scholarly journals A unifying concept of animal breeding programs

2020 ◽  
Author(s):  
H. Simianer ◽  
A. Ganesan ◽  
L. Buettgen ◽  
N.T. Ha ◽  
T. Pook

ABSTRACTModern animal breeding programs are constantly evolving with advances in breeding theory, biotechnology and genetics. Surprisingly, there seems to be no generally accepted succinct definition of what exactly a breeding program is, neither is there a unified language to describe breeding programs in a comprehensive, unambiguous and reproducible way. In this work, we try to fill this gap by suggesting a general definition of breeding programs that also pertains to cases where genetic progress is not achieved through selection, but e.g. through transgenic technologies, or the aim is not to generate genetic progress, but e.g. to maintain genetic diversity. The key idea of the underlying concept is to represent a breeding program in modular form as a directed graph that is composed of nodes and edges, where nodes represent cohorts of breeding units, usually individuals, and edges represent breeding activities, like ‘selection’ or ‘reproduction’. We claim, that by defining a comprehensive set of nodes and edges it is possible to represent any breeding program of arbitrary complexity by such a graph, which thus comprises a full description of the breeding program. This concept is implemented in a web-based tool (MoBPSweb, available at www.mobps.de) which is described in a companion paper, and has a link to the R-package MoBPS (Modular Breeding Program Simulator) to simulate the described breeding programs. The approach is illustrated by showcasing three different breeding programs of increasing complexity. Finally, potential limitations of the concept are indicated and extensions to other fields, like plant breeding, are discussed.

2020 ◽  
Vol 11 (2) ◽  
Author(s):  
R Chris Gaynor ◽  
Gregor Gorjanc ◽  
John M Hickey

Abstract This paper introduces AlphaSimR, an R package for stochastic simulations of plant and animal breeding programs. AlphaSimR is a highly flexible software package able to simulate a wide range of plant and animal breeding programs for diploid and autopolyploid species. AlphaSimR is ideal for testing the overall strategy and detailed design of breeding programs. AlphaSimR utilizes a scripting approach to building simulations that is particularly well suited for modeling highly complex breeding programs, such as commercial breeding programs. The primary benefit of this scripting approach is that it frees users from preset breeding program designs and allows them to model nearly any breeding program design. This paper lists the main features of AlphaSimR and provides a brief example simulation to show how to use the software.


Author(s):  
R. Chris Gaynor ◽  
Gregor Gorjanc ◽  
John M. Hickey

AbstractThis paper introduces AlphaSimR, an R package for stochastic simulations of plant and animal breeding programs. AlphaSimR is a highly flexible software package able to simulate a wide range of plant and animal breeding programs for diploid and autopolyploid species. AlphaSimR is ideal for testing the overall strategy and detailed design of breeding programs. AlphaSimR utilizes a scripting approach to building simulations that is particularly well suited for modeling highly complex breeding programs, such as commercial breeding programs. The primary benefit of this scripting approach is that it frees users from preset breeding program designs and allows them to model nearly any breeding program design. This paper lists the main features of AlphaSimR and provides a brief example simulation to show how to use the software.


1980 ◽  
Vol 60 (2) ◽  
pp. 253-264 ◽  
Author(s):  
A. J. McALLISTER

In the last decade the dairy cattle population has declined to a level of 1.9 million cows in 1978 with about 56% of these cows bred AI and nearly 20% of the population enrolled in a supervised milk recording program. The decline in cow numbers has been accompanied by an increase in herd size and production per cow. The current breeding program of the dairy industry is a composite of breeding decisions made by AI organizations, breeders who produce young bulls for sampling and all dairymen who choose the sires and dams of their replacement heifers. Estimates of genetic trend from 1958–1975 for milk production in the national milk recorded herd range from 21 to 55 kg per year for the four dairy breeds with Holsteins being 41 kg per year. Both differential use of superior proven sires and improved genetic merit of young bulls entering AI studs contribute to this genetic improvement. Various national production and marketing alternatives were examined. Selection is a major breeding tool in establishing a breeding program to meet national production requirements for milk and milk products once the selection goal is defined. AI and young sire sampling programs will continue to be the primary vehicle for genetic improvement through selection regardless of the selection goal. The current resources of milk-recorded cows bred AI is not being fully utilized to achieve maximum genetic progress possible from young sire sampling indicate that the number of young bulls sampled annually in the Holstein breed could be tripled with the existing milk-recorded and AI bred dairy cow population. Expanded milk recording and AI breeding levels could increase the potential for even further genetic improvement. The potential impact of selection for other traits, crossbreeding and the use of embryo transfer of future breeding programs is highlighted.


