Hedi HAMMAMI (2009). Genotype by Environment Interaction for Production Traits of Holsteins Using Two Countries as Model: Luxembourg and Tunisia (Doctoral thesis). Gembloux, Belgium, Gembloux Agricultural University, 170 p., 30 tabl., 16 fig. Summary. Under globalization, breeding organizations are selecting animals and exchanging germplasm across various environments. Ignoring genotype by environment interaction (G x E) may affect the efficiency of breeding strategies and limit outcomes from cooperation between breeding programs. Quantifying the effectiveness of indirect selection and effects of G x E for different breeds is therefore necessary. The objective of this thesis was to evaluate the magnitude of G x E for milk yield using Luxembourg and Tunisian Holstein populations. In fact, these two countries rely considerably on importation of superior genes from diverse origins for their breeding programs. This study needed records on both the genotype and the environment. In the first part of this thesis, genetic ties between the two populations were studied. Additive relationships and genetic similarity were important and genetic links have been strengthened with time which allowed the analysis of the phenotypic expression of daughters of common sires under each of these tow production environments. In the second part, genetic parameters for production traits of Tunisian Holsteins were estimated by a test-day random regression model (RRTD). Heritability estimates for 305-d milk, fat and protein yields were low to moderate (0.12 to 0.18) suspecting difficulties of high-producing cows to express their potential under limiting production conditions. In the third part, G x E for milk yield and persistency were investigated using character state models, where milk yield in each country was considered as a separate trait, and where the country border delimitation was designed as an environmental character state. A RRTD sire model was applied and was extended to a RRTD animal model. Significant G x E was detected for milk yield and persistency by both models. Large differences in genetic and permanent environmental variances between the two countries were observed. Genetic correlations for 305-d milk yield and persistency between Luxembourg and Tunisian Holsteins were 0.50 and 0.43 (sire model) and 0.60 and 0.36 (animal model). Moreover, low rank correlations obtained between estimated breeding values of common sires translate a significant re-ranking between the two environments. At the end of this thesis, a herd management (HM) parameter reflecting feeding and management intensity was defined. Three HM levels were identified in each country and G x E was investigated within- and across-environments. Significant G x E was detected between the Tunisian HM levels, whereas, only heterogeneous genetic variance for milk yield with limited re-ranking of sires across the three Luxembourg environments was observed. Overall, this thesis shows that under constraining environmental effects, selection for adaptive traits among economically valuable traits under their specific conditions is needed for low-input systems. When satisfactory feeding resources, management and husbandry practices are available, high degree environmental sensitivity is desired and the use of a high yielding breed may be encouraged.

Incluir como ag?ncias financiadoras: Funda??o de Amparo ? Pesquisa do Estado de Minas Gerais (FAPEMIG), Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (CAPES), Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq). / Submitted by Jos? Henrique Henrique (jose.neves@ufvjm.edu.br) on 2018-01-05T18:15:19Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) thaiza_silva_campideli.pdf: 3972827 bytes, checksum: d46dcbd4e39c922c90034d3992c8ad54 (MD5) / Approved for entry into archive by Rodrigo Martins Cruz (rodrigo.cruz@ufvjm.edu.br) on 2018-01-19T16:55:01Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) thaiza_silva_campideli.pdf: 3972827 bytes, checksum: d46dcbd4e39c922c90034d3992c8ad54 (MD5) / Made available in DSpace on 2018-01-19T16:55:01Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) thaiza_silva_campideli.pdf: 3972827 bytes, checksum: d46dcbd4e39c922c90034d3992c8ad54 (MD5) Previous issue date: 2017 / Esta pesquisa foi realizada com o objetivo de avaliar a sensibilidade dos valores gen?ticos aos n?veis diet?ticos de lisina digest?vel para caracter?sticas de desempenho e medidas morfom?tricas de til?pias do Nilo da linhagem tailandesa. Vinte