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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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The scope for manipulating the polyunsaturated fatty acid content of beef:a review

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Journal of Animal Science and Biotechnology 2016年第3期7卷 299-311页

作者： Payam Vahmani Cletos Mapiye Nuria Prieto David C.Rolland Tim A.Mc Allister Jennifer L.Aalhus Michael E.R.Dugan agriculture and agri-food canada Lacombe Research Centre Department of Animal Sciences Faculty of Agri SciencesStellenbosch University Department of agricultural Food and Nutritional SciencesUniversity of Alberta agriculture and agri-food canada Lethbridge Research Centre

Since 1950, links between intake of saturated fatty acids and heart disease have led to recommendations to limit consumption of saturated fatty acid-rich foods, including beef. Over this time, changes in food consumption patterns in several countries including canada and the USA have not led to improvements in health. Instead, the incidence of obesity, type II diabetes and associated diseases have reached epidemic proportions owing in part to replacement of dietary fat with refined carbohydrates. Despite the content of saturated fatty acids in beef, it is also rich in heart healthy cis-monounsaturated fatty acids, and can be an important source of long-chain omega-3（n-3） fatty acids in populations where little or no oily fish is consumed. Beef also contains polyunsaturated fatty acid biohydrogenation products,including vaccenic and rumenic acids, which have been shown to have anticarcinogenic and hypolipidemic properties in cell culture and animal models. Beef can be enriched with these beneficial fatty acids through manipulation of beef cattle diets, which is now more important than ever because of increasing public understanding of the relationships between diet and health. The present review examines recommendations for beef in human diets, the need to recognize the complex nature of beef fat, how cattle diets and management can alter the fatty acid composition of beef, and to what extent content claims are currently possible for beef fatty acids.

关键词： Beef Biohydrogenation products Lipids n-3 fatty acids Rumenic acid Vaccenic acid

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Effect of Land Use on Soil Phosphorus Sorption-Desorption Under Intensive agricultural Practices in Plastic-Film Greenhouses

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Pedosphere 2014年第3期24卷 367-377页

作者： YANG Guang-Rong HAO Xi-Ying LI Chun-Li LI Yong-Mei agriculture and agri-food canada Lethbridge Research Centre Yunnan agricultural University

With rapid urbanization and economic growth, Chinese traditional rice-legume production is increasingly replaced by vegetable and horticultural flower production, which could affect soil properties. This study was conducted near Kunming City, Yunnan Province, Southwest China to investigate how soil phosphorus （P） sorption and desorption processes respond to land use changes and to relate P sorption and desorption parameters to soil properties. Soil samples （0-20, 20-40, 40-60, 60-80 and 80-100 cm） were collected from five sites representing four land use types： rice-legume production in a two-crop, one-year rotation （Rice）, vegetable production in open fields （Vegetable）, recent （〈 3 years） conversion from open fields to plastic-film greenhouse vegetable and flower production at two sites （VFCS1 and VFCS2）, and longer-term （〉 10 years） plastic-film greenhouse vegetable and flower production （VFCL）. The changes in land use affected soil pH, electrical conductivity, available N and P and organic carbon content in topsoil and subsoil. In turn, these changes of soil properties influenced soil P sorption capacity. The P sorption maximum （Smax） was affected by land use types, soil sampling depth and their interactions （P 〈 0.0001）. For surface soil, Smax was in the order of Rice （1 380 mg kg-1）〉 VFCL （1 154 mg kg-1）〉 VFCS2 （897 mg kg-1）〉 VFCS1 （845 mg kg-1）〉 Vegetable （747 mg kg-1）. The lowest Sm^x generally occurred at the surface （except for Rice at 80-100 cm） and increased with depth. The amount of P desorbed during the 8 successive extractions was in the range 23%-44% of sorbed P, and was not affected by land use types or sampling depths. The decreases in Smax suggested that soil P sorption capacity decreased when rice-legume production converted to more intensive vegetation and flower production and caution should be exercised when applying P fertilizer to minimize potential leaching and runoff P loss to the environment.

关键词： flower production P sorption maximum rice-legume production vegetable production

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Implications of butyrate and its derivatives for gut health and animal production

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Animal Nutrition 2018年第2期4卷 151-159页

作者： ANDrea Bedford Joshua Gong Guelph research and Development centre Agriculture and Agri-food Canada

Butyrate is produced by microbial fermentation in the large intestine of humans and *** serves as not only a primary nutrient that provides energy to colonocytes, but also a cellular mediator regulating multiple functions of gut cells and beyond, including gene expression, cell differentiation, gut tissue development, immune modulation, oxidative stress reduction, and diarrhea *** there are a large number of studies in human medicine using butyrate to treat intestinal disease, the importance of butyrate in maintaining gut health has also attracted significant research attention to its application for animal production, particularly as an alternative to in-feed *** to the difficulties of using butyrate in practice(i.e., offensive odor and absorption in the upper gut), different forms of butyrate,such as sodium butyrate and butyrate glycerides, have been developed and examined for their effects on gut health and growth performance across different *** and its derivatives generally demonstrate positive effects on animal production, including enhancement of gut development, control of enteric pathogens, reduction of inflammation, improvement of growth performance(including carcass composition), and modulation of gut *** benefits are more evident in young animals, and variations in the results have been *** present article has critically reviewed recent findings in animal research on butyrate and its derivatives in regard to their effects and mechanisms behind and discussed the implications of these findings for improving animal gut health and *** addition, significant findings of medical research in humans that are relevant to animal production have been cited.

