Made available in DSpace on 2014-06-11T19:26:42Z (GMT). No. of bitstreams: 0 Previous issue date: 2004-01-28Bitstream added on 2014-06-13T18:54:59Z : No. of bitstreams: 1 santacruzoviedo_vr_me_botfca.pdf: 253923 bytes, checksum: d788e43f5154fa351b3082b8b6f18339 (MD5) / Foram conduzidos dois experimentos na FCA/UNESP, objetivando avaliar a depressão causada por endogamia com sucessivas gerações de autofecundação em uma população de pepino do tipo japonês. No primeiro experimento foram avaliadas características de produção de frutos imaturos no período de 21/08/2002 à 29/11/2002 em ambiente protegido. No segundo experimento foram avaliadas características de produção e qualidade de sementes no período de 12/03/2003 à 13/06/2003 em condições de campo. A partir do intercruzamento entre plantas do híbrido Natsu suzumi foi obtida a geração F2, considerada como população S0. Obtiveram-se progênies S1, S2, S3, S4 e S5, através de autofecundações sucessivas pelo método do SSD ('Single Seed Descent'). Ao partir da mistura ao acaso de sementes de progênies com igual número de autofecundações sucessivas foram obtidas cinco populações denominadas de população S1 a população S5. Foram sete tratamentos (híbrido Natsu suzumi, populações S0 a S5) e o delineamento experimental foi em blocos ao acaso, com seis e quatro repetições no primeiro e segundo experimento, respectivamente e cinco plantas por parcela nos dois experimentos. No primeiro experimento (frutos imaturos) foram avaliados, número de folhas, comprimento da haste principal, número e massa de frutos, total e comercial, número de nós e porcentagem de brotações. No segundo experimento (frutos maduros) avaliaram-se características relacionadas com produção (número e massa de sementes por planta e por fruto) e qualidade de sementes (teste padrão de germinação, primeira contagem de sementes, índice de velocidade de germinação, massa de 100 sementes). Foram realizadas as análises de variância para cada característica, e as médias dos tratamentos foram comparadas pelo teste de Tukey (%). Também foram realizados análises de variância apenas com as seis... / Two experiments were set up at FCA/UNESP. The objective of this work was to evaluate the inbreeding depression with successive generations of self pollination in a cucumber Japanese population. It was studied one population F2 obtained from a commercial hybrid (Natsu suzumi) considered as S0 population. In the first experiment were appraised characteristics of production of immature fruits in the period of 21/08/2002 to 29/11/2002 in protected cultivation. In the second experiment were appraised seed production and quality in the period of 12/03/2003 to 13/06/2003 in open field conditions. It was obtained progenies S1, S2, S3, S4 and S5 through the 'Single Seed Descent' methodology. It was used randomized blocks with seven treatments (different generations of self pollination - S0 to S5 and the hybrid Natsu suzumi) six and four replicates in the first and second experiment and five plants per plot in both. In the first experiment (immature fruits) were evaluated number of leaves, length of the main stem, number and weight of fruits, total and commercial, number of nodes and vines percentage. In the second experiment (mature fruit) characteristic related with production were evaluated (number and weight of seeds per plant and per fruit) and quality of seeds (germination test, first counted of seeds, index of germination speed and weight of 100 seeds). The variance analyses were accomplished each characteristic and the averages of the treatments were compared by the test of Tukey (%). Also accomplished just with the six inbreed generations to evaluate the possible inbreeding depression (without including the commercial hybrid). In the comparison among the population differences were not observed for the characteristics appraised showing there were not production loss for inbreeding in this population. However, for the characteristics length of the main stem, number of total fruit, weight of seeds per fruit and seed number per fruit the commercial.

