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

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

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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 m

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

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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 *** 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://***/bioinformatics_ tools/mADPipeline/***).

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

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Sequencing a Juglans regia×*** 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 *** genomes of interspecific hybrids are usually comprised of haploid genomes of parental *** exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa×*** using a novel combination of single-molecule sequencing and optical genome mapping *** resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere *** termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb *** centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes,many of them *** 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 *** was shown to be asymmetric with one subgenome exhibiting greater gene loss than the *** asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the *** the importance of ***×*** hybrids as potential walnut rootstocks,we catalogued disease resistance genes in the parental genomes and studied their chromosomal *** 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 *** B and D homeoalleles of hexaploid bread wheat are thought to be either a pseudogene or expressed at a low level,*** function of the low expressed allele on chromosome 5 D(5 Dq) was still *** identified a compact spike and dwarf mutant of Sumai 3,NAUH164,by EmS mutagenesis,and the mutant gene was designated as ***23 was mapped to a physical interval of 8.5 mb on chromosome 5 DL,in which the 5 Dq was *** present study,the 5 Dq/q’ were cloned from wild type Sumai 3 and its *** 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 *** SNP resulted in an Ala416 Thr mutation and changed the structure of 5 Dq *** expression change was observed for 5 AQ in the wild type and the *** the 5 Dq expression was significantly up-regulated in leaves,stems and spikes of NAUH164 than those in Sumai *** in the wild type Sumai 3,the Ta-miR172 expression was down regulated in leaf,stem and spike of the *** may due to the induced mismatch to *** further study the relationship of 5 Dq’ with Rht23,a SNP-based co-dominant marker,was *** analysis using a(NAUH164×Alondra’s) RIL population showed that the marker allele was co-segregated with the Rht23 mutant *** results suggest that Rht23 was a 5 Dq point mutation,which led to plant dwarf and compact spike *** 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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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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TeV astronomy

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Frontiers of physics 2013年第6期8卷 714-747页

作者： frank m. Rieger max-Planck-Institut fiir Kernphysik P.O. Box 103980 69029 Heidelberg Germany Institut de Ciencies de L'Espai (IEEC-CSIC) Campus UAB Torte C5 08193 Bellaterra Spain Dublin Institute for Advanced Studies 31 Fitzwilliam Place Dublin 2 Ireland European Associated Laboratory for Gamma-Ray Astronomy jointly supported by CNRS and MPG

With the successful realization of the current-generation of ground-based detectors, TeV Astronomy has entered into a new era. We review recent advances in VHE astronomy, focusing on the potential of Imaging Atmospheric Cherenkov Telescopes （IACTs）, and highlight astrophysical implications of the results obtained within recent years.

关键词： TeV astronomy gamma-rays Cherenkov telescopes high-energy astrophysics

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Influence of groundwater depth on species composition and community structure in the transition zone of Cele oasis

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Journal of Arid Land 2010年第4期2卷 235-242页

作者： frank m. THOmAS Department of Geobotany University of Trier Behringstraβe 21 54296 Trier Germany

The paper analyzes the hypothesis that the distribution of dominant plant species and characteristics of plant communities are related to groundwater depth. The results showed that variations of groundwater depth impacted distributions and characteristics of dominant plant communities. However, besides groundwater depth, the community composition and species diversity were also influenced by physiognomy of the habitat. Based on the similarity coefficient, the differences between dominant plant communities were significant at different groundwater depths. Compared with other results relating to desert vegetation and groundwater depth, variations of community distribution were similar at the large spatial scale. However, in this extremely arid region, there were significant differences in community type and community succession when compared with other arid regions, especially in relationship to deep groundwater depth. With groundwater depth from deep to shallow, communities transformed with the sequence of Alhagi communities, Tamarix spp. communities, Populus communities, Phragmites communities, and Sophora communities. At groundwater depth of less than 6.0 m, the community type and composition changed, and the species diversity increased. Among these dominant species, Tamarix exhibited the biggest efficiency in resource utilization according to niche breadth, which means it possessed the best adaptability to environmental conditions at the oasis margins.

