Os objetivos deste trabalho foram estimar os efeitos genéticos fixos atuando sobre uma população sintética e testar diferentes modelos e metodologias neste processo de estimação. Os efeitos genéticos fixos testados foram os efeitos aditivos direto e materno de raça e não aditivos diretos e maternos de heterose, perdas epistáticas e complementariedade. Os modelos testados incluem alternada e conjuntamente todos estes efeitos. As metodologias de regressão de cumeeira e regressão por quadrados mínimos foram comparadas assim como dois métodos distintos para determinação do ridge parameter. Uma população sintética, envolvendo as raças Angus e Nelore foi utilizada. Foram utilizados 294.045 registros de desmame e 148.443 registros de sobreano de uma população sintética envolvendo as raças Angus e Nelore. Foram estudadas as seguintes características: ganho de peso do nascimento ao desmame (WG), escores de conformação (WC), precocidade (WP) e musculatura (WM) coletados ao desmame, ganho de peso do desmame ao sobreano (PG), escores fenotípicos de conformação (PC), precocidade (PP) e musculatura (PM) e perímetro escrotal (SC) coletados ao sobreano. Na maioria das análises, os efeitos genéticos fixos estimados foram estatisticamente significativos. O modelo completo, incluindo todos os efeitos genéticos fixos foi o mais indicado nas duas metodologias testadas. Na estimação por regressão de quadrados mínimos, o modelo mais parcimonioso foi o que incluiu apenas os efeitos aditivos de raça e não aditivos de heterose (dominância) e na estimação por regressão de cumeeira o mais parcimonioso foi o aquele que incluiu, além dos dois já referidos, os efeitos não aditivos de perdas epistáticas. As metodologias mostraram-se equivalentes, para os modelos que incluíram apenas efeito aditivo de raça e não aditivo de heterose. Todavia com a inclusão dos efeitos não aditivos de perdas epistáticas e/ou complementariedade, a regressão de cumeeira mostrou-se mais indicada até o momento em que os dados atingiram um determinado volume e estrutura, com grande parte das classes de composições raciais representadas na amostra e, a partir daí os modelos se mostraram equivalentes. Na comparação entre os métodos de determinação do ridge parameter, o mais indicado foi o método que identifica o menor valor possível que produz fatores de inflação de variância abaixo de 10 para todos os regressores estimados. / The objectives of this study were to estimate the fixed genetic effects acting on a synthetic population, as well as test different models and methodologies in this estimation process. The tested fixed genetic effects were the direct and maternal breed additive and direct and maternal heterosis, epistatic loss and complementarity non-additive effects The tested models include alternate and together all these effects. The ridge regression and least square regression methodologies were compared and were also compared two different methods for determining the ridge parameter to use in the ridge regression. A synthetic beef cattle population, involving Angus and Nellore in several breed combinations was used. 294,045 records at weaning and 148,443 records at yearling were used. The traits of weight gain from birth to weaning (WG), phenotypic scores of conformation (WC), precocity (WP) and muscling (WM) collected at weaning, weight gain from weaning to yearling (PG), phenotypic scores of conformation (PC), precocity (PP) and muscles (PM) collected at yearling and scrotal circumference (SC) were used in the analyzes. In most of analyzes, the estimated fixed genetic effects were statistically significant. The complete model, including all fixed genetic effects was the most suitable in the two tested methodologies. In the estimation by least squares regression, the most parsimonious model was the model that included only breed additive and non-additive heterosis (dominance) effects and in the estimation by ridge regression the most parsimonious model was that included, besides the breed additive and non-additive heterosis (dominance) effects, the non-additive epistatic loss effects. Comparing the two methodologies, for models that include only breed additive and non-additive heterosis effects, methodologies proved to be equivalent; with the inclusion of non-additive epistatic loss and / or complementarity effects, ridge regression was more indicated originally. After reached a certain volume and structure, with much of classes of breeds represented in the sample. Both least squares and ridge regression were equivalent. Comparing the methods for determining the ridge parameter, the best method was that which identifies the smallest possible value that produces the variance inflation factors below 10 for all estimated regressors.