Made available in DSpace on 2014-06-11T19:32:15Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-01-25Bitstream added on 2014-06-13T20:43:04Z : No. of bitstreams: 1 guidolin_dgf_dr_jabo.pdf: 427451 bytes, checksum: 084dc7a803aeb9d016055543a1cf6b98 (MD5) / O monitoramento dos resultados de um programa de seleção de bovinos de corte serve para avaliar o progresso genético alcançado e para que os resultados obtidos sirvam de elementos orientadores de ações futuras. Neste trabalho, os objetivos foram estimar parâmetros genéticos e tendências genéticas para características de importância econômica em bovinos da raça Guzerá, estimar parâmetros populacionais e os coeficientes de endogamia e relaciona-los com valores genéticos e com o índice de seleção recomendado para a raça (MGT). Para isto, dados de 18.491 animais, oriundos de 43 fazendas foram cedidos pelo Programa de Avaliação Genética da Raça Guzerá (PAGRG). As características estudadas foram área de olho de lombo (AOL), espessura de gordura entre a 12ª e a 13ª costela (EG), espessura de gordura na garupa (EGP8), idade ao primeiro parto (IPP), perímetro escrotal aos 365 (PE365) e 450 (PE450) dias de idade, período de gestação (PG), peso adulto da vaca (PAV), peso corporal ao nascimento (PN), aos 120 (P120), aos 210 (P210), aos 365 (P365), aos 450 (P450) dias de idade e produtividade acumulada em fêmeas (PAC). Os parâmetros populacionais estimados foram taxa de endogamia por geração, tamanho efetivo da população, intervalo de gerações e o número efetivo de fundadores e de ancestrais. Os parâmetros genéticos e valores genéticos foram estimados pelo método da máxima verossimilhança restrita, em análises uni e bi-características. Tendências genéticas foram obtidas por regressão linear das médias dos valores genéticos anuais, em função do ano de nascimento. A estatística t foi usada e a hipótese nula considerava o coeficiente da regressão como sendo zero. As características apresentaram suficiente variação genética aditiva, sendo passíveis de seleção e estas se mostraram favoravelmente correlacionadas geneticamente, exceto... / Monitoring the results of a breeding program for beef cattle is used to evaluate the genetic progress achieved and the results serve as guiding elements for future actions. In this work, the objectives were to estimate genetic parameters and genetic trends for traits of economic importance in Guzerat beef cattle, estimate population parameters and coefficients of inbreeding and its relationship with breeding values and the selection index recommended for the breed (MGT).For this, data from 18,491 animals from 43 farms were granted by the Programa de Avaliação Genética da Raça Guzerá (PAGRG). The traits studied were rib eye area (REA), fat thickness between the 12th and 13th rib (FT), rump fat thickness (RF), age at first calving (AFC), scrotal circumference at 365 (SC365) and 450 (SC450) days of age, gestation length (GL), mature weight of the cow (MWC), body weight at birth (BWB), 120 (BW120), 210 (BW210), 365 (BW365) and 450 days of age (BW450) and cumulative productivity in females (AP). The population parameters estimated were rate of inbreeding per generation, effective population size, generation interval and the effective number of founders and ancestors. The genetic parameters, breeding values were estimated by restricted maximum likelihood, by one and two-trait analysis. Genetic trends were calculated from a linear regression of mean predicted breeding values (PBV) based on birth year. At-statistic was used to test the hypothesis that the regression coefficient for each equation is equal to zero. The traits showed sufficient additive genetic variation, being capable to respond to selection and proved to be genetically correlated among them, except AP, FT and RF, which showed low genetic correlations with other traits. The genetic trend indicated that the animal’s mean breeding value has changed over time for the traits studied... (Complete abstract click electronic access below)

