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Modeling and simulation of recurrent phenotypic and genomic selections in plant breeding under the presence of epistasis

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The Crop Journal 2020年第5期8卷 866-877页

作者： Mohsin Ali Luyan Zhang Ian DeLacy Vivi Arief Mark Dieters Wolfgang H.Pfeiffer Jiankang Wang Huihui Li National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China School of Agriculture and Food Sciences The University of QueenslandBrisbaneQLD 4072Australia harvestplus challenge programme c/o International Food Policy Research Institute(IFPRI)1201 Eye StNWWashingtonDC 20005USA

Recurrent selection is an important breeding method for population improvement and selecting elite inbreds or fixed lines from the improved ***,a computer simulation tool called QuMARS has been developed,which allows the simulation and optimization of various recurrent selection *** major objective in this study was to use the QuMARS tool to compare phenotypic recurrent,marker-assisted recurrent,and genomic selections(abbreviated respectively as PS,MARS and GS)for both short-and long-termbreeding ***,twomarker selection models were considered,i.e.,stepwise(Rstep)and forward regressions(Forward).For GS,three prediction models were considered,i.e.,genomic best linear unbiased predictors(GBLUP),ridge regression(Ridge),and regression by Moore-Penrose general inverse(InverseMP).To generate genotypes and phenotypes for a given individual during simulation,one additive and two epistasis genetic models were considered with three levels of *** demonstrated that selection responses from GBLUP-based GS and MARS(Forward)were consistently greater than those from PS under the additive model,particularly in early selection *** contrast,selection response from PS was consistently superior over MARS and GS under epistatic *** the two epistasis models,total genetic variance and the additive variance component were increased in some cases after *** simulation,we concluded that GS and PS were effective recurrent selection methods for improved breeding of targeted traits controlled by additive and epistatic quantitative trait loci(QTL).QuMARS provides an opportunity for breeders to compare,optimize and integrate new technology into their conventional breeding programs.

关键词： breeding elite additive

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The challenge of defining rare genetic programs by single-cell RNA sequencing:Insights from phloem studies

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Molecular Plant 2024年第1期17卷 22-25页

作者： Xiaomin Liu Pawel Roszak YkäHelariutta State Key Laboratory of Tree Genetics and Breeding College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing 100083China The Sainsbury Laboratory University of CambridgeCB21TN CambridgeUK Wood Development Group University of Helsinki00100 HelsinkiFinland Organismal and Evolutionary Biology Research programme Faculty of Biological and Environmental Sciences and Viikki Plant Science CentreUniversity of Helsinki00100 HelsinkiFinland

Single-cell RNA sequencing technology provides unprecedented opportunities to capture the spatiotemporal aspects of genetic programs that drive cell *** is a subtype of vascular tissue that is crucial for transporting sugars,proteins,and other organic *** critical role in the redistribution of carbon between photosynthetically active“source”organs(leaves,shoots)and“sink”tissues/organs incapable of fixing carbon(wood,storage organs,root system,etc.)has made phloem development and its transcriptional regulation a prime research focus.

关键词： organs sugar rare

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Diversification of primary gene pool through introgression of resistance to foliar diseases from synthetic amphidiploids to cultivated groundnut(Arachis hypogaea L.)

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The Crop Journal 2014年第Z1期2卷 110-119页

作者： Varsha Kumari M.V.C.Gowda Vinod Tasiwal Manish K.Pandey Ramesh S.Bhat Nalini Mallikarjuna Hari D.Upadhyaya Rajeev K.Varshney Department of Genetics and Plant Breeding University of Agricultural Sciences Dharwad International Crops Research Institute for the Semi-Arid Tropics Department of Plant Pathology University of Agricultural Sciences Dharwad Department of Biotechnology University of Agricultural Sciences Dharwad CGIAR Generation challenge programme c/o CIMMYT

Groundnut(Arachis hypogaea L.)is widely grown and consumed around the world and is considered to have originated from a single hybridization event between two wild *** utilization of wild germplasm in breeding programs has been restricted by reproductive barriers between wild and cultivated species and technical difficulties in making large numbers of *** to overcome these hurdles have resulted in the development of synthetic amphidiploids,namely ISATGR 278-18(Arachis duranesis×Arachis batizocoi)and ISATGR 5B(Arachis magna×***),which possess several desirable traits,including resistance to foliar diseases that generally cause huge yield losses annually in groundnut growing areas of Asia,America,and *** an objective to improve foliar disease resistance,the primary gene pool was diversified by introgressing foliar disease resistance in five cultivated genotypes(ICGV 91114,ICGS 76,ICGV 91278,JL 24,and DH 86)from synthetic amphidiploids using a backcross breeding *** introgression lines with resistance to two foliar diseases(rust and late leaf spot)were identified with levels of resistance equal to the *** backcross derived lines have shown a wide range of variation for several morphological and agronomic *** lines,after further evaluation and selection,can serve as donors in future breeding programs aimed atdeveloping improved cultivars with desirable agronomic traits,high resilience to biotic/abiotic stresses and a broadened genetic base.