关键词： Butyrate Butyrins Antibiotic alternatives Gut health Nutrition Animal production

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Synopsis of Leymus Hochst.(Triticeae:Poaceae)

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Journal of Systematics and Evolution 2009年第1期47卷 67-86页

作者： Bernard R.BAUM Eastern Cereals and Oilseeds research centre Agriculture and Agri-Food CanadaCentral Experimental Farm

Leymus is a genus in the Triticeae tribe, Poaceae. The taxa of this genus are allopolyploid species which possess the Ns and Xm genomes. According to cytological, cytogenetic and molecular genetic analyses, some species of Hystrix and Elymus ought to be transferred to this genus. A world revision of the genus Leymus is needed. In this paper we summarize experimental results, provide a key to sections, species and varieties, and list all the taxa we recognize in Leymus with their synonyms. This synopsis is a new taxonomic system to be used for the revision of Leymus.

关键词： genome Leymus new taxonomic system section species varieties

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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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Proteomics analysis of Trichoplusia ni midgut epithelial cell brush border membrane vesicles

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Insect Science 2019年第3期26卷 424-440页

作者： Muhammad Afzal Javed Cathy Coutu David A. Theilmann Martin A. Erlandson Dwayne D. Hegedus Saskatoon research and Development centre Agriculture and Agri-Food Canada Saskatoon Saskatchewan Canada Summerland research and Development centre Agriculture and Agri-Food Canada Summerland British Columbia Canada Department of food & Bio-Product Sciences University of Saskatchewan Saskatoon Saskatchewan Canada

The insect midgut epithelium is composed of columnar, goblet, and regenerative cells. Columnar epithelial cells are the most abundant and have membrane protrusions that form the brush border membrane (BBM) on their apical side. These increase surface area available for the transport of nutrients, but also provide opportunities for interaction with xenobiotics such as pathogens, toxins and host plant allelochemicals. Recent improvements in proteomic and bioinfbrmatics tools provided an opportunity to determine the proteome of the T. ni BBM in unprecedented detail. This study reports the identification of proteins from BBM vesicles (BBMVs) using single dimension polyacrylamide gel elec? trophoresis coupled with multi-dimensional protein identification technology. More than 3000 proteins were associated with the BBMV of which 697 were predicted to possess either a signal peptide, at least one transmembrane domain or a GPI-anchor signal. Of these, bioinfbrmatics analysis and manual curation predicted that 185 may be associated with the BBMV or epithelial cell plasma membrane. These are discussed with respect to their predicted functions, namely digestion, nutrient uptake, cell signaling, development, cell-cell interactions, and other functions. We believe this to be the most detailed proteomic analysis of the lepidopteran midgut epithelium membrane to date, which will provide information to better understand the biochemical, physiological and pathological processes taking place in the larval midgut.

关键词： brush border membrane vesicles midgut proteomic analysis Trichoplusiani

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Characterization of starch morphology, composition, physicochemical properties and gene expressions in oat

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Journal of Integrative agriculture 2015年第1期14卷 20-28页

作者： ZHENG Ke JIANG Qian-tao WEI Long ZHANG Xiao-wei MA Jian CHEN Guo-yue WEI Yu-ming Mitchell Fetch Jennifer LU Zhen-xiang ZHENG You-liang Triticeae research Institute Sichuan Agricultural University Lethbridge research centre Agriculture and Agri-Food Canada Cereal research centre Agriculture and Agri-Food Canada Key Laboratory of Southwestern Crop Germplasm Utilization Ministry of Agriculture/Sichuan Agricultural University

Starch is the major carbohydrate in oat （Avena sativa L.） and starch formation requires the coordinated actions of several synthesis enzymes. In this study, the granule morphology, composition and physicochemical properties of oat starch, as well as the expressions of starch synthesis genes were investigated during oat endosperm development. Under the scanning electron microscopy （SEM）, we observed that the unique compound granules were developed in oat endosperms at 10 days post anthesis （DPA） and then fragmented into irregular or polygonal simple granules from 12 DPA until seed maturity. The amylose content, branch chain length of degree of polymerization （DP=13-24）, gelatinization temperature and percentage of retrogradation were gradually increased during the endosperm development; whereas the distribution of short chains （DP=6-12） were gradually decreased. The relative expressions of 4 classes of 13 starch synthesis genes characterized in this study indicated that three expression pattern groups were significantly different among gene classes as well as among varied isoforms, in which the first group of starch synthesis genes may play a key role on the initiation of starch synthesis in oat endosperms.