Made available in DSpace on 2014-06-11T19:32:15Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-09-12Bitstream added on 2014-06-13T20:43:05Z : No. of bitstreams: 1 000736380.pdf: 3145920 bytes, checksum: eb9040463ecaf8a423ca7772cda63410 (MD5) / Esta tese compreende quatro diferentes estudos conduzidos a fim de avaliar estratégias alternativas para aumentar a eficiência de seleção genômica (GS) em programas de melhoramento animal. Um primeiro estudo foi desenvolvido com a finalidade de avaliar a performance preditiva de diferentes métodos estatísticos com base na informação de painéis de marcadores densamente distribuídos ao longo do genoma. Cinco diferentes características de uma população real de camundongos foram analisadas. Verificou-se que métodos com grandes diferenças conceituais apresentaram performance preditiva similar em algumas situações, também havendo variação na performance relativa dos métodos em função da característica analisada. O uso de diferentes variáveis resposta (pseudo-fenótipos) para estimação de efeitos de marcadores foi avaliado num segundo estudo, por meio da simulação de uma grande população de bovinos de corte, para a qual predições genômicas foram obtidas usando um procedimento de múltiplas etapas. Houve evidência de que provas desregredidas (dEBV) são mais apropriadas do que valores genéticos preditos (EBV) e médias ajustadas de desempenho da progênie (PYD), tanto para o treinamento de modelos quanto para a validação de predições genômicas. No terceiro estudo, procurou-se avaliar consequências em longo-prazo da aplicação de GS numa população de bovinos de corte sob seleção. Verificou-se grande benefício da aplicação de GS em cenários simulando seleção para características de qualidade de carne e reprodução de fêmeas. Houve evidência de que pode-se esperar maior benefício para GS, quando comparada à seleção por BLUP, no caso de características oligogênicas. Também foi possível inferir que em aplicações de GS, o uso de um critério de seleção em que se atribui maior peso a alelos favoráveis de menor frequência poderia proporcionar... / Improvements in production levels and product quality are needed in livestock systems to meet the growing world demand for animal-source foods. Besides this increasing demand, the productive sector must deal with constraints related to competition for land, greenhouse gas emissions and also due to hardening legislation in the fields of environment and animal welfare (FAO, 2011). In this context, animal breeding has played and will continue to play an important role to improve the efficiency of such production systems, especially in terms of competitiveness, safety, sustainability and biodiversity conservation (Harlizius et al., 2004). The main objective of animal breeding programs is to improve the performance of the next generations, through identification and reproduction of the animals with better genetic pool to efficiently produce in a specific environment (herein, superior animals). In the last decades, animal breeders succeeded in achieving this goal, mostly through the application of statistical tools grounded in quantitative genetics theory, what could be called as 'classical animal breeding'. In this case, the traditional prediction of the genetic merit of individuals (estimated breeding values, EBV) is obtained based on information of pedigree and phenotypes (own records and measures on relatives). With the advent of dense molecular marker panels, the implementation and design of breeding programs, especially in dairy cattle, had changed dramatically as a consequence of incorporating this new information to identify superior animals earlier and more precisely. Pioneer simulation studies drew attention of animal breeders to the possibility of making accurate predictions of the genetic merit of individuals by using genotypic information from dense marker panels, a process known as genomic selection (GS) (Nejati-Javaremi et al., 1997; Meuwissen et al., 2001). Other influential work ...

Made available in DSpace on 2015-07-13T12:10:25Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-12-17. Added 1 bitstream(s) on 2015-07-13T12:25:14Z : No. of bitstreams: 1 000835692.pdf: 541240 bytes, checksum: bec6b6659cf4eaceddcb3c897b0c930f (MD5) / Em bovinos da raça Brahman criados no Brasil a diversidade genética pode diminuir ao longo dos anos e pode ser ainda menor para animais estabulados, além disso, espera-se que a variância fenotípica de características reprodutivas pode ser pouco explicada pela variância genética. Portanto, objetivou-se avaliar o comportamento da diversidade genética durante um período de 18 anos e de animais estabulados por meio da análise de pedigree e estimar os parâmetros genéticos para as características idade ao primeiro parto (IPP), intervalo entre partos (IEP), reconcepção (REC) e habilidade de permanência (HABP) em bovinos da raça Brahman, visando o desenvolvimento de estratégias de seleção para o progresso genético da raça. O pedigree foi analisado de três maneiras: considerando toda a informação de pedigree (Pt); dividindo as informações de pedigree em dois períodos de 1994 a 2004 (P1) e de 2005 a 2012 (P2), de acordo com nível médio endogâmico; e dividindo os dados de pedigree de acordo com a condição de criação dos animais, a pasto (Ppasto) e estabulado (Pest). Os valores dos