e nove fam?lias de irm?os completos foram produzidas pelo acasalamento de 21 machos e 29 f?meas. A distribui??o entre os tanques foi feita aleatoriamente, por fam?lia, ap?s marca??o dos peixes, entre 94 a 109 dias de idade, at? formar um lote inicial de vinte alevinos por tanque, totalizando 700 peixes. ? idade aproximada de 150 dias os peixes foram aleatoriamente redistribu?dos no sistema, at? formar lotes com aproximadamente 138 peixes por n?vel de lisina digest?vel na dieta. Os peixes foram alimentados quatro vezes ao dia com dietas contendo diferentes n?veis de lisina digest?vel: 1,43; 1,53; 1,63; 1,73; e 1,83% nas idades entre 94 a 150 dias; e 1,28; 1,38; 1,48; 1,58 e 1,68% a partir da idade de 150 at? 255 dias. As informa??es individuais das til?pias (peso, comprimento total, comprimento padr?o, comprimento de cabe?a, altura e largura) foram padronizadas para 150, 185, 220 e 255 dias de idade. A partir de ent?o foram calculados o ganho de peso total, o ganho de peso di?rio, rela??o entre cabe?a e comprimento padr?o, rela??o entre largura e altura e a rela??o entre comprimento padr?o e comprimento total. Para as an?lises foi utilizado modelo de regress?o aleat?ria, sob modelo animal uni-caracter?stica. Foram testados modelos de ordens 2 e 3 do polin?mio de Legendre para o efeito fixo e ordem 2 para os efeitos gen?tico aditivo e de fam?lia e testados modelos com vari?ncia residual homog?nea (1classe) a heterog?nea (2, 3, e 4 classes). Os modelos que proporcionaram melhor ajuste na maioria das caracter?sticas foram os que consideraram vari?ncia residual homog?nea. De forma geral, os valores da correla??o de posto foram altas. As normas de rea??o de 25 til?pias tailandesas amostradas aleatoriamente indicaram altera??o na sensibilidade dos valores gen?ticos de algumas caracter?sticas ?s mudan?as no n?vel nutricional de lisina digest?vel. Observou-se, portanto, que as til?pias apresentam altera??o nos valores gen?ticos, sugerindo de maneira geral, a exist?ncia da intera??o gen?tipo x n?veis de lisina digest?vel para caracter?sticas, o que pode acarretar em sele??o de diferentes animais nos diferentes ambientes. / Disserta??o (Mestrado) ? Programa de P?s-Gradua??o em Zootecnia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 2017. / This research was carried out with the aim of evaluating the sensitivity of breeding values to dietary digestible lysine level for performance traits and morphometric measurements of Nile tilapia of Thai lineage. Twenty-nine full sib families were produced by mating 21 males and 29 females. The distribution among the tanks was randomized by family, after marking the fish, between 94 and 109 days of age, until forming an initial batch of twenty fingerlings per tank, totaling 700 fish. At the approximate age of 150 days the fish were randomly redistributed into the system until they formed lots with approximately 138 fish per level of digestible lysine in the diet. Four times a day the fishes were fed diets containing different levels of lysine: 1.43; 1.53; 1.63; 1.73 and 1.83% in the growing phase; and 1.28; 1.38; 1.48; 1.58 and 1.68% in the finishing phase. The individual tilapia information (weight, total length, standard length, head length, height and width) were standardized for 150, 185, 220 and 255 days of age. From then on the weight gain, daily weight gain, head to standard length ratio, width to height ratio and the relationship between standard length and total length were calculated. . For the analyses, a random regression model was used under a single animal model. Legendre polynomial models of 2 and 3 orders were tested for the fixed effect, and of order 2 for the additive and family genetic effects. In addition, models were also tested using homogeneous residual variance (1 class) and heterogeneous variance (2, 3, and 4 classes). The models that provide better fit in most of the characteristics were those that considered homogeneous residual variance. In general, the rank correlations of breeding values of pairs of dietary digestible lysine levels were high. The reaction norms of 25 randomly sampled Thai tilapia showed change in the sensitivity of breeding values of some traits to changes in dietary digestible lysine level. Therefore, it was observed that breeding values of tilapia traits generally changed along the environment gradient, suggesting the existence of genotype x dietary digestible lysine level interaction which can lead to the selection of different fishes in different environments.