FundaÃÃo de Amparo à Pesquisa do Estado do Cearà / O objetivo deste trabalho foi de analisar as caracterÃsticas de crescimento, reprodutivas e de habilidade materna de vÃrios grupos genÃticos compostos pelas raÃas Santa InÃs, Somalis Brasileira, Dorper, Poll Dorset, e seus cruzamentos, avaliando os diversos fatores genÃticos e nÃo genÃticos envolvidos. Foram utilizados registros de peso ao nascer (PN), peso ao desmame (PD), ganho de peso do nascimento ao desmame (GP), peso total de crias ao nascimento por matriz (PTCN), peso total de crias ao desmame por matriz (PTDC), idade ao primeiro parto (IPP), intervalo de partos (IDP) e perÃodo de gestaÃÃo (PG), no perÃodo de 1998 a 2007. Os dados foram oriundos de animais da Gaasa e Alimentos LTDA, localizada no MunicÃpio de Inhumas-GO, uma fazenda assistida pelo Programa de Melhoramento GenÃtico de Caprinos e Ovinos de Corte (GENECOC), pertencente à Empresa Brasileira de Pesquisa AgropecuÃria - Embrapa Caprinos. Os modelos de anÃlises foram definidos pelo procedimento MIXED do pacote estatÃstico SAS, apÃs a verificaÃÃo das restriÃÃes e limitaÃÃes dos dados. As avaliaÃÃes dos efeitos genÃticos aditivos e nÃo aditivos, e as estimativas dos componentes de (co)variÃncia foram obtidos pelo mÃtodo da mÃxima verossimilhanÃa restrita (REML), usando um algoritimo livre de derivadas, sob um modelo animal, utilizando o programa Multiple Trait Derivative-Free Restricted Maximum Likelihood (MTDFREML). Para as caracterÃsticas PN, PD e GP, utilizou-se o modelo animal considerando como aleatÃrios os efeitos genÃticos aditivos direto e maternos, o efeito de ambiente permanente materno e os efeitos residuais, enquanto os efeitos fixos foram os de grupo de contemporÃneos, interaÃÃo do sexo com o tipo de nascimento e classe de idade da mÃe, alÃm das (co)variÃveis para a obtenÃÃo das estimativas dos efeitos genÃticos aditivos diretos de cada raÃa, do efeito da heterose individual e heterose materna e do efeito de recombinaÃÃo. Para as caracterÃsticas PTCN, PTCD, IDP e PG, incluÃram-se o efeito genÃtico aditivo direto e o efeito de ambiente permanente do animal como aleatÃrios e os efeitos de grupo de contemporÃneas, ordem de parto e interaÃÃo do sexo com o tipo de nascimento das crias como fixos, alÃm das (co)variÃveis para a obtenÃÃo das estimativas do efeito genÃtico aditivo direto de cada raÃa, da heterose individual e de recombinaÃÃo. Jà para a IPP foram incluÃdos estes mesmos efeitos, exceto o efeito de ambiente permanente do animal. As anÃlises do desempenho mÃdio do rebanho para as caracterÃsticas estudadas foram de 3,75 kg, 14,91 kg, 0,200 kg/dia, 4,82 kg, 16,21 kg, 604,11 dias, 283,07 dias e 150,51 dias, respectivamente para PN, PD, GP, PTCN, PTCD, IPP IDP e PG. As estimativas para a diferenÃa genÃtica aditiva entre as raÃas ovinas foram significativas para todas as caracterÃsticas, exceto para o IDP. Os efeitos de heterose individual e materna tambÃm foram significativos para todas as caracterÃsticas, exceto para o PN (individual e materna) e para o GP (individual). Foi observada significativa perda por recombinaÃÃo para PD, GP, IPP e PG. As estimativas de herdabilidade para as PN, PD e GP foram de 0,38, 0,14 e 0,10, respectivamente, para herdabilidade direta e de 0,27, 0,09 e 0,04, respectivamente, para herdabilidade materna. Jà as estimativas de herdabilidade direta para PTCN, PTCD, IPP, IDP e PG foram de 0,19, 0,05, 0,21, 0,02 e 0,10, respectivamente. Foi observada a reduÃÃo do desempenho em vÃrias das caracterÃsticas estudadas, em funÃÃo de perdas por recombinaÃÃo. Isto significa que a formaÃÃo de uma populaÃÃo sintÃtica a partir das raÃas envolvidas neste estudo à uma aÃÃo bastante complexa, exigindo um rigoroso e bem conduzido processo de seleÃÃo para neutralizar