Comparison of selective genotyping strategies for prediction of breeding values in a population undergoing selection

Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0), and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection candidates). Lower correlations between genomic-based estimates of breeding values (GEBV) and true breeding values (TBV) were obtained when using the Bottom strategy. For Random, Extreme, and Less Related strategies, the correlation between GEBV and TBV became slightly larger as selection intensity decreased and was largest when no selection occurred. These 3 strategies were better than the Top approach. In addition, the Extreme, Random, and Less Related strategies had smaller predictive mean squared errors (PMSE) followed by the Top and Bottom methods. Overall, the Extreme genotyping strategy led to the best predictive ability of breeding values, indicating that animals with extreme yield deviations values in a reference population are the most informative when training genomic selection models.

Comparison of logistic and neural network models to fit to the egg production curve of White Leghorn hens

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Growth curve in Santa Ines sheep

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Relações lineares múltiplas entre deslocamentos químicos em RMN 13C de haletos alifáticos

Os deslocamentos químicos de RMN 13C de carbonos a , b , g e d de 17 conjuntos de haletos (F, Cl Br e I) alifáticos, inclusive compostos mono, bi e tricíclicos, podem ser reproduzidos por uma equação linear de duas constantes e duas variáveis do tipo : d R-X = A*d R-X1 + B*d R-X2 onde A e B são constantes obtidas por regressão multilinear a partir de deslocamentos químicos de 13C; d R-X, o deslocamento químico de 13C do composto com halogênio (R-X); d R-X1 e d R-X2 deslocamentos químicos de outros haletos. Para brometos (R-X) alifáticos a melhor correlação foi obtida com os dados de fluoretos (R-X1) e iodetos (R-X2) com R2 de 0,9989 e desvio médio absoluto (DM) de 0,39ppm. Para cloretos (R-X) a melhor correlação foi com dados de brometos (R-X1) e iodetos (R-X2) com R2 de 0,9960 e DM de 0,76ppm. Para fluoretos (R-X) a melhor correlação foi com brometos (R-X1) e iodetos (R-X2) com R2 de 0,9977 e DM de 1,10ppm e para iodetos (R-X) foi com fluoretos (R-X1) e brometos (R-X2) com R2 de 0,9972 e desvio médio absoluto de 0,60 ppm.

Non-linear growth models for bullfrog tadpoles

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Comparação entre os estimadores de mínimos quadrados ordinários e mínimos desvios absolutos em modelos de regressão linear simples -: uma aplicação na energia na agricultura

Pós-graduação em Agronomia (Energia na Agricultura) - FCA

Associação e seleção genômica para características relacionadas à eficiência reprodutiva de fêmeas da raça Nelore

Pós-graduação em Zootecnia - FCAV

Ratios of dijet production cross sections as a function of the absolute difference in rapidity between jets in proton-proton collisions at root s=7 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Efeitos ambientais e genéticos sobre peso, perímetro escrotal e escores de avaliação visual à desmama em bovinos da raça Canchim

Os efeitos de ano e época de nascimento, propriedade, sexo do bezerro, regime alimentar, idade do bezerro e idade da vaca ao parto, os efeitos aditivos direto e materno da raça Charolesa e o efeito de heterose materna entre as raças Charolesa e zebu foram avaliados pelo método dos quadrados míninos sobre características de importância econômica, como peso, perímetro escrotal e escores visuais de conformação frigorífica, de umbigo e de pelame à desmama em bovinos da raça Canchim. Utilizaram-se dados de 12.334 animais Canchim nascidos de 1999 a 2005. O ano e a época de nascimento, a propriedade, o regime alimentar e a idade da vaca ao parto (linear e quadrático) tiveram efeitos significativos sobre todas as características estudadas. Houve efeitos do sexo sobre o peso do bezerro à desmama e o escore de umbigo; da idade do bezerro sobre peso, perímetro escrotal e escores de conformação frigorífica e de pelame; e das proporções de Charolês no bezerro e na mãe sobre o peso, a conformação frigorífica e a qualidade de pelagem; e da heterozigose materna sobre peso, perímetro escrotal e escores de conformação frigorífica e de umbigo. Os efeitos aditivos diretos da raça Charolesa como desvio do zebu foram negativos sobre peso, conformação frigorífica e qualidade da pelagem à demama, enquanto os efeitos aditivos maternos foram positivos. Os efeitos heteróticos maternos foram positivos sobre peso, perímetro escrotal e escores de conformação frigorífica e de umbigo. em geral, essas fontes de variação devem ser consideradas nas estimativas de parâmetros genéticos e nas avaliações genéticas dos animais Canchim para as características estudadas.

Soil compaction by machine traffic and least limiting water range related to soybean yield

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Soil resistance to penetration and least limiting water range for soybean yield in a haplustox from Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Seleção para peso pós-desmama em um rebanho Gir. 1. Resposta direta e correlacionada em 21 anos de seleção

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Phosphorus bioavailability in diets for growing horses

A study of phosphorus (P) metabolism was carried out using 12 month old Brasileiro de Hipismo breed of horses to determine the P bioavailability available from feeds commonly fed to horses in Brazil. Five different diets were formulated to contain approximately equivalent levels of crude protein and digestible energy, as well as to supply at least 22 g P/horse/day (NRC, 1989). All 5 diets contained 40% Bermuda coastal hay plus 60% concentrate. The 5 different concentrates contained: C1 (corn+ cottonseed meal) C2 (corn grain+soybean meal) C3 (corn+sugarcane yeast), C4 (oat+cottonseed meal), and C5 (oat+soybean meal). The radioisotope (32)p was injected with 30 NIB. Blood, feces and urine were collected for 7 days to evaluate endogenous fecal P and true absorption. Analysis of variance of P intake showed differences due to dietary effects (P < 0.05). Concentrate C3 had the lowest intake (79.68 mg/ kg BW). All of the diets produced positive P retention. Absolute values for P concentrations in plasma, urine, feces and endogenous feces did not vary between diets. Values for endogenous fecal P were independent of the level of P intake, so the correlation between P intake and P endogenous was not significant. P bioavailability values were 50.75; 40.98; 43.50; 51.03 and 57.68% for diets C1 through C5, respectively. However, differences in P bioavailability were found (P < 0.05) between diets. Diets C2 and C3 had lower P bioavailability than the other diets. The P bioavailability of all dietary treatments in this study exceeded NRC (1989) postulations of 35% true P absorption in diets not supplemented with inorganic P. The results of this study indicate that inorganic P supplementation is not needed for growing yearlings fed common Brazilian feeds. Considering the high cost of P supplementation and the risk of environmental P contamination, inorganic phosphorus supplementation for growing yearlings may not be required. (c) 2007 Elsevier B.V. All rights reserved.

Least limiting water range in soil under crop rotations and chiseling

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)