The formation of simple linear models for predicting the breeding values of animals

2020 ◽  
Author(s):  
А.Е. КАЛАШНИКОВ ◽  
J. PŘIBYL ◽  
А.А. КОЧЕТКОВ ◽  
Т.М. АХМЕТОВ ◽  
Р.Р. ШАЙДУЛЛИН ◽  
...  
Keyword(s):  
Information System ◽  
Basic Principle ◽  
Linear Models ◽  
Residual Error ◽  
International Standards ◽  
Rating System ◽  
Breeding Value ◽  
Matrix Equations ◽  
Mathematical Apparatus ◽  
Breeding Values

Представлен основной принцип оценки племенной ценности при помощи линейных моделей (матричных уравнений) согласно общепринятым мировым стандартам (BLUP). Дан алгоритм и описан математический аппарат для реализации системы оценки и выбора лучших племенных животных для дальнейшей селекции. Представлены основные принципы построения работоспособной системы оценки племенной ценности в современном формате в соответствии с требованиями ISAG/ICAR (Interbull). Описана необходимость формирования единой информационной системы баз данных (ИС БД) для хранения информации о первичном учете, идентификации и данных о продуктивности животных. Представлено описание принципа проверки достоверности линейных моделей по величине остаточной ошибки и соответствия модели наследования по Менделю. The basic principle of estimating breeding value using linear models (matrix equations) according to generally accepted international standards (BLUP) is performed. An algorithm is showed and a mathematical apparatus is described for implementing a system for estimating and selecting the best breeding animals for further reproduction. The main principles of building a workable breeding values rating system in a modern format in concordance with the claims of ISAG / ICAR (Interbull) are given down. The necessity of forming a unified database information system (IS DB) for keeping information about primary registration, identification and data on animal productivity is declared. The description of the principle of checking up the reliability of linear models by the value of the residual error and the conformity of the Mendel model of inheritance is presented.

Potential biases of incomplete linear models in heritability estimation and breeding value prediction

1999 ◽  
Vol 29 (6) ◽  
pp. 724-736 ◽  
Author(s):  
P X Lu ◽  
D A Huber ◽  
T L White
Keyword(s):  
Genetic Variance ◽  
Linear Models ◽  
Additive Genetic Variance ◽  
Genetic Effect ◽  
Breeding Value ◽  
Additive Genetic Effect ◽  
Unbalanced Data ◽  
Breeding Values ◽  
Incomplete Model ◽  
Heritability Estimation

Potential biases associated with incomplete linear models in the estimation of heritability and the prediction of breeding values have been investigated. Results indicate that estimates of additive genetic variance and heritability as well as predicted parental breeding values from incomplete models will inevitably be biased as long as the true variance components of ignored effects are not zero. While models ignoring the interaction effect of males and females (SCA) × environment (E) interaction downwardly biased the estimates of additive genetic variance and heritability, models ignoring SCA and (or) the additive genetic effect (GCA) × E interaction yielded upward biases. The magnitudes of biases are functions of population genetic architecture, mating design, and field experimental design and can be precisely assessed with formulae derived for balanced data. Numerical simulations using unbalanced data of different mating and field experimental designs suggest that the formulae from balanced data can be used to approximate the minimum biases associated with unbalanced data. Because of the magnitudes of biases for some typical forest genetic scenarios, it is suggested that models ignoring SCA and (or) GCA × E should be avoided when the numbers of test sites and crosses per parent are small. However, incomplete model ignoring SCA × E interaction may be used to reduce computational demand with only negligible consequences.

MODELS FOR PREDICTING THE BREEDING VALUE OF ANIMALS IN GENOMIC EVALUATION

2020 ◽  
Author(s):  
А.Е. КАЛАШНИКОВ ◽  
J. PŘIBYL ◽  
А.А. КОЧЕТКОВ ◽  
Т.М. АХМЕТОВ ◽  
Р.Р. ШАЙДУЛЛИН ◽  
...  
Keyword(s):  
Linear Models ◽  
Animal Husbandry ◽  
International Standards ◽  
Genetic Identification ◽  
Breeding Value ◽  
Software Environment ◽  
Genetic Traits ◽  
Marker Selection ◽  
Qualified Personnel ◽  
Genetic Value