estes efeitos indesejÃveis. Nas condiÃÃes do presente estudo, os genes da raÃa Somalis Brasileira contribuÃram para um melhor desempenho reprodutivo. Por outro lado, conduziu a reduÃÃo no ganho de peso, quando comparado Ãs demais raÃas estudadas / The aim of this study was to analyze growth, reproductiv e and maternal traits from Santa InÃs, Brazilian Somali, Dorper and Poll Dorset breeds and its crosses, evaluating the genetic and non-genetic factors presented. Records of birth weight (BW), weaning weight (WW), weight gain from birth to weaning (WG), litter weig ht at birth (LWB), litter weight at weaning (LWW), age at first lambing (AFL), lambing interval (LI) and gestation length (GL), between 1998 and 2007, were utilized. Data were from animals of the Gaasa e Alimentos LTDA, located in Inhumas-GO, a herd assisted by Programa de Melhoramento GenÃtico de Caprinos e Ovinos de Corte (GENECOC), of Empresa Brasileira de Pesquisa AgropecuÃria - Embrapa Caprinos. The analysis models were defined by MIXED procedure of the statistical package SAS, after verification of restrictions and limitations of data. The evaluations of additives and non-additives genetic effects, and the estimates of (co)variance components were obtained by Restricted Maximum Likelihood method (REML), using a derivative-free algorithm under animal model, using the software Multiple Trait Derivative-Free Restricted Maximum Likelihood (MTDFREML). For the traits BW, WW and WG, the animal model accomplished direct and maternal addictive genetic effects, maternal permanent environmental effect and residual effects as aleatory, while the fixed effects were contemporary group, interaction of sex with birth type and class of the mother's age, besides the(co)variables for the obtaining of the estimates of direct addictive genetic effects of each breed, individual heterosis effects, maternal heterosis effects and recombination e ffects. For the traits LWB, LWW, LI and GL, direct addictive genetic effects and individual permanent environmental effects were included in the model as aleatory and contemporary group, lactation order and in teraction of the sex with birth type effects as fixed, besides the (co)variables for the obtaining of the estimates of direct addictive genetic effect s breed, individual heterosis effects and recombination effects. Already for AFL, all effects were included, except the individual permanent environmental effect. The averages for the the studied traits were 3,75 kg, 14,91 kg, 0,200 kg/day, 4,82 kg, 16,21 kg, 604,11 days, 283,07 days and 150,51 days for BW, WW, WG, LWB, LWW, AFL, LI and GL, respectively. The estimates for the addictive genetic differences among the breeds were also significant for all the traits, except for LI. The individual and maternal heterosis were also significant for all the traits, ex cept for BW (individual and maternal) and WG (individual). Significant recombination losses were observed for WW, WG, AFL and GL. The direct heritabilities for BW, WW and WG were 0,38, 0,14 and 0,10, respectively, while maternal heritabilities for the same traits were 0,27, 0,09 and 0,04, respectively. Already the direct heritabilities for LWB, LWW, AFL, LI and GL were 0,19, 0,05, 0,21, 0,02 and 0,10. Reduction of performance were observed in many studied traits due losses by recombination. This means that the formation of a synthetic breed from the breeds involved in this study is a complex action, requiring a rigorous and well conducted process of selection to neutralize these undesirable effects. In the conditions of this study, the genes of Brazilian Somali contributed to improve reproductive performance. On the other hand, it contributed to reduction of weight gain when compared to the other breeds studied.