关键词： Groundnut Peanut Wild species Wide crosses Interspecific hybridization

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The Power of Integrative Approaches to Develop Markers for Maize Molecular Breeding

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分子植物育种 2007年第2期5卷 199-200页

作者： J.M. Ribaut Generation challenge programme c/o CIMMYT Km. 45 Carretera México-Veracruz El Batán Texcoco Estado de Mexico C. P. 56130 Mexico

Recent advances in genomics and bioinformatics now offer real opportunities for dissecting complex traits into their component sub-traits, which will simplify the process of developing the tools necessary to

关键词：玉米分子育种基因表达干旱

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A Comprehensive Transcriptome Assembly of Pigeonpea （Cajanus cajan L.） using Sanger and Second-Generation Sequencing Platforms

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Molecular Plant 2012年第5期5卷 1020-1028页

作者： Himabindu Kudapa Arvind K. Bharti Steven B. Cannon Andrew D. Farmer Benjamin Mulaosmanovi Robin Kramer Abhishek Bohra Nathan T. Weeks John A. Crow Reetu Tuteja Trushar Shah Sutapa Dutta Deepak K. Gupta Archana Singh Kishor Gaikwad Tilak R. Sharma Gregory D. May Nagendra K. Singh Rajeev K. Varshney International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru 502324 india National Center for Genome Resources (NCGR) Santa Fe NM 87505 USA United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn Insects and Crop Genetics Research Unit Ames IA USA National Research Centre on Plant Biotechnology (NRCPB) Indian Agricultural Research Institute New Delhi 110 012 India Department of Agronomy Iowa State University Amens IA USA CGIAR Generation challenge programme (GCP) c/o ClMMYT 06600 Mexico DF Mexico

A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript as- sembly contigs （TACs） with an N50 of 1510 bp, the largest one being -8 kb. Of the 21 434 TACs, 16 622 （77.5%） could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions （ISRs）. By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping posi- tions at the chromosome level were predicted for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of eight genotypes. While 116 markers were validated, 70 markers showed one to three alleles, with an average of 0.16 polymorphism information content （PIC） value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.

关键词： Cajanus cajan (L.) second-generation sequencing transcriptome assembly intron spanning region (ISR)markers.

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Application of Optimization Principle in Landmark University Project Selection under Multi-Period Capital Rationing Using Linear and Integer Programming

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Open Journal of Optimization 2019年第3期8卷 73-82页

作者： Nathaniel Kayode Oladejo Department of Physical Sciences Mathematics Programme Landmark University Nigeria

The current structure of Landmark University (LU) was induced by raising a generation of solution providers through a qualitative and life-applicable training system that focuses on values and creative knowledge by making it more responsive and relevant to the modern-day demands of demonstration, industrialization and development. The challenge facing Landmark University is the question of which of its numerous projects they should invest to give maximum output with minimum input. In this paper, we maximize the Net Present Value (NPV) and maintain the net discount cash overflow of each project per period as contained and extracted as the secondary data of cash inflows of the Landmark University (LU) monthly financial statement and annual reports from 2012 to 2017 of which the documents have been regrouped as small and large scale projects as many enterprises make more use of the trial-and-error method and as such firms have been finding it difficult in allocating scarce resources in a manner that will ensure profit maximization and/or cost minimization with a simple and accurate decision making by the company through an optimization principle in selecting LU project under multi-period capital rationing using linear programming (LP) and integer programming (IP). The annual net cash flow which is the difference between the cash inflows and cash outflows during each period for the project was estimated and recorded. The discount factors were estimated at cost of capital of 10% for each cash flow per period with the corresponding NPV at 10% which revealed that the optimal decision achieves maximum returns of $110 × 102 and this assisted the project manager to select a large number of the variable projects that can maximize the profit which is far better than relying on an ad-hoc judgmental approach to project investment that could have cost 160 × 102 for the same project. Sensitivity analysis on the project parameters are also carried out to test the extent to which pro

关键词： Optimization Linear Integer Programming Sensitivity Investment Maximize Net Present Value

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Sustainable Land Management

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Journal of Environmental Protection 2016年第4期7卷 502-506页

作者： Molla Mekonnen Alemu United Nations Development programme Freetown Sierra Leone

In one way or another, one out of three people are being affected by land degradation. It is estimated that, about every year, 75 billion tonnes of soil material are being lost worldwide as a result of land degradation. Recent findings also showed that about 2 billion hectares of land were severely degraded, in some cases in an irreversible way, all these caused a severe damage to local ecologies as well as contributed a lot for climate change and its associated effects on the wellbeing of humanity. Apart from this, the major portion of most developing countries population are still dependent on the un-mechanized and primitive forms agriculture, livestock production, forestry and fishery, and their livelihood and options for economic development are directly linked to the quality of the land and its resources. The objective of this article is to reaffirm the role of Sustainable Land Management in the process of agricultural development, the main source of livelihood in the developing countries. The paper initially explored the basic concept and principles of sustainable management. Causes of land degradation, the prime challenge of sustainable land management and development are also dealt in detail.