关键词： oat starch granule morphology composition physicochemical property gene expression

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Multi‑omics integration identifies regulatory factors underlying bovine subclinical mastitis

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Journal of Animal Science and Biotechnology 2024年第3期15卷 987-1007页

作者： Mengqi Wang Naisu Yang Mario Laterriere David Gagne Faith Omonijo Eveline M.Ibeagha‑Awemu agriculture and agri‑food canada Sherbrooke Research and Development CentreSherbrookeQCCanada Department of Animal Science Universite LavalQuebec CityQCCanada Quebec research and Development centre Agriculture and Agri-Food CanadaQuebec CityQCCanada

Background Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy ***-omics approaches enable the comprehensive investigation of the complex interactions between mul-tiple layers of information to provide a more holistic view of disease ***,this study investigated the genomic and epigenomic signatures and the possible regulatory mechanisms underlying subclinical mastitis by integrating RNA sequencing data(mRNA and lncRNA),small RNA sequencing data(miRNA)and DNA methylation sequencing data of milk somatic cells from 10 healthy cows and 20 cows with naturally occurring subclinical mastitis caused by Staphylococcus aureus or Staphylococcus *** Functional investigation of the data sets through gene set analysis uncovered 3458 biological process GO terms and 170 KEGG pathways with altered activities during subclinical mastitis,provided further insights into subclin-ical mastitis and revealed the involvement of multi-omics signatures in the altered immune responses and impaired mammary gland productivity during subclinical *** abundant genomic and epigenomic signatures with sig-nificant alterations related to subclinical mastitis were observed,including 30,846,2552,1276 and 57 differential methylation haplotype blocks(dMHBs),differentially expressed genes(DEGs),lncRNAs(DELs)and miRNAs(DEMs),***,5 factors presenting the principal variation of differential multi-omics signatures were *** important roles of Factor 1(DEG,DEM and DEL)and Factor 2(dMHB and DEM),in the regulation of immune defense and impaired mammary gland functions during subclinical mastitis were *** of the omics within Factors 1 and 2 explained about 20%of the source of variation in subclinical ***,networks of impor-tant functional gene sets with the involvement of multi-omics signatures were demonstrated,which contributed to a comprehensive view of the possible regu

关键词： Candidate discriminant multi-omics signature Gene Long non-coding RNA Methylation haplotype block MicroRNA Multi-omics integration Natural killer cell mediated cytotoxicity pathway Staphylococcus aureus infection pathway

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Evaluation of host resistance and fungicide application as tools for the management of root rot of field pea caused by Aphanomyces euteiches

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The Crop Journal 2019年第1期7卷 38-48页

作者： Longfei Wu Kan-Fa Chang Sheau-Fang Hwang Robert Conner Rudolph Fredua-Agyeman David Feindel Stephen E.Strelkov Department of agricultural Food and Nutritional Science University of Alberta Crop Diversification centre North Alberta Agriculture and Forestry agriculture and agri-food canada Morden Research and Development Centre

Aphanomyces root rot(ARR) of field pea(Pisum sativum), caused by Aphanomyces euteiches, can cause severe root damage, wilting, and large yield losses under wet soil conditions. To identify ways to manage this disease, the effect of A. euteiches inoculum density on field pea was studied under greenhouse and field conditions in 2015 and 2016. Increases in inoculum density reduced seedling emergence, root nodulation, and plant vigor, and resulted in increased root rot severity in both field and greenhouse tests. Seed treatments with the fungicides Apron Advance(thiabendazole + fludioxonil + metalaxyl) + Vibrance(difenoconazole + metalaxylM + sedaxane), INTEGO Solo(ethaboxam), BAS 516F(boscalid + pyraclostrobin), BAS 720F(metalaxyl + pyraclostrobin + fluxapyroxad), and BAS 516F + BAS 720F(3:1) were evaluated for their efficacy against ARR. All seed treatments except Apron Advance + Vibrance reduced root rot severity under controlled conditions. BAS 516F, BAS 720F and INTEGO Solo improved plant vigor and all treatments reduced seedling blight to varying degrees under greenhouse conditions, but not in the field. A collection of 22 pea genotypes was evaluated for resistance to root rot in field plot experiments. Line 00–2067 showed the least severe root rot symptoms,whereas ‘Spring D' showed the lowest reduction in yield. The results suggest that there may be an opportunity to combine partial host resistance and fungicidal seed treatments to adequately manage ARR of field pea.

关键词： Aphanomyces euteiches Field pea Fungicides Inoculum density Resistance

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