coeficientes endogâmicos (F) foram de 0,31%, 0,07%, 0,50%, 0,30% e 0,22% para Pt, P1, P2, Ppasto, Pest, respectivamente. Os intervalos de geração (IG) para Pt, P1, P2, Ppasto, Pest foram de 4,73, 3,35, 4,50, 4,65, 4,81 anos, respectivamente. Para os resultados dos parâmetros com base na probabilidade de origem do gene: número de fundadores (Nf), número efetivo de fundadores (fe), número efetivo de ancestrais (fa) e número efetivo de genomas remanescentes (fg), fe > fa > fg em todas as situações e ocorreu uma diminuição nos valores dos parâmetros estimados entre períodos (P1 e P2) e entre condição de criação (Ppasto e Pest). As razões fe/fa e fg/fe foram próximas de 1, indicando que não houve gargalo genético e que o processo de deriva genética foi pequeno. Para estimar os parâmetros... / The genetic diversity in Brahman cattle in Brazil may decrease over the years and can be even lower for stabled animals, moreover, it is expected that the phenotypic variance of reproductive characteristics can be little explained by genetic variance. The aims of this study were to evaluate the behavior of genetic diversity over a period of 18 years and stabled animals by pedigree analysis and estimates genetic parameters for ge at first interval (IPP), calving interval (IEP), reconception (REC) and stayability (HABP) reproductive traits of Brahman cattle in Brazil, aiming to develop selection strategies for genetic progress of breed. The pedigree was analyzed in three ways: considering all the pedigree information (Pt); dividing the pedigree information in two periods from 1994 to 2004 (P1) and from 2005 to 2012 (P2), according inbreeding; and dividing the pedigree data according to breeding management of animals on pasture (Ppasto) and stabled (Pest). Coefficient inbreeding (F) values were 0,31%, 0,07%, 0,50%, 0,30% and 0,22% for Pt, P1, P2, Ppasto, Pest, respectively. Generation intervals (IG) values for Pt, P1, P2, Ppasto, Pest were 4,73, 3,35, 4,50, 4,65, 4,81 years, respectively. For the results of the parameters based on the probability of gene origin: number of founders (Nf), effective number of founders (f e ), effective number of ancestors (f a ) and founder genome equivalents (f g ), in all situations f e > f a > f g and there was a decrease in values of estimated parameters between periods (P1 e P2) and between breeding management (Ppasto e Pest). Values close to 1 observed for f e /f a and f g /f e show no genetic bottleneck and the process of genetic drift was small. For estimate the genetic parameters for reproductive traits, two-trait analyzes were used, using the linear animal model for IEP and IPP and the animal threshold model for REC and HABP. The mean heritability were ...

Orientador: Ricardo da Fonseca / Co-orientador: Fabiana Martins Costa Maia / Banca: Claudia Maria Bertan Membrive / Banca: Henrique Nunes de Oliveira / Resumo: Em bovinos da raça Brahman criados no Brasil a diversidade genética pode diminuir ao longo dos anos e pode ser ainda menor para animais estabulados, além disso, espera-se que a variância fenotípica de características reprodutivas pode ser pouco explicada pela variância genética. Portanto, objetivou-se avaliar o comportamento da diversidade genética durante um período de 18 anos e de animais estabulados por meio da análise de pedigree e estimar os parâmetros genéticos para as características idade ao primeiro parto (IPP), intervalo entre partos (IEP), reconcepção (REC) e habilidade de permanência (HABP) em bovinos da raça Brahman, visando o desenvolvimento de estratégias de seleção para o progresso genético da raça. O pedigree foi analisado de três maneiras: considerando toda a informação de pedigree (Pt); dividindo as informações de pedigree em dois períodos de 1994 a 2004 (P1) e de 2005 a 2012 (P2), de acordo com nível médio endogâmico; e dividindo os dados de pedigree de acordo com a condição de criação dos animais, a pasto (Ppasto) e estabulado (Pest). Os valores dos coeficientes endogâmicos (F) foram de 0,31%, 0,07%, 0,50%, 0,30% e 0,22% para Pt, P1, P2, Ppasto, Pest, respectivamente. Os intervalos de geração (IG) para Pt, P1, P2, Ppasto, Pest foram de 4,73, 3,35, 4,50, 4,65, 4,81 anos, respectivamente. Para os resultados dos parâmetros com base na probabilidade de origem do gene: número de fundadores (Nf), número efetivo de fundadores (fe), número efetivo de ancestrais (fa) e número efetivo de genomas remanescentes (fg), fe > fa > fg em todas as situações e ocorreu uma diminuição nos valores dos parâmetros estimados entre períodos (P1 e P2) e entre condição de criação (Ppasto e Pest). As razões fe/fa e fg/fe foram próximas de 1, indicando que não houve gargalo genético e que o processo de