Представлен основной принцип оценки племенной ценности при помощи линейных моделей согласно общепринятым мировым стандартам, применяемым в геномной оценке GEBV. Алгоритм и математический аппарат GEBV основан на методе BLUP и имеет своей целью расчет величин племенной (генетической) ценности с учетом передачи генетических признаков по наследству. Рассмотрены принципы и формирование математической и программной среды GEBV для применения данных генотипирования по SNP (генетические чипы) и маркерной селекции, а также данных генетической идентификации животных. GEBV представляет собой прогноз племенной ценности молодых животных, для которых нет в наличии данных о собственной продуктивности или продуктивности потомства. Оценка племенной ценности их родителей и предков по другим родственным потомкам и сверстникам позволяет при применении в оценке данных генотипирования по нейтральным маркерам и маркерам продуктивности (SNP) производить прогноз племенной ценности сразу после рождения животных. GEBV дает возможность уточнять оценку племенной ценности молодых животных по BLUP, сократить время анализа, увеличить достоверность существующей оценки по BLUP, снизить расходы на содержание, увеличить точность определения родства, наследуемости признаков, ускорить отбор животных, сократить генерационный интервал. Применение метода BLUP в геномной оценке требует подготовки новых квалифицированных кадров в университетах и научных учреждениях ввиду их острого дефицита в практическом животноводстве и масштабной селекции. The basic principle of evaluating breeding values using linear models in accordance with generally accepted international standards used in genomic assessment is presented. The algorithm and mathematical apparatus for it is based on the BLUP method in order to calculate the values of the breeding (genetic) value, taking into account the transmission of genetic traits by inheritance. The principles and formation of a mathematical and software environment for genomic assessment for the use of genotypic data according to SNPs (genetic chips) and marker selection, as well as data of animal genetic identification are considered. GEBV is a prediction of the breeding value of young animals for which there is no available data on their own productivity or the productivity of their progeny. The evaluation of the breeding value of their parents and progenitors by other related descendants and peers allows for the use of genotyping data for neutral markers and productivity markers (SNP) to make a prediction of the breeding value immediately after the birth of animals. GEBV makes it possible to improve the evaluation of the breeding value of young animals by SNP, with decrease the analysis time, increase the reliability of the GEBV analysis with existing software, reduce cost of maintenance, increase the accuracy of determining relationships, heritabilities of traits, accelerate the selection of animals, bring the generation interval. The use of the GEBV method of simple and genomic assessment requires the training of new qualified personnel in universities and scientific institutions due to their acute shortage in practical animal husbandry and selection.

scholarly journals A note on genetic parameters and accuracy of estimated breeding values in honey bees

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Evert W. Brascamp ◽  
Piter Bijma
Keyword(s):  
Honey Bees ◽  
Variance Components ◽  
Genetic Parameters ◽  
Additive Genetic Variance ◽  
Breeding Value ◽  
Phenotypic Variance ◽  
Breeding Values ◽  
Estimated Breeding Values ◽  
Additive Genetic Relationship ◽  
The Relationship

Abstract Background In honey bees, observations are usually made on colonies. The phenotype of a colony is affected by the average breeding value for the worker effect of the thousands of workers in the colony (the worker group) and by the breeding value for the queen effect of the queen of the colony. Because the worker group consists of multiple individuals, interpretation of the variance components and heritabilities of phenotypes observed on the colony and of the accuracy of selection is not straightforward. The additive genetic variance among worker groups depends on the additive genetic relationship between the drone-producing queens (DPQ) that produce the drones that mate with the queen. Results Here, we clarify how the relatedness between DPQ affects phenotypic variance, heritability and accuracy of the estimated breeding values of replacement queens. Second, we use simulation to investigate the effect of assumptions about the relatedness between DPQ in the base population on estimates of genetic parameters. Relatedness between DPQ in the base generation may differ considerably between populations because of their history. Conclusions Our results show that estimates of (co)variance components and derived genetic parameters were seriously biased (25% too high or too low) when assumptions on the relationship between DPQ in the statistical analysis did not agree with reality.