Thesis (M.Sc. (Animal Production)) -- University of Limpopo, 2021 / Initial analysis was conducted to test significance of dam parity, litter size, birth season, birth year, kidding season and kidding age on lactation milking performance of various milk production traits and components, as well as to calculate phenotypic correlation between dam kidding age and these traits. Analysis of variance (ANOVA) was carried out using 16 407 non-pedigreed lactation records to test for non-genetic significant effects, while Pearson’s correlation coefficients were calculated using Minitab software. The second analysis included 2 960 fully pedigreed lactation records that were analysed to estimate (co) variance components and direct heritability values for milk production and component traits applying uni-variate linear analysis, as well as genetic and phenotypic correlations between them using bi-variate linear analysis. Both analyses used secondary data of all grade and registered Saanen goats participating in the official Milk Recording and Performance Testing Scheme of the Animal Improvement Institute of the Agricultural Research Council of South Africa. From ANOVA, dam parity and year of birth significantly influenced (p < 0.05) all traits investigated, with better lactation milking performances estimated in 3rd parity groups and animals born during recent years respectively. Birth season only affected (p < 0.05) MY, urea and NR with animals born during spring season yielding a better lactation milking performance. Kidding season influenced (p < 0.05) all traits except PY and urea, with highest lactation milking performance estimated in animals kidding during spring season. All traits except FY and PY were significantly influenced (p < 0.05) by litter size, with multiple litter kidding groups yielding highest, while kidding age effects were not significant (p > 0.05) on NR, SCCI and urea. Pearson’s correlation estimations showed negative associations between kidding age (rp = -0.30, -0.004, - 0.057, -0.051, -0.015, -0.265 and -0.271 for urea, MY, FY, PY, LY, NR and P respectively) except for SCCI (rp= 0.189). From uni-variate and bi-variate linear analyses, direct heritability estimates ranged from moderate to high (h2 = 0.42 ± 0.03, 0.38 ± 0.03, 0.39 ± 0.03, 0.22 ± 0.03, 0.40 ± 0.03, 0.38 ± 0.03, 0.28 ± 0.05 and 0.20 ± 0.03 for MY, FY, PY, LY, Urea, NR, P and SCCI respectively), with MY having highest value. Genetic correlation estimates between MY and traits such as FY, PY, urea, NR and P were all high and positive indicating favorable correlated responses (rg =0.97, 0.94, 0.95, 0.99 and 0.74 respectively). Furthermore, phenotypic correlation estimates between MY and these traits except P (rp = 0.33) were close to their respective genetic xv correlation values (rp=0.95, 0.91, 0.92 and 0.92 for FY, PY, urea and NR respectively). Genetic correlation between MY and LY, and between MY and SCCI were not significant (p > 0.05), while phenotypic correlations between MY and these traits were significant (p <0.05), positive and low (rp=0.03 and 0.02 for LY and SCCI respectively). It was concluded that non-genetic factors determine to what extent the genetic potential of an animal is expressed thus, their inclusion in genetic evaluation models is crucial. Selecting for increased MY would increase herd lactation NR and improve lactation milking performance of other traits such as FY, PY and P. Selection against SCCI needs to be applied more in the population to avoid losses attributed to intra mammary infections / National Research Foundation (NRF)

Made available in DSpace on 2016-12-08T16:44:34Z (GMT). No. of bitstreams: 1 PGPV11MA038.pdf: 1217077 bytes, checksum: 00344fc81180f6d99a71b0ff111924e8 (MD5) Previous issue date: 2011-02-09 / Curtobacterium wilt has become one of the most important emerging diseases in bean plants. Studies aimed at identifying sources of resistance and to know the genetic control of disease are essential for the development of resistant cultivars. The aim of this study was to identify bean genotypes resistant to curtobacterium wilt and determine the inheritance of resistance of this disease on bean, to enable the development of resistant cultivars in a breeding program. Were evaluated 72 genotypes, among which are 67 accessions of the Active Germplasm Bank of beans at the Universidade do Estado de Santa Catarina (UDESC). It was possible to identify Xan 159 as being tolerant to the disease, because it showed