deriva genética foi pequeno. Para estimar os parâmetros... / Abstract: The genetic diversity in Brahman cattle in Brazil may decrease over the years and can be even lower for stabled animals, moreover, it is expected that the phenotypic variance of reproductive characteristics can be little explained by genetic variance. The aims of this study were to evaluate the behavior of genetic diversity over a period of 18 years and stabled animals by pedigree analysis and estimates genetic parameters for ge at first interval (IPP), calving interval (IEP), reconception (REC) and stayability (HABP) reproductive traits of Brahman cattle in Brazil, aiming to develop selection strategies for genetic progress of breed. The pedigree was analyzed in three ways: considering all the pedigree information (Pt); dividing the pedigree information in two periods from 1994 to 2004 (P1) and from 2005 to 2012 (P2), according inbreeding; and dividing the pedigree data according to breeding management of animals on pasture (Ppasto) and stabled (Pest). Coefficient inbreeding (F) values were 0,31%, 0,07%, 0,50%, 0,30% and 0,22% for Pt, P1, P2, Ppasto, Pest, respectively. Generation intervals (IG) values for Pt, P1, P2, Ppasto, Pest were 4,73, 3,35, 4,50, 4,65, 4,81 years, respectively. For the results of the parameters based on the probability of gene origin: number of founders (Nf), effective number of founders (f e ), effective number of ancestors (f a ) and founder genome equivalents (f g ), in all situations f e > f a > f g and there was a decrease in values of estimated parameters between periods (P1 e P2) and between breeding management (Ppasto e Pest). Values close to 1 observed for f e /f a and f g /f e show no genetic bottleneck and the process of genetic drift was small. For estimate the genetic parameters for reproductive traits, two-trait analyzes were used, using the linear animal model for IEP and IPP and the animal threshold model for REC and HABP. The mean heritability were ... / Mestre

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No. of bitstreams: 1 Tese - Ederly Santos Silva.pdf: 1737064 bytes, checksum: 3f36097378fc3cdeb2502d467b6793ac (MD5) Previous issue date: 2011-08-01 / FAPEAM - Fundação de Amparo à Pesquisa do Estado do Amazonas / Copaibas are trees that are native to tropics, with nine species found in Brazilian Amazonia. Copaiba trees produce an oil-resin that is found in secretory channels located in the trunks. Copaifera reticulata is the predominant species in the Tapajós National Forest. The socioeconomic aspects of the communities of Pedreira and São Domingos, who are authorized to collect copaiba, and the phytodemographic, genetic and physical-chemical aspects of the copaiba populations available to these communities were analyzed, with the objective of subsidizing future actions of copaiba management in the Tapajós Flona. In the socioeconomic study, semi-structured interviews with the communities extractors elucidated the current local situation with respect to the extraction of copaiba. In the phytodemographic study, the species was identified, the density of potentially productive individuals was quantified, and these were mapped. Microsatellite markers developed by Embrapa Genetic Resources and Biotechnology were used for the genetic analyses. The physical-chemical parameters used were density and viscosity of the oil-resin, as these are associated with potential uses and for the chemical study it was the refraction index, acidity, saponificacion and éster. The management of copaiba is technologically simple, but the extractors identified numerous difficulties, including less advantage in the sale of the oil-resin than formerly, showing that the situation in the past that stimulated them is very different from the current situation, especially in the commercialization process. The density of productive trees in the collection area of Km 67 was 5,5 and of Km 72 was 6,2, with 200 adult individuals geo-referenced. The largest number of productive trees was in the diameter class 51-70 cm, totaling 88 trees, and the largest diameter found was 120 cm. To C. reticulata it presents an oil-resin with viscosity 9 (mPa.s) very variable and it lowers acidity (mg of KOH/g), which could serve as a basis for oil-resin differentiation. With the six microsatellite loci that transferred, 78 alleles were observed. The genetic diversity (He) varied from 0.59 to 0.85 per locus, considered high for Neotropical tree species; however, the observed heterozygosity was smaller than the expected heterozygosity by the Hardy-Weinberg equilibrium in the collection areas, demonstrating a reasonable level of inbreeding (f = 0.375 to 