scholarly journals Development of the stock exchange information system

2006 ◽  
Vol 16 (2) ◽  
pp. 265-284
Author(s):  
Radojko Miladinovic
Keyword(s):  
Information System ◽  
Project Management ◽  
Capital Market ◽  
Stock Exchange ◽  
International Standards ◽  
Software Project ◽  
Software Project Management ◽  
Exchange Information ◽  
Countries In Transition ◽  
Continuous Trading

The stock exchange represents the key institution for the development of capital market of any country. Thus the information system of every stock exchange must satisfy very strict international standards. The development of these systems is particularly difficult in countries in transition, due to intense economic and legal changes, lack of technical and financial resources, lack of experience and knowledge in the area of the capital market business, etc. Therefore the special software project management methodology for their realization must be clearly defined. In the development process of the Belgrade Stock Exchange (BSE) information system a new software project management methodology for its realization has been defined, the application of which is illustrated through a series of different development stages of the Belgrade Stock Exchange information system. In order to make all the problems more comprehensive, only the continuous trading method is described, being the most frequently used trading method in the world.

scholarly journals SELECTING SAFETY PACKAGE COMPONENTS OF ENTERPRISE INFORMATION SYSTEM FOLLOWING REQUIREMENTS OF STANDARD LEGAL DOCUMENTS

2018 ◽  
Vol 18 (3) ◽  
pp. 333-338
Author(s):  
E. A. Vitenburg ◽  
A. A. Levtsova
Keyword(s):  
Information System ◽  
Information Security ◽  
International Standards ◽  
Protection System ◽  
Enterprise Information System ◽  
Enterprise Information ◽  
Research Results ◽  
Legal Documents ◽  
The Russian Federation ◽  
Selection Of

Introduction. Production processes quality depends largely on the management infrastructure, in particular, on the information system (IS) effectiveness. Company management pays increasingly greater attention to the safety protection of this sphere. Financial, material and other resources are regularly channeled to its support. In the presented paper, some issues on the development of a safety enterprise information system are considered.Materials and Methods. Protection of the enterprise IS considers some specific aspects of the object, and immediate threats to IT security. Within the framework of this study, it is accepted that IS are a complex of data resources. A special analysis is resulted in determining categories of threats to the enterprise information security: hacking; leakage; distortion; loss; blocking; abuse. The connection of these threats, IS components and elements of the protection system is identified.  The requirements of normative legal acts of the Russian Federation and international standards regulating this sphere are considered. It is shown how the analysis results enable to validate the selection of the elements of the IS protection system.Research Results. A comparative analysis of the regulatory literature pertinent to this issue highlights the following. Different documents offer a different set of elements (subsystems) of the enterprise IS protection system. To develop an IS protection program, you should be guided by the FSTEC Order No. 239 and 800-82 Revision 2 Guide to ICS Security.Discussion and Conclusions. The presented research results are the basis for the formation of the software package of intellectual support for decision-making under designing an enterprise information security system. In particular, it is possible to develop flexible systems that allow expanding the composition  of the components (subsystems).

scholarly journals Genomic selection for white spot syndrome virus resistance in whiteleg shrimp boosts survival under an experimental challenge test

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marie Lillehammer ◽  
Rama Bangera ◽  
Marcela Salazar ◽  
Sergio Vela ◽  
Edna C. Erazo ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Genetic Improvement ◽  
White Spot Syndrome Virus ◽  
Random Mating ◽  
Challenge Test ◽  
White Spot ◽  
Breeding Value ◽  
Genomic Breeding ◽  
Breeding Values ◽  
White Spot Syndrome

AbstractWhite spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The development of resistant shrimp populations is an attractive option for management of the disease. However, heritability for WSSV resistance is generally low and genetic improvement by conventional selection has been slow. This study was designed to determine the power and accuracy of genomic selection to improve WSSV resistance in Litopenaeus vannamei. Shrimp were experimentally challenged with WSSV and resistance was evaluated as dead or alive (DOA) 23 days after infestation. All shrimp in the challenge test were genotyped for 18,643 single nucleotide polymorphisms. Breeding candidates (G0) were ranked on genomic breeding values for WSSV resistance. Two G1 populations were produced, one from G0 breeders with high and the other with low estimated breeding values. A third population was produced from “random” mating of parent stock. The average survival was 25% in the low, 38% in the random and 51% in the high-genomic breeding value groups. Genomic heritability for DOA (0.41 in G1) was high for this type of trait. The realised genetic gain and high heritability clearly demonstrates large potential for further genetic improvement of WSSV resistance in the evaluated L. vannamei population using genomic selection.