关键词： Sustainable Land Management

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Mapping mountain areas: learning from Global, European and Norwegian perspectives

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Journal of Mountain Science 2019年第1期16卷 1-15页

作者： Martin F.PRICE Tor ARNESEN Erik GL?ERSEN Marc J.METZGER Centre for Mountain Studies Perth College University of the Highlands and Islands Mountain Research programme Eastern Norway Research Institute Spatial Foresight Territorial Policy Support and Research Research Institute of Geography and the Lived Environment School of GeoSciences University of Edinburgh

Defining the spatial extent of mountain areas has long been a challenge. In the present century, the availability of digital elevation models(DEMs) incorporated into geographic information systems(GIS) has allowed the definition of mountain areas based on topographic and other criteria. This paper presents the various delineations of mountains that have been prepared at three scales – global, regional(Europe), and national – and explores the reasons and processes leading to these delineations, and how they have been used. A detailed case study is then presented for Norway. Overall, two types of approaches to mapping mountains have been taken: first, considering mountains per se, based on elevation and/or topography; second, considering them among other categories, e.g., landforms or biogeographical, environmental or landscape zones. All attempts to map mountain areas derive essentially from the objectives of those commissioning and/or undertaking the work; a unitary definition remains unlikely.

关键词： Mountains Mapping Geographic information systems Europe Norway Topography

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Do supplemental perches influence electrocution risk for diurnal raptors?

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Avian Research 2020年第2期11卷 139-149页

作者： Roberto Sánchez Javier Sánchez Javier Oria Francisco Guil Fundación CBD-Hábitat C/Gustavo Fernández Balbuena28002 MadridSpain Tragsa Group C/Conde de Peñalver8428006 MadridSpain Boscaje S.L. Plaza Conde de Cheste540001 SegoviaSpain Ministry for the Ecological Transition and the Demographic challenge Plaza San Juan de la CruzS/N28071 MadridSpain

Background:Power lines are amongst the main causes of mortality for birds *** drives the population dynamics of several threatened species of raptors,at local and global *** the many solutions that have been tested to minimize this threat are supplemental perches;however,their efficiency has rarely been ***:We designed 43 transects in 4 districts in mainland Portugal to gather data from birds perching on pylons with or without supplemental *** 2015 to 2018,transects were surveyed by car at least *** analyzed the factors driving the use of these supplemental perches,and we analyzed if there were differences in the perceived risk(calculated from measurements and not from field surveys)depending on whether the perching was on pylons with or without supplemental ***:We recorded 548 perches of 14 *** conditions seemed to play a role in birds’choice of pylons with supplemental perches versus pylons without supplemental *** also indicated a strong influence of observational *** use of models showed us an important specific effect in the selection of supplemental perches where available:there are some species with a greater tendency to perch on supplemental perches,even when they use both pylons with and without supplemental *** most of the analyzed species and species groups,perceived risk was higher in pylons without supplemental perches compared to pylons with supplemental perches,but there were differences between ***:Supplemental perches may be a useful and efficient tool for mitigating raptor ***,there are many influential factors affecting their success,and their effectiveness with different species groups is not *** studies show higher electrocution rates for certain species and devices and thus,their efficacy must be *** propose a two-step validation process,first in controlled conditions and then in the

关键词： Aquila adalberti Circaetus gallicus Diurnal raptors Electrocution Power lines Pylons

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Compounds of traditional Chinese medicine and neuropathic pain

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Chinese Journal of Natural Medicines 2020年第1期18卷 28-35页

作者： LI Shun-Hua LI Lin YANG Ru-Nan LIANG Shang-Dong Neuropharmacology Laboratory of Physiology Department Medical School of Nanchang UniversityNanchang 330006China Undergraduate Student of Class 155 of Nanchang University Queen Marry University of London Joint programme Nanchang 330006China Jiangxi Provincial Key Laboratory of Autonomic Nervous Function and Disease Nanchang 330006China

Neuropathic pain(NP)has become a serious global health issue and a huge clinical challenge without available effective treatment.P2 receptors family is involved in pain transmission and represents a promising target for pharmacological *** Chinese medicine(TCM)contains multiple components which are effective in targeting different pathological mechanisms involved in *** from traditional analgesics,which target a single pathway,TCMs take the advantage of multiple components and multiple targets,and can significantly improve the efficacy of treatment and contribute to the prediction of the risks of *** of TCM acting at nucleotide P2 receptors in neurons and glial cells could be considered as a potential research direction for moderating neuropathic *** review summarized the recently published data and highlighted several TCMs that relieved NP by acting at P2 receptors.

关键词： Traditional Chinese medicine Diabetic neuropathic pain HIV-gp120-associated neuropathic pain Chronic constriction injury Nucleotide receptors

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