0.419), probably due to a clumped distribution. The analysis with Structure did not identify two populations based on the collection areas, but two genetic groupings based on different combinations of alleles. Most of the genetic variation was found within the collection areas (97%), with weak genetic differentiation among the areas (Fst = 0.030). A little less genetic variation it was found within the genetic groups (93%), with a corresponding increase in divergence (Fst = 0.070). The noncorrespondence between collection areas and genetic groupings could be due to unknown historical events, but, combined with the high genetic diversity founds, suggests that the current levels of inbreeding won't be a problem for a management plan, although the isolation of the Tapajós Flona in the future could contribute to elevate inbreeding to worrying levels. The information presented here will serve as a baseline for future comparison, guiding improvements in the management plan. / As copaíbas são árvores nativas da região tropical das quais nove espécies podem ser encontradas na Amazônia brasileira. As árvores de copaíba produzem um óleo-resina que é encontrado em canais secretores localizados no tronco das árvores. Copaifera reticulata é a espécie predominante na área deste estudo. Foram analisados os aspectos socioeconômicos das Comunidades de Pedreira e São Domingos na Flona do Tapajós, Santarém, Pará, por serem autorizadas a coletar copaíba na Flona, e os aspectos fito-demográficos, genéticos e físicos das populações de copaibeiras disponíveis a estas comunidades, com objetivo de subsidiar futuras ações de manejo de copaíba na Flona. No estudo socioeconômico, realizouse entrevistas semi-estruturadas com os extratores das comunidades para saber a real situação local quanto a extração do produto. No estudo fito-demográfico, identificou-se a espécie, quantificou-se a densidade dos indivíduos que foram potencialmente produtivos, e mapeou-se as árvores. Marcadores microssatélites desenvolvidos pela Embrapa Recursos Genéticos e Biotecnologia serão utilizados para as análises genéticas. Os parâmetros escolhidos para o estudo físico foram a determinação da densidade e viscosidade do óleo-resina por serem relacionados aos usos potenciais, e para o estudo químico foram os índices de refração, acidez, saponificação e éster. O processo de manejo da copaíba apresenta tecnologia simples para a retirada do óleo-resina, mas os extratores apontaram muitas dificuldades em relação ao manejo da espécie. Extrativistas afirmaram que atualmente tem-se menos vantagem na venda do óleo-resina de copaíba do que antigamente, indicando que a situação no passado que os estimulava é bem diferente do quadro atual, necessitando de apoio no processo de comercialização. As densidades dos indivíduos na área de coleta do Km 67 foi 5,5 indivíduos por hectare e no Km 72 foi 6,2 indivíduos por hectare, e 200 indivíduos adultos foram georeferenciados. O maior número de matrizes produtivas encontram-se na classe diamétrica 51-70 cm, totalizando 88 árvores, e o maior diâmetro encontrado foi 120 cm de DAP. A C. 7 reticulata apresenta um óleo-resina com viscosidade (mPa.s) muito variável e baixa acidez (mg de KOH/g), podendo servir de base para diferenciação de óleos-resina. Com os seis locos microssatélites que transferiram foram observados 78 alelos. A diversidade genética (He) variou de 0,59 a 0,85 por locos, considerada alta para a maioria das espécies neotropicais; no entanto, a heterozigosidade observada foi menor que a heterozigosidade esperada pelas proporções do EHW para as áreas de estudo, demonstrando um razoável nível de endogamia (f = 0,375 a 0,419) nas áreas de coleta, provavelmente devido a sua distribuição agrupada. As análises com Structure não identificaram duas populações baseadas nas áreas de coleta, mas sim dois agrupamentos genéticos baseados em conjuntos distintos de alelos. A maior parte da variação genética foi encontrada dentro das áreas de coleta (97%), enquanto encontrou-se uma fraca diferenciação genética entre as áreas (FST = 0,030). Um pouco menos de variação genética foi encontrada dentro dos grupos genéticos (93%), com um aumento correspondente na divergência (FST = 0,070). A não correspondência entre áreas de coleta e agrupamentos genéticos poderia ser devido a eventos históricos desconhecidos, mas, combinada com a alta diversidade encontrada, sugere que a endogamia atual não será um problema para um plano de manejo, embora o isolamento da Flona no futuro poderia contribuir para elevar a endogamia a níveis preocupantes. As informações aqui apresentadas servirão como linha base para comparação futura, orientando melhorias no plano de manejo.