2018 ◽  
Author(s):  
Giovanny Covarrubias-Pazaran

AbstractIn the last decade the use of mixed models has become a pivotal part in the implementation of genome-assisted prediction in plant and animal breeding programs. Exploiting the use genetic correlation among traits through multivariate predictions has been proposed in recent years as a way to boost prediction accuracy and understand pleiotropy and other genetic and ecological phenomena better. Multiple mixed model solvers able to use relationship matrices or deal with marker-based incidence matrices have been released in the last years but multivariate versions are scarse. Such solvers have become quite popular in plant and animal breeding thanks to user-friendly platforms such as R. Among such software one of the most recent and popular is the sommer package. In this short communication we discuss the update of the package that is able to run multivariate mixed models with multiple random effects and different covariance structures at the level of random effects and trait-to-trait covariance along with other functionalities for genetic analysis and field trial analysis to enhance the genome-assisted prediction capabilities of researchers.


Sugar Tech ◽  
2021 ◽  
Author(s):  
Thomas Dumont ◽  
Laurent Barau ◽  
Audrey Thong-Chane ◽  
Jordan Dijoux ◽  
Mathilde Mellin ◽  
...  

AbstractAll over the world, sugarcane breeding programs are developing new, high-yielding cultivars that are resistant to major diseases to improve the profitability and sustainability of the sugar-energy industries they serve. In Reunion Island, sugarcane genetic improvement efforts began in 1929. Many challenges had to be overcome. Continuous breeding efforts have been made to develop varietal resistances to control some major diseases and are still going on today. Given the extreme agroclimatic diversity that characterizes the different production areas of the industry, it was necessary to gradually develop a large network of seven decentralized breeding programs to support genetic progress throughout the whole industry. This article provides an overview of the sugarcane breeding program of Reunion. It describes historical achievements and gives detailed information about germplasm development, variety exchanges, breeding program and selection scheme and procedures. A review is also made on applied genetics research activities supporting variety improvement. Further progress depends on the optimized functioning of the current breeding program, which has never been so largely extended in terms of target environments. The article discusses prospects of genomics breeding applications in the complex genetic context of sugarcane, which will require large multidisciplinary collaborations.


Author(s):  
Torsten Pook ◽  
Lisa Büttgen ◽  
Amudha Ganesan ◽  
Ngoc-Thuy Ha ◽  
Henner Simianer

Abstract In this work, we introduce a new web-based simulation framework (”MoBPSweb”) that combines a unified language to describe breeding programs with the simulation software MoBPS, standing for ’Modular Breeding Program Simulator’. Thereby, MoBPSweb provides a flexible environment to log, simulate, evaluate, and compare breeding programs. Inputs can be provided via modules ranging from a Vis.js-based environment for” drawing” the breeding program to a variety of modules to provide phenotype information, economic parameters, and other relevant information. Similarly, results of the simulation study can be extracted and compared to other scenarios via output modules (e.g. observed phenotypes, the accuracy of breeding value estimation, inbreeding rates), while all simulations and downstream analysis are executed in the highly efficient R-package MoBPS.


2009 ◽  
Vol 66 (3) ◽  
pp. 309-316 ◽  
Author(s):  
Cláudia Erna Lange ◽  
Luiz Carlos Federizzi

The success of a genetic breeding program in a certain period can be assessed by the genetic gain observed. Genetic progress can be estimated from the multi environmental trials (MET) data which are routinely carried out by annual species breeding programs for the assessment of new commercial cultivars. A data set of 20 years of MET of advanced soybean lines derived from four breeding programs was used to estimate and to compare the genetic gains obtained for three soybean maturity groups (early, medium and late) in four cropping regions of the State of Rio Grande do Sul. The estimated yield gains ranged from 0.0 to 71.5 kg ha-1 year-1 (3.49% per year), depending on the maturity group and region, which suggests that the genetic breeding effort does not have a similar effect among the maturity groups or benefit the regions equally. There was no evidence of genetic progress for the early maturity group in any of the four regions, whereas gains in Regions I and IV were comparatively greater than those in Regions II and III. The objectives of the soybean breeding program in the region should be redirected. Since not all the experimental lines used to estimate genetic gains were commercially released, the reported genetics gains were achieved by the breeding programs rather than those achieved by the cropping systems.


2010 ◽  
Vol 7 (1) ◽  
Author(s):  
Julius D. Nugroho

<!--[if gte mso 9]><xml> <w:WordDocument> <w:View>Normal</w:View> <w:Zoom>0</w:Zoom> <w:PunctuationKerning /> <w:ValidateAgainstSchemas /> <w:SaveIfXMLInvalid>false</w:SaveIfXMLInvalid> <w:IgnoreMixedContent>false</w:IgnoreMixedContent> <w:AlwaysShowPlaceholderText>false</w:AlwaysShowPlaceholderText> <w:Compatibility> <w:BreakWrappedTables /> <w:SnapToGridInCell /> <w:WrapTextWithPunct /> <w:UseAsianBreakRules /> <w:DontGrowAutofit /> <w:UseFELayout /> </w:Compatibility> <w:BrowserLevel>MicrosoftInternetExplorer4</w:BrowserLevel> </w:WordDocument> </xml><![endif]--><!--[if gte mso 9]><xml> <w:LatentStyles DefLockedState="false" LatentStyleCount="156"> </w:LatentStyles> </xml><![endif]--> <!--[if gte mso 10]> <mce:style><! /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} --> <!--[endif]--> <p class="Style2" style="text-indent: 0cm;">Matoa (<em>Pometia pinnata</em>) is a local fruit of<span>&nbsp; </span>Papua (formerly called Irian Jaya) which has high potensial to develop as comercial fruit. Highly significant genetic resources of matoa potentially for breeding program in Papua are being threatened as a result of cutting down trees for fruit harvesting and of forest exploitation for timber. Besides the loss of genetic resources facing now, other major problems should be consider for conservation and domestication of this fruit tree species i.e. lack of silviculture and agronomy knowledge for further breeding programs; matoa production only for local market; and inadequate government policy for matoa breeding program. Strategy developed for matoa conservation and domestication should also concern about time limited due to the fast loss of genetic poll. This paper provides a general overview of strategy for conservation and domestication of <em>Pometia pinnata</em> with special reference to Papua.</p>