the lowest average scores for symptoms of bacterial wilt and is indicated for use in breeding programs to develop resistant cultivars. The study of inheritance of resistance to bacterial wilt was accomplished through a complete diallel of five parents (IAC Carioca Aruã, IAC Carioca Pyatã, IAC Carioca Tybatã, SCS Guará and Pérola) and through study of six generations of people IAC Carioca Aruã x Guara and IAC Carioca Pyatã x Pérola. Diallel analysis showed that although both the additive effects and non-additive are involved, the additive effect is more important in controlling the curtobacterium wilt. The IAC Carioca Pyatã had the highest general combining ability and is recommended for use in breeding programs that aim to develop resistant genotypes. The analysis of the means of generations between genotypes tolerant x susceptible (IAC Carioca Aruã x SCS Guará and IAC Carioca Pyatã x Pérola), demonstrates the importance of the additive effects on the character determination. Analyses of variance of six generations agree with the results found by the analysis of averages, where the additive effect has greater importance for the inheritance of curtobacterium wilt. The narrow sense heritability was around 35%, demonstrating that it is possible to gain with the selection of resistant individuals / A murcha de curtobacterium tem se mostrado uma das doenças emergentes mais importantes na cultura do feijão. Estudos que visem identificar fontes de resistência e conhecer o controle genético da doença são fundamentais para o desenvolvimento de cultivares resistentes. O objetivo deste trabalho foi identificar genótipos de feijão resistentes à murcha de curtobacterium e estudar a herança da resistência desta doença em feijão, para possibilitar o desenvolvimento de cultivares resistentes em programas de melhoramento. Foram avaliados 72 genótipos, dentre os quais estão 67 acessos pertencentes ao Banco Ativo de Germoplasma de Feijão da Universidade do Estado de Santa Catarina (UDESC). Foi possível identificar a linhagem Xan 159 como tolerante à doença, pois apresentou as menores médias para as notas dos sintomas da murcha de curtobacterium, sendo indicado para uso em programas de melhoramento para o desenvolvimento de cultivares resistentes. O estudo da herança da resistência à murcha de curtobacterium foi realizado, através de um dialelo completo com cinco genitores (IAC Carioca Aruã, IAC Carioca Pyatã, IAC Carioca Tybatã, Pérola e SCS Guará) e através do estudo das seis gerações da populações IAC Carioca Aruã x Guará e IAC Carioca Pyatã x Pérola. A análise dialélica mostrou que, embora ambos os efeitos aditivos e não-aditivos estão envolvidos, o efeito aditivo é mais importante no controle da murcha de curtobacterium. O genótipo IAC Carioca Pyatã apresentou a maior capacidade geral de combinação e é recomendado para uso em cruzamentos dirigidos que objetivam o desenvolvimento de genótipos resistentes. A análise das médias das gerações entre genótipos tolerantes x suscetíveis (IAC Carioca Aruã x SCS Guará e IAC Carioca Pyatã x Pérola), demonstra a importância dos efeitos aditivos para a determinação do caráter. As análises das variâncias das seis gerações concordam com os resultados encontrados pela análise das médias, onde o efeito aditivo possui maior importância para a herança da murcha de curtobacterium. A herdabilidade no sentido restrito foi em torno de 35%, demonstrando que há possibilidade de obter ganhos com a seleção de indivíduos resistentes

A rich diversity of social behaviours exists in the animal kingdom, and these behaviours have evolved to perform a variety of adaptive functions. Social behaviours show variation both among and within species, however the mechanisms that give rise to this variation are not well understood. Using fruit flies (Drosophila melanogaster), my goal was to uncover the genetic and behavioural mechanisms that underpin natural variation in two different social behaviours: sociability and sexual aggression. First, I showed that sociability, which is the tendency of animals to engage in friendly activities together, is influenced by indirect genetic effects (IGEs), and that encounters among individuals drive these effects (Chapter 2). I then showed that sociability and social plasticity have low-moderate heritability (Chapter 3), and sociability is not correlated between the sexes or with activity. I then generated lineages of flies with high and low sociability using artificial selection (Chapter 