This multifaceted study primarily aimed at understanding the genetic make-up of captive versus wild cheetah (Acinonyx jubatus) populations in South Africa, with a specific emphasis on a valuable gene pool of a recessive phenotype that is increasingly being maintained in captive population country-wide. The current literature on cheetah genetics has very little information on diversity levels of wild South African cheetahs, and no information on founder dynamics and genetic make-up of South African captive populations. Decisions on cheetah relocations are being made, implementing current conservation policy, from assumptions on origin and relatedness. This research compared population genetic parameters within the largest South African captive cheetah population to free-ranging Namibian and South African conspecifics. The study addressed concerns regarding excessive Namibian genetic introgression into the native captive population and established the extent of genetic variability and Namibian ancestry within the captive population. The study has attempted to address the rising concern among conservation officials with respect to illegal trade of wild-captured cheetahs, wild caught cheetahs that are sold as captive-bred after implanting a microchip. In addition to establishing routine parentage verification using genetic markers that are polymorphic in this species, this study established a technique powerful enough to estimate ancestry in cheetahs of unknown antecedents. The potential of spatial Bayesian clustering to differentiate the point of origin of unknown cheetahs was exploited and in addition, a database for future forensic efforts to address the problem of illegal trade was established. The captive population that was part of this dataset proved to be quite admixed, excepting for the King lineage which was distinct. The second aspect of this study investigated complex conditions such as development of gastritis, renal conditions and/or susceptibility to infections and its relation to pedigree and marker based inbreeding levels. Heritability values for important breeding traits were estimated from pedigree records of 532 cheetahs and are reported for the first time. Gastritis was weakly correlated to the expression of the King trait. Finally, a smaller cohort of the captive pedigree that segregates for a recessive colour variant called the King phenotype was tested for the assumption that the variation is a mutation of the tabby locus described in domestic cats. Genetic linkage analysis was done by testing microsatellite markers detected linked to Tabby for linkage to a conserved region in the cheetah that potentially codes for the King coat colour. Genetic linkage analysis was not detected between the King locus and the domestic cat microsatellite markers used for this study, with LOD scores remaining non-significant for all the markers. / Thesis (PhD)--University of Pretoria, 2011. / Production Animal Studies / unrestricted

The ability of natural selection to promote and preserve genetic variation at Major Histocompatibility Complex (MHC) class I loci was examined in two fish species known to have low genetic variation either as a consequence of their breeding system or population structure. The tempo and modes of molecular evolution acting on these loci has also been discussed. The marine killifish Rivulus marmoratus is the only vertebrate known to exist in nature in homozygous form. The findings of this study suggest that MHC class I genes at one locus in R. marmoratus have rapidly accumulated variation, particularly in region of the gene encoding functional important domains. This rapid accumulation of variation is likely due to the increased intensity of natural selection acting on these genes resulting from the homozygosity of the species. The contention that the variation characterized at one MHC locus is of recent origin is further supported by an analysis of the mitochondrial control region if R. marmoratus, which suggests that the individuals included in this study are recently diverged. The variation characterized here is the first evidence of genetic variation at coding loci in this species, and may be evidence of the cost of homozygosity for R. marmoratus. Variation at a single MHC class I locus was also characterized in several members of the Death Valley pupfish species complex. Two of these species, Cyprinodon diabolis and Cyprinodon salinus have undergone intense historical or ongoing population bottlenecks. Despite the action of random genetic drift acting on these species, both maintain multiple MHC class I alleles at one locus. The alleles characterized in C. diabolis and C. salinus were also recovered from other members of the Death Valley complex. This suggests that overdominant natural selection has acted to maintain ancestral genetic variation at this locus in both species. This result has important implications for the design of conservation programs for these endangered species, and may have broader implications for the design of captive breeding programs of species with highly reduced population sizes in general. / Ph. D.

