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This thesis presents a statistical approach which incorporates pedigree information in the form of relationship matrices into the analysis of standard agricultural genetic trials, where elite lines are tested. Allowing for the varying levels of inbreeding of the lines which occur in these types of trials, the approach involves the partitioning of the genetic effect of lines into additive genetic effects and non-additive genetic effects. The current methodology for creating relationship matrices is developed and in particular an approach to create the dominance matrix under full inbreeding in a more efficient manner is presented. A new method for creating the dominance matrix assuming no inbreeding is also presented. The application of the approach to the single site analyses of wheat breeding trials is shown. The wheat lines evaluated in these trials are inbred lines so that the total genetic effect of each of the lines is partitioned into an additive genetic effect and an epistatic genetic effect. Multi-environment trial analysis is also explored through the application of the approach to a sugarcane breeding trial. The sugarcane lines are hybrids and therefore the total genetic effect of each hybrid is partitioned into an additive genetic effect, a heterozygous dominance genetic effect and a residual non-additive genetic effect. Finally, the approach for inbred lines is examined in a simulations study where the levels of heritability and the genetic variation as a proportion of total trial variation is explored in single site analyses. / Thesis (Ph.D.) - University of Adelaide, School of Agriculture, Food and Wine, 2008

Thesis--University of Washington. / Vita. Another copy has number: Thesis 27614. Bibliography: leaves [152]-155.

Massive declines in the latter half of the 20th century left black rhinoceros populations perilously close to extinction with only approximately 3600 individuals remaining, in contrast to estimated census numbers of over 100,000 individuals in 1900. While Diceros bicornis bicornis is the second most abundant subspecies of black rhino, behind D. b. minor, relatively few genetic studies have focused on this taxon. I used polymorphic DNA microsatellite markers to describe population structure in this subspecies. Using these genetic markers, the goals of this study were: i) to characterize the genetic variability of D.b. bicornis individuals (n = 170) found in Etosha National Park, Namibia, using seven DNA microsatellite markers, ii) to determine if there is population structure within Etosha National Park, using both traditional Wright’s F-statistics and a Bayesian model that requires no a priori population assignment, iii) to determine relatedness amongst founding and newly introduced black rhinoceroses held in private game farms throughout Namibia, using moment estimators of relatedness; and iv) to determine parentage of game farm rhinos with partial or no pedigree data available, using likelihood-based methods. I found that: i) the levels of genetic diversity in D.b. bicornis from Etosha National Park are consistent with previously published studies using microsatellite markers, and are relatively high; ii) the population structure within Etosha National Park is ambiguous using traditional F-statistics, but can be subdivided into three diagnosable clusters (western, central and eastern) using a Bayesian approach; iii) a relatively high degree of relatedness exists among founding members of game farm rhinos; and iv) assignments of parentage had greater success when there were fewer candidate parents and support the notion that black rhinoceroses are polygynous. / Thesis (Master, Biology) -- Queen's University, 2009-06-01 10:18:14.064