Submitted by Jos? Henrique Henrique (jose.neves@ufvjm.edu.br) on 2018-03-20T18:00:43Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) namibia_rizzari_leite.pdf: 3000386 bytes, checksum: 4ad82a1678a4c363522c1631a2cdead0 (MD5) / Approved for entry into archive by Rodrigo Martins Cruz (rodrigo.cruz@ufvjm.edu.br) on 2018-03-29T14:18:22Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) namibia_rizzari_leite.pdf: 3000386 bytes, checksum: 4ad82a1678a4c363522c1631a2cdead0 (MD5) / Made available in DSpace on 2018-03-29T14:18:22Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) namibia_rizzari_leite.pdf: 3000386 bytes, checksum: 4ad82a1678a4c363522c1631a2cdead0 (MD5) Previous issue date: 2017 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico (CNPq) / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior (Capes) / Funda??o de Amparo ? Pesquisa do Estado de Minas Gerais (FAPEMIG) / Esta pesquisa foi realizada com o objetivo de avaliar o efeito da intera??o gen?tipo x n?veis de lisina digest?vel das dietas sobre caracter?sticas morfom?tricas e de desempenho de til?pias do Nilo, variedade GIFT, em fase de crescimento. O experimento foi constitu?do de duas fases, sendo que na primeira as til?pias foram alimentadas dos 90 aos 150 dias de idade com dietas contendo percentuais de lisina iguais a 1,43, 1,53, 1,63, 1,73 e 1,83 e na segunda fase, dos 151 aos 255 dias, os percentuais de lisina das dietas foram iguais a 1,28, 1,38, 1,48, 1,58 e 1,68. As til?pias foram pesadas dos 90 aos 255 dias de idade com intervalos de aproximadamente 30 dias, foram calculados o ganho de peso total e o ganho de peso di?rio e, posteriormente, as idades foram ajustadas para 90 e 150 dias na primeira fase, e 185, 220 e 255 dias na segunda fase. As medidas de altura, largura, comprimento de cabe?a, comprimento padr?o e comprimento total das til?pias foram coletadas aos 150 dias de idade. A partir desses dados, foram calculadas as rela??es cabe?a/comprimento padr?o, comprimento padr?o/comprimento total e largura/altura. Modelos de regress?o aleat?ria, por meio do modelo animal uni caracter?stica, foram utilizados para avaliar a sensibilidades dos valores gen?ticos aos n?veis de lisina digest?vel das dietas, plotando-se as normas de rea??o de 25 peixes amostrados aleatoriamente para as diferentes caracter?sticas para demonstrar o padr?o de comportamento dos valores gen?ticos das caracter?sticas ao longo do gradiente ambiental. Foram testados modelos com homogeneidade (1 classe) e heterogeneidade de vari?ncia residual (2, 3 e 4 classes). Modelos com heterogeneidade de vari?ncia residual foram mais adequados para avalia??o gen?tica da maioria das caracter?sticas das til?pias na primeira fase e modelos com homogeneidade de vari?ncia residual para a maioria das caracter?sticas de desempenho das til?pias avaliadas na segunda fase. Os valores gen?ticos das til?pias, em ambas as fases, variaram entre os n?veis de lisina estudados para a maioria das caracter?sticas, indicando a presen?a de intera??o gen?tipo x ambiente. No geral, as herdabilidades e vari?ncias gen?ticas aditivas variaram de baixas a altas magnitudes. As correla??es de Spearman, assim como as normas de rea??o, indicaram reordenamento dos valores gen?ticos ao longo do gradiente ambiental, sugerindo a presen?a de intera??o gen?tipo x ambiente. A sele??o para desempenho e medidas morfom?tricas de til?pias GIFT deve ser realizada no n?vel de lisina da dieta com a qual as til?pias ser?o alimentadas. / Disserta??o (Mestrado) ? Programa de P?s-Gradua??o em Zootecnia, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 2017. / This research was carried out with the objective of evaluating the effect of genotype x levels of digestible lysine of the diets on morphometric and performance characteristics of Nile tilapia, GIFT variety, in the growing phase. The experiment consisted of two phases, and in the first the tilapia were fed from 90 to 150 days of age diets containing lysine percentages equal to 1.43, 1.53, 1.63, 1.73 and 1.83. In the second phase, from 151 to 255 days, the lysine percentages of the diets were 1.28, 1.38, 1.48, 1.58 and 1.68. Tilapia were weighed from 90 to 255 days of age at intervals of approximately 30 days. Total weight gain and daily weight gain were calculated and, subsequently, were adjusted for 90 and 150 days in the first phase, and 185 , 220 and 255 days in the second phase. The measurements of height, width, head length, standard length and total length of tilapias were collected at 150 days of age. From these data, the head / standard length ratios, standard length / total length and width / height ratios were calculated. Single trait random regression modes were used in the analyses and the reaction norm plots of 25 randomly sampled fishes were used to demonstrate the sensitivity of breeding values to dietary digestible lysine level. Models with homogeneity (1 class) and heterogeneity of residual variance (2, 3 and 4 classes) were tested. Models considering heterogeneity of residual variance were more adequate for genetic evaluation of most of the characteristics of tilapia in the first phase