Population structure in five African beef cattle breeds in South Africa was investigated, to assess the effect of animal recording in management of genetic diversity and genetic improvement. Pedigree records of 247,173 Afrikaner, 57,561 Boran, 198,557 Drakensberger, 256,692 Nguni and 55,309 Tuli breed were analysed using the online POPREP software system. Pedigree completeness over six generations varied with the lowest completeness in the Boran and the highest in the Afrikaner.The average generation interval ranged between 6.0 to 6.4 years. The rates of inbreeding per year were 0.03%, 0.04%, 0.06%, 0.07% and 0.08% in Boran, Nguni, Afrikaner, Drakensberger and Tuli respectively. Effective population sizes were 89, 107, 122, 191 and 364 in Tuli, Afrikaner, Drakensberger, Nguni and Boran respectively. Inbreeding and effective population size for the Boran was not a true reflection due to poor pedigree recording. These results indicate that none of the breeds are in critical limits of endangerment. Breeding values were regressed on birth year of each breed for weight traits; Kleiber ratio and scrotal circumference from 1986 to 2012. Genetic trends were stable for birth weights except the Afrikaner and Tuli. Genetic progress has been made in weaning and post weaning weights for all the breeds except for limited progress in the Nguni. Kleiber ratio and scrotal circumference in all measured breeds have shown good progress. The results of this study confirmed that recording of pedigree and performance records are effective in maintenance of genetic diversity and genetic improvement through selection based on EBVs of recorded traits. / Dissertation (MScAgric)--University of Pretoria, 2014. / tm2015 / Animal and Wildlife Sciences / MScAgric / Unrestricted

The objectives of this study were to: (1) quantify levels of genetic intermixing in remnant Illinois eastern woodrat populations augmented with Ozark woodrats, and (2) assess genetic health and population viability in remnant and reintroduced woodrat populations. This dissertation is arranged into 3 chapters. DNA extractions, microsatellite genotyping, and mtDNA haplotype sequencing were conducted for individuals from the western Shawnee National Forest (WSNF) (i.e., LaRue Pine Hills [LPH], Fountain Bluff, Horseshoe Bluff), eastern Arkansas (AR), southern Missouri (MO), and 5 locations in the eastern Shawnee National Forest (ESNF), Illinois. Genetic data provided a strong signal in STRUCTURE which confirmed MO, AR, and LPH were genetically distinct populations prior to the genetic augmentation at LPH. Following augmentation, eastern woodrats in ESNF and WSNF have experienced admixture with introduced populations, increased allelic richness, decreased inbreeding, and increased effective population size, while genetic swamping was not observed. Haplotypes from both introduced populations were observed after augmentation at LPH but neither were detected in adjacent remnant populations. Reintroduced populations in the ESNF are acting as a single population and descendants consist of primarily AR and MO individuals. Admixture was apparent in all ESNF populations and haplotypes from all source populations persisted. Effective population size was largest at Garden of the Gods but all 5 populations had similar allelic richness and heterozygosity. In the ESNF, migration is not supported between study populations and additional habitat management may be needed. Future population monitoring of the ESNF population should focus efforts in the 3 central populations which are likely source populations. Future eastern woodrat management efforts should focus on (1) connectivity between ESNF populations and (2) connectivity in the WSNF amongst remnant populations and between remnant and reintroduced populations in the central Shawnee National Forest. I recommend the establishment of migration corridors by decreasing canopy cover in the forested matrix and the establishment of artificial rock outcrops in the form of boulder piles along migration corridors. My study indicates that genetic augmentations can be a beneficial management action in isolated eastern woodrat populations having experienced loss in gene flow, while reintroductions can benefit woodrats in areas believed to have experienced local extirpation. I also recommend identifying genetic structure of source populations for genetic augmentations and reintroductions beforehand to confirm multiple source populations, genetic variation, and introduction of multiple alleles. As rodents often have short lifespans and individual reintroductions may fail to establish, genetic augmentations and reintroductions should include the relocation of multiple individuals over time via soft release.