2016 ◽  
Vol 14 (1) ◽  
pp. 1122-1124 ◽  
Author(s):  
Ricardo Almeida ◽  
Małgorzata Guzowska ◽  
Tatiana Odzijewicz

AbstractIn this short note we present a new general definition of local fractional derivative, that depends on an unknown kernel. For some appropriate choices of the kernel we obtain some known cases. We establish a relation between this new concept and ordinary differentiation. Using such formula, most of the fundamental properties of the fractional derivative can be derived directly.


2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1633.2-1634
Author(s):  
F. Cosan ◽  
O. M. Gedar

Background:Reactive arthritis (ReA) is defined by 1999 ACR criteria as arthritis preceding a bacterial genitourinary (GUS) or gastrointestinal (GIS) infection in 3 days-6 weeks and evidence of triggering infection. Recently, ReA is classified as SpA and patients who do not fulfill SpA criteria are classified as undifferentiated spondyloarthritis (USpA) according to ASAS/EULAR SpA classification criteria.Objectives:In several case reports which are associated with other infective agents are reported and the definition is extended for some clinicians so that SpA which is occurred after any infection is called as ReA. On the other hand, some researchers still accept the classical definition of ReA. The problem with the heterogeneity of opinions and unstandardized definition of ReA hinders studies about pathogenesis and standardization of treatments. In this study, we aimed to determine the spectrum of the use of the definition of reactive arthritis in publications in PubMed between 2009-2019.Methods:The ReA keyword is searched in PubMed for the years between 2009-2019. 248 different publications have been identified and included in this research. 89 articles, 47 reviews, 108 case reports, 2 guidelines, and 2 editorials reviewed for the definition of ReA.Results:Only 42.7% (106 patients) of these publications meet the classical definition which suggests ReA after only GIS and GUS infections. In 4 (1.6%) of the publications ReA was defined after GIS, GUS and oropharyngeal infections; in 3 (1,2%) of the publications after any bacterial infection; in 9 (3.6%) of the publications after any infection. In 8 (3.2%) of the publications, ReA and USPA was used correspondingly. In 39 (15,7%) of the publications the term agent related, ReA was used without making a general definition for ReA. 79 publications (31,9%) have not defined ReA.According to causative agent and ReA relationship, in 64 (24,6%) general infective agents, in 75 (30,2%) classical agents, in 22 (8,9%) other bacterial agents, in 23 (9,3%) streptococcus, in 10(4%) intravesical BCG, in 6 (2.4%) HIV, in 6 (2.4%) tuberculosis, in 12 (4,8%) clostrudium difficle, in 2 (0.8%) parasites were reported. In 31 (12,5%) of the publications the causative agent for the ReA was unknown, the diagnosis was made clinically.Conclusion:In this study, it is aimed to draw attention terminology intricacy and the need for the standardization of the definition of ReA and USpA. It is clear that to standardize the definition of Rea and USpA is necessary. Between 2009-2019 there are reported cases diagnosed as ReA associated with bacterial infections (especially with Clostridium difficile, streptococcus and tuberculosis infections), and viral infections (by a majority with HIV), and parasitic infections. It is not clear if we need to define them classically or define them as USPA. Another important consideration is the necessity of extended laboratory investigations to find out the real causative agent even if the patient is clinically diagnosed with ReA. The requirement of the differentiation between ReA and USpA must be revealed for therapeutic researches.References:[1]A proposal for the classification of patients for clinical and experimental studies on reactive arthritis. Pacheco-Tena C, Burgos-Vargas R, Vázquez-Mellado J, Cazarín J, Pérez-Díaz JA. J Rheumatol. 1999 Jun;26(6):1338-46.[2]The Assessment of SpondyloArthritis International Society classification criteria for peripheral spondyloarthritis and for spondyloarthritis in general. Rudwaleit M, van der Heijde D, Landewé R, Akkoc N, Brandt J, Chou CT, Dougados M, Huang F, Gu J, Kirazli Y, et al. Ann Rheum Dis. 2011;70:25–31.Disclosure of Interests:None declared


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