4). The evolved lineages had significantly diverged sociability which was not associated with fitness measures or nearest-neighbor distances, but was negatively correlated with intrasexual aggression (Chapter 4). Finally, in sexual aggression, which I quantified as male forced copulation rate, I showed that evolved differences and differences due to social plasticity were both associated with the differential expression of many genes, but only a few of these genes were significant in both (Chapter 5). I also showed that these sets of genes are enriched in neuropeptide hormone and serotonin gene ontology categories, and that 4 of 7 chosen genes were validated for their effects on sexual aggression. Overall, this thesis sheds light on the complex mechanisms that underlie variation in these social behaviours, and it paves the way for future research to further elucidate some of these mechanisms, especially on the genetic basis of sociability using the evolved lineages I generated. / Thesis / Doctor of Philosophy (PhD) / Individual animals tend to vary in many traits including social behaviours. Using fruit flies, my goal was to understand what causes individuals to vary in two social behaviours: sociability and sexual aggression. I found that highly sociable flies tended to influence other flies to become more sociable due to a change in how much these flies interacted. I also found that individual differences in sociability are moderately heritable, and the genetic variation contributing to this is different between the sexes. Also, less sociable flies tended to be more aggressive than highly sociable flies. Finally, for sexual aggression, I showed that variation in a male’s success in forcibly mating with a female was associated with changes in the expression of hundreds of genes, but these changes were mostly unique for evolved versus environmentally induced variation. Future work will similarly look to identify genes involved with individual differences in sociability.

The evolution of extra-group paternity (EGP) is a contentious issue in evolutionary biology. This thesis examines the factors and adaptive benefits driving EGP in a high-density, group-living population of European badgers (Meles meles). To improve power to assign parentage, I isolated and characterised 21 new polymorphic microsatellite markers. I genotyped 83% of 1410 badger trapped 1987‒2010 using 35 autosomal microsatellite markers. Maternity and paternity were assigned at 80% confidence ca. 82% of individuals. 48% of paternities were extra-group, where 85% were attributable to neighbouring-group males and EGP was detected in 47% of litters; thus badger social group do not correspond with a breeding unit. I tested whether indirect genetic benefits explain these high EGP rates. (1) ‘Good-gene-as-heterozygosity Hypothesis’: Paternal heterozygosity, but not maternal or an individual’s own heterozygosity, associated positively with first-year survival probability. Under benign environmental conditions, cubs fathered by more heterozygous males had a higher first year survival probability. Despite this correlation, the EGP rate per litter correlated with neither average nor maximum within-group heterozygosity of candidate fathers. (2) Fitness benefit Hypothesis: Extra-group offspring (EGO) had lower first-year survival probability and lived 1.3 years less than within-group offspring (WGO). Female WGO produced more litters and offspring over their lifetime than female EGO, whereas male EGO produced more offspring than male WGO. (3) Inbreeding avoidance hypothesis: The EGP rate within a litter increased with greater average pair-wise relatedness between mothers and within-group candidate fathers. No inbreeding depression on first-year survival probability was detected, but small sample sizes limited statistical power. Socio-ecologically, at the litter level, EGP correlated negatively with the number of within-group candidate fathers, and positively with neighbouring-group candidate fathers. In conclusion, EGP in badgers may reduce inbreeding and be maintained in the population through a sex-specific antagonistic selection and indirect genetic benefits may occur when the total fitness benefits of producing extra-group sons outweigh the costs of producing extra-group daughters. These indirect genetic benefits only partially explain the evolution of promiscuity in European badgers, highlighting that evolutionary factors underlying promiscuity remain unclear.