and models considering homogeneity of residual variance for most of the performance characteristics of tilapia evaluated in the second phase. The breeding values of tilapia, in both phases, varied among the lysine levels studied for most of the traits, indicating the presence of genotype x environment interaction. In general, heritabilities and additive genetic variances varied from low to high magnitude. Spearman correlations, as well as the reaction norms, suggested rearrangement of breeding values along the environmental gradient, again indicating the presence of genotype x environment interaction. The selection for performance and morphometric traits of tilapia GIFT strain should be performed at the lysine level of the diet with which the tilapia will be fed.

Un des principaux enjeux de l’amélioration des plantes consiste aujourd’hui à faire face au changement climatique, en assurant un rendement élevé et plus stable dans des systèmes agricoles économes en intrants (eau, fertilisants) et respectueux de l’environnement. Les nouvelles variétés de blé devront non seulement être tolérantes aux stress hydriques et aux fortes températures, mais aussi continuer à être productives avec des apports limités en fertilisation, tout en maintenant une qualité du grain adaptés aux différents usages. De nouvelles méthodes de prédiction des réponses des blés à ces stress sont indispensables pour avancer dans cette direction. Dans ce travail, nous avons tout d’abord identifié les stress qui régissaient les interactions entre génotypes et les environnements (GxE) dans les essais considérés, puis développé un modèle génomique de l’adaptation à un stress environnemental (Factorial Regression genomic Best Linear Unbiased Prediction ou FR-gBLUP), en particulier pour le stress hydrique. En émettant l’hypothèse que plus des variétés de blés sont génétiquement proches, plus elles répondront de façon similaire à un stress environnemental donné, nous avons mesuré par validation croisée des gains de précision de prédiction par rapport à un modèle additif variant entre 3.5% et 15.4%. Des simulations complètent l’étude en démontrant que plus la part de variance expliquée par les réponses au stress considéré est importante, plus le modèle FR-gBLUP apporte un gain de précision. Pour prédire les réponses variétales à un stress particulier, les environnements doivent être finement caractérisés pour les stress limitant le développement des plantes. En nous intéressant plus particulièrement au stress azoté en France, nous avons établi des indicateurs de stress à partir d’un modèle de culture, et les avons comparés à des indicateurs classiques, tels que le type de conduite azotée ou l’azote disponible. Nous avons ainsi mis en évidence l’intérêt des modèles de culture pour caractériser les interactions GxE et pour prédire la réponse génomique au stress azoté, à condition que le signal d’interaction soit assez fort. Au-delà de l’application potentielle de ces méthodes pour la sélection ou la recommandation de variétés de blés plus adaptées ou plus résistantes au changement climatique, les résultats de ce travail démontrent aussi l’intérêt de la complémentarité des approches éco-physiologiques et génétiques. / In a climate change context, assuring high and stable yield in more sustainable agricultural systems is a major challenge for plant breeding. We are aiming for future wheat varieties which will be heat and drought tolerant, and also productive in limited fertilization input environments. New prediction methods of the response to these stresses are needed to move forward. In this study, we first identified stresses that generated interactions between genotypes and environments (GxE) in our experimental trials and then developed a genomic model for adaptation to a particular environmental stress (Factorial Regression genomic Best Linear Unbiased Prediction ou FR-gBLUP), in our case drought. This model hypothesizes that the more individuals are genetically close, the more their response to a stress will resemble. We used cross-validations to measure prediction accuracy gains compared to an additive model and observed gains between 3.5% and 15.4%. Besides, simulation studies showed that the more the variance explained by the responses to the stress is important, the more the FR-gBLUP model will improve the additive model. Furthermore, fine characterization of the stresses limiting the plants’ growth is required to predict varietal responses to a particular stress. We focused on the particular case of nitrogen stress in France. By establishing crop model based stress indicators and comparing them to classical indicators, such as the management system or the available nitrogen, we pointed out the interest of crop model to characterize GxE interactions and to predict the genomic response to nitrogen stress, as long as the GxE interaction signal is strong enough. Beyond the potential applications of these methods for breeding or recommendation for varieties more adapted or tolerant to environmental stresses, this study also raises the interest of coupling eco-physiological and genetics approaches.