关键词： groundwater depth community characteristic niche breadth oases Taklamakan desert

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HIV protease:late action to prevent immune detection

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Signal Transduction and Targeted Therapy 2021年第5期6卷 1408-1409页

作者： Konstantin m.J.Sparrer frank Kirchhoff Institute of molecular Virology Ulm University Medical CenterUlmGermany

A recent study published in Science by Wang and colleagues shows that premature activation of the HIV-1 protease leads to caspase activation and recruitment domain 8(CARD8)inflammasome-mediated pyroptosis of infected macrophages and CD4+T cells(Fig.1).These findings might help to improve approaches aiming to eliminate the latent viral reservoirs upon HIV-1 *** invading viral pathogens trigger the innate immune system and are usually rapidly controlled and eventually *** sense viral intruders via so-called pattern recognition receptors(PRRs)capable of detecting pathogen-associated molecular patterns(PAmPs)allowing discrimination between self and *** many cases,these patterns are viral nucleic acids that show pathogen-specific structures or emerge at the wrong localization in the ***,activation of PRRs by their respective ligands leads to the induction of various anti-viral signaling cascades,among them the inflammasome.

关键词： eventually action eliminate

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Endoscopic papillectomy: Data of a prospective observational study

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World Journal of Gastroenterology 2013年第27期19卷 4316-4324页

作者： Uwe Will Anne-Kathrin müller frank Fueldner Igor Wanzar frank meyer Department of Gastroenterology Municipal Hospital Department of Surgery University Hospital

AIm:To investigate the clinical value of endoscopic papillectomy indicated by feasibility and safety of the procedure in various diseases of the papilla in a representative number of patients in a setting of daily clinical and endoscopic practice and care by means of a systematic prospective observational study. mETHODS:Through a defined time period, all consecutive patients with tumor-like lesions of the papilla, who were considered for papillectomy, were enrolled in this systematic bicenter prospective observational study, and subdivided into 4 groups according to endoscopic and endoscopic ultrasonography (EUS) findings as well as histopathological diagnosis:adenoma; carcinoma/ neuroendocrine tumor (NET)/lymphoma; papilla into which catheter can not be introduced; adenomyomatosis, respectively. Treatment results and outcome were characterized by R0 resection, complication, recurrence rates and tumor-free ***:Over a 7-year period, 58 patients underwent endoscopic papillectomy. main symptoms prompting to diagnostic measures were unclear abdominal pain in 50% and cholestasis with and without pain in 44%. Overall, 54/58 patients [inclusion rate, 93.1%; sex ratio, males/females = 25/29 (1:1.16); mean age, 65 (range, 22-88) years] were enrolled in the study. Prior to papillectomy, EUS was performed in 79.6% (n = 43/54). Group 1 (adenoma, n = 24/54; 44.4%):91.6% (n = 22/24) with R0 resection; tumor-free survival after a mean of 18.5 mo, 86.4% (n = 19/22); recurrence, 13.6% (n = 3/22); minor complications, 12.5% (n = 3/24). Group 2 (carcinoma/NET/lymphoma, n = 18/54; 33.3%):75.0% (n = 10/18) with R0 resection; tumor-free survival after a mean of 18.5 (range, 1-84) mo, 88.9% (n = 8/9); recurrence, 11.1% (n = 1/9). Group 3 (adenomyomatosis, n = 4/54; 7.4%). Group 4 (primarily no introducible catheter into the papilla, n = 8; 14.8%). The overall complication rate was 18.5% (n = 10/54; 1 subject with 2 complications):Bleeding, n = 3; pancreatitis, n = 7; perforat

关键词： Papilla of Vater Papillectomy Endoscopic ultrasonography Adenoma Carcinoma Carcinoid-like tumor Adenomyomatosis

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