Selection of parents and estimation of genetic parameters using BLUP and molecular methods for lentil (Lens culinaris Medik.) breeding program in Argentina

2019 ◽  
Vol 56 (1) ◽  
pp. 12-25
Author(s):  
Carolina Bermejo ◽  
Federico Cazzola ◽  
Fernando Maglia ◽  
Enrique Cointry
Keyword(s):  
Quantitative Traits ◽  
Genetic Parameters ◽  
Selection Process ◽  
Recombinant Inbred Lines ◽  
Correlation Coefficients ◽  
Cost Effective ◽  
Molecular Data ◽  
Breeding Value ◽  
Breeding Values ◽  
High Yields

AbstractThe most important objective of lentil breeding programs is to develop new genotypes that are genetically more productive. Besides, it is necessary that the varieties obtained have short flowering cycles to allow the later sowing of summer crops. Selection is based through phenotypic means; however, we argue it should be based on genetic or breeding values because quantitative traits are often influenced by environments and genotype–environment interactions. The objectives of this study were to: (i) identify genotypes with the highest merit; (ii) estimate genetic parameters to know the genetic control of morphological traits in macrosperma and microsperma lentil types using best linear unbiased prediction (BLUP). Twenty-five recombinant inbred lines (RILs) from six F4 families selected on the basis of precocity and high yields were tested in four environments for important quantitative traits. The analysis of variance showed significant differences between genotypes, environments, and genotype–environment interactions for all the traits. Seven macrosperma- and two microsperma-type RILs were selected. Based on average ranking from breeding values and molecular data obtained with sequence-related amplified polymorphism (SRAP), the same genotypes were selected. Genotypic coefficients of variation, heritability across and by environment, and genetic correlation coefficients using BLUP were obtained. According to our results BLUP could replace molecular analysis methods because the selection process was simpler, more cost-effective, and more accurate. The breeding value of parents would give a better ranking of their genetic value than would their phenotypic value; therefore, the selection efficiency would be enhanced and the genetic gain would be more predictable. The selected genotypes could become potential commercial varieties or be used as parental lines in future hybridization programs.

Genetic line × concentrate level interactions for milk production and feed efficiency in dairy cattle

1992 ◽  
Vol 72 (2) ◽  
pp. 227-236 ◽  
Author(s):  
S. Wang ◽  
G. L. Roy ◽  
A. J. Lee ◽  
A. J. McAllister ◽  
T. R. Batra ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Milk Production ◽  
Milk Yield ◽  
Feed Efficiency ◽  
Production Efficiency ◽  
Breeding Value ◽  
Environment Interaction ◽  
Genetic Line ◽  
Breeding Values ◽  
Concentrate Level

Early first lactation data from 2230 cows of five research herds of Agriculture Canada were used to study the interactions of genetic line by concentrate level, and sire by concentrate level and to estimate breeding values of sires. The genetic lines were defined as Holstein (H), Ayrshire (A), and H × A or A × H (C). The interactions of sire by concentrate level were studied separately using progeny of five different mating groups: G1, H sires mated to H cows; G2, H sires mated to H, A and C cows; G3, A sires mated to A cows; G4, A sires mated to H, A and C cows; and G5, C sires mated to C cows. The interactions of genetic line by concentrate were significant (P < 0.05) for 56- to 112-d milk yield (MY112), corrected 56-to 112-d milk yield (CMY112) and feed efficiency (EFMY112 = MY112/TDN consumption). H and C cows produced more milk and were more efficient than A cows when fed high levels of concentrate. The H cattle possess a greater capacity to convert the concentrate into milk, while A cattle reach maximum milk production earlier than H cattle. The interactions of sire by concentrate were statistically significant for MY112, EFMY112 and CMY112 in G1 (P < 0.01), and G2 (P < 0.01). The breeding values of sires for MY112 were estimated using BLUP for all of the H line (BLUP-T), for half of the population consuming low amounts of concentrate (BLUP-L) and for the other half consuming high amounts (BLUP-H). A significant reranking of sires was found among the three groups. Key words: Genotype × environment interaction, milk production, efficiency, breeding value, dairy cattle

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