Annual Legumes Soil N Soil Organic C Green manure Deer Browse Forage Cropping Systems

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Legume Green manure and Intercropping for High Biomass Sorghum Production

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Agricultural Sciences 2024年第6期15卷 605-621页

作者： Clark B. Neely Francis m. Rouquette Jr. Cristine L. S. morgan frank m. Hons William L. Rooney Gerald R. Smith Department of Soil and Crop Science Washington State University Pullman WA USA Texas A&m AgriLife Research Overton TX USA Soil Health Institute Morrisville NC USA Department of Soil and Crop Science Texas A&M University College Station TX USA

Before the advent of cheap, synthetic fertilizers, legumes were commonly used as green manure crops for their ability to fix atmospheric nitrogen (N). A three-year study at Overton, TX examined legume integration into high-biomass sorghum (Sorghum bicolor L.) production systems on a Lilbert loamy fine sand recently cultivated after a fertilized bermudagrass [Cynodon dactylon (L.) Pers.] pasture. In this split-split plot design, ‘Dixie’ crimson clover (Trifolium incarnatum L.) and ‘Iron and Clay’ cowpea (Vigna unguiculata L.) were integrated into a high-biomass sorghum production system to evaluate impacts on N concentration, C concentration, and yield of high-biomass sorghum and their impacts on soil total N and soil organic carbon (SOC). main plots were split into crimson clover green manure (CLGm) and winter fallow (FALL) followed by three sub-plots split into warm-season crop rotations: cowpea green manure (CPGm), cowpea-sorghum intercrop (CPSR), and sorghum monocrop (SORG). Three N fertilizer treatments (0, 45, 90 kg N∙ha−1) were randomized and applied as sub-sub plots. The CLGm increased (P sorghum biomass yield (16.5 t Dm∙ha−1) 28% in year three but had no effect in the first two years. The CPSR treatment reduced sorghum yield up to 62% compared to SORG;whereas CPGm increased sorghum yield 56% and 18% the two years following cowpea incorporation. Rate of N fertilizer had no effect on sorghum biomass yield. Decrease in SOC and soil N over time indicated mineralization of organic N and may explain why no N fertilizer response was observed in sorghum biomass yield. Cowpea showed strong potential as a green manure crop but proved to be too competitive for successful intercropping in high-biomass sorghum production systems.

关键词： High-Biomass Sorghum Legumes Green manure Intercrop Cowpea Crimson Clover Soil Organic Carbon Soil Nitrogen

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