The goal of this thesis is to get acquainted with methods of determining bone mineral density from appropriate tissue types in diagnostic CT data and possibly modifying or extending them in order to make the bone quality diagnosis more reliable. The thesis begins by introducing the issue of determining bone quality. Next, a method that takes cortical bone deformations into account as well as bone mineral density is introduced. Accuracy assessment based on opinion of a medical expert suggests positive outcome of future objective accuracy assessment utilizing so far unavailable base of calibrated CT data, that is needed before deployment into clinical practice. If the accuracy of the suggested method is confirmed this way, this work provides a so far absent tool for fully automatic preventive diagnostics of osteoporosis.

<p>Breeding for improved animal welfare is paramount for increasing the long-term sustainability of the animal food industry. In this context, the main objectives of this dissertation were to understand the genetic and genomic background of welfare indicators in livestock and evaluate the feasibility of single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) for performing genomic selection in beef cattle. This dissertation includes five studies. First, we aimed to test and identify an optimal ssGBLUP scenario for crossbreeding schemes. We simulated multiple populations differing based on the genetic background of the trait, and then we tested alternative models, such as multiple-trait weighted ssGBLUP. Even though more elaborated scenarios were evaluated, a single-trait ssGBLUP approach was recommended when genetic correlation across populations were higher than 0.70. The goal of the second study was to identify genomic regions controlling behavior traits that are conserved across livestock species. We systematically reviewed genomic regions associated with behavioral indicators in beef and dairy cattle, pigs, and sheep. The genomic regions identified in this study were located in genes previously reported controlling human behavioral, neural, and mental disorders. In the third study we used a large dataset (675,678 records) from North American Angus cattle to investigate the genetic background of temperament, a behavioral indicator, recorded on one-year-old calves, and provide the models and protocols for implementing genomic selection. We reported a heritability estimate equal to 0.38 for yearling temperament, and it was, in general, genetically favorably correlated with other productivity and fertility traits. Candidate genomic regions controlling yearling temperament were also identified. The fourth study was based on temperament recorded on North American Angus cows from 2 to 15 years of age (797,187 records). The goal was to understand the genetic and genomic background of temperament across the animal’s lifetime. By fitting a random regression model, we observed that temperament is highly genetically correlated across time. However, animals have differential learning and behavioral plasticity (LBP; changes of the phenotype overtime), although the LBP heritability is low. In our last study we evaluated foot scores (foot angle, FA; and claw set, CS) in American (US) and Australian (AU) Angus cattle aiming to assess the genetic and genomic background of foot scores and investigate the feasibility of performing an across-country genomic evaluation (~1.15 million animals genotyped). Foot scores are heritable (heritability from 0.22 to 0.27), and genotype-by-environment interaction was observed between US and AU Angus populations (genetic correlation equal to 0.61 for FA and 0.76 for CS). An across-country genomic prediction outperformed within-country evaluations in terms of predictivity ability (bias, dispersion, and validation accuracy) and theoretical accuracies. We have also identified genes associated with FA and CS previously reported in human’s bone structure and repair mechanism. In conclusion, this dissertation presents a comprehensive genetic and genomic characterization of welfare indicators (temperament and foot scores) in (inter)national livestock populations. </p>