Submitted by RAFAEL LARA TONUSSI null (rafaeltonussi@yahoo.com.br) on 2017-01-18T17:45:01Z No. of bitstreams: 1 tese_Rafael_Lara_Tonussi.pdf: 1385325 bytes, checksum: ea9dbc49d8fec3ee26a2a139e1dd0baf (MD5) / Rejected by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br), reason: Solicitamos que realize uma nova submissão seguindo a orientação abaixo: Incluir o número do processo de financiamento FAPESP nos agradecimentos da dissertação/tese. Corrija esta informação e realize uma nova submissão com o arquivo correto. Agradecemos a compreensão on 2017-01-23T19:14:45Z (GMT) / Submitted by RAFAEL LARA TONUSSI null (rafaeltonussi@yahoo.com.br) on 2017-01-24T10:46:09Z No. of bitstreams: 1 tese_Rafael_Lara_Tonussi.pdf: 1384474 bytes, checksum: 3424ccffa913eaba43458f131eef937b (MD5) / Approved for entry into archive by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br) on 2017-01-25T16:33:51Z (GMT) No. of bitstreams: 1 tonussi_rl_dr_jabo.pdf: 1384474 bytes, checksum: 3424ccffa913eaba43458f131eef937b (MD5) / Made available in DSpace on 2017-01-25T16:33:51Z (GMT). No. of bitstreams: 1 tonussi_rl_dr_jabo.pdf: 1384474 bytes, checksum: 3424ccffa913eaba43458f131eef937b (MD5) Previous issue date: 2016-12-14 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Reprodutores múltiplos (RM) é o sistema de manejo mais comum em produção de bovinos de corte principalmente devido a facilidade e baixo custo de manejo. No entanto, RM não permite a identificação de paternidade, tornando o pedigree incompleto um dos principais obstáculos para avaliações genéticas precisas. Existe um crescente interesse na investigação do uso de dados genômicos em modelos com paternidade incerta, visando aumentar a acurácia e diminuir o viés nas avaliações genéticas. Portanto, o objetivo desse estudo foi investigar a aplicação do BLUP e single step genomic BLUP (ssGBLUP) em diferentes cenários com paternidade incerta utilizando dados simulados e reais em bovinos de corte. Foram simulados genótipos, pedigree e fenótipos para idade ao primeiro parto (IPP) e peso aos 550 dias (P550) utilizando herdabilidades baseadas em dados reais (0,12 para IPP e 0,34 para P550). O genoma foi simulado com um comprimento total de 2.333 cM, com 735.293 marcadores bialélicos e 7.000 QTL distribuídos aleatoriamente ao longo dos 29 cromossomos. Foi assumido que os QTLs explicaram 100% da variância genética. Para QTL, a quantidade de alelos variou aleatoriamente de dois a quatro por loci. Foram estudados cenários com 0%, 25%, 50%, 75% e 100% de RM e foram testados quatro tipos de escalas entre as matrizes G e A22. A acurácia e viés foram calculados para cincos grupos: ALL = todos os animais; BULL = apenas touros; GEN = animais genotipados, FEM = fêmeas e YOUNG = machos jovens. O uso da informação genômica no modelo (ssGBLUP) apresentou acurácia maior (variando de 0,31 a 0,97) do que o BLUP tradicional (variando de 0,05 a 0,97), especialmente no grupo YOUNG. No estudo com dados reais, todos os modelos incluíram grupos de contemporâneos e classe de idade da vaca como efeitos fixos. A acurácia do valor genético (EBV / GEBV) foi calculada em cada cenário para oito grupos de animais: ALL = todos os animais, BULL = apenas touros com dez ou mais progênies; GEN = animais genotipados, GENwithPHEN = animais genotipados com fenótipos, GENwithoutPHEN = animais genotipados sem fenótipos, YOUNG = machos e fêmeas jovens sem fenótipos, YwithoutGEN = animais jovens sem fenótipos e genótipos e YwithGEN = animais jovens sem fenótipos e com genótipos. As acurácias do EBV (método BLUP) variaram de 0,02 a 0,46 para P455 e 0,04 a 0,18 para IPP, enquanto que as acurácias do GEBV (ssGBLUP) variaram de 0,13 a 0,48 para P455 e 0,16 a 0,33 para IPP. Os resultados obtidos com dados simulados e reais mostraram que acurácias do EBV e GEBV diminuíram à medida que as proporções de RM aumentaram. Além disso, o uso da informação genômica na avaliação genética pelo ssGBLUP aumentou a acurácia da avaliação, especialmente para animais com menos informações e para animais jovens. / Multiple service sire (MS) is the most common mating system in extensive beef production systems mainly due the facility and low management cost. However, MS does not allow the paternity identification, which makes the incompleteness of pedigree one of the main obstacles for accurate genetic evaluations. There is a grown interest to investigate the use of genomic data in uncertain paternity models aiming to increase the accuracy and to decrease bias in genetic evaluations. Therefore, the objective of this study was to investigate the application of BLUP and single step genomic BLUP (ssGBLUP) under different scenarios of uncertain paternity, using simulated and real data in beef cattle population. Genotypes, pedigree, and phenotypes for age at first calving (AFC) and weight at 550 days (W550) were simulated using heritabilities based on real data (0.12 for AFC and 0.34 for W550). The simulated genome had a total length of 2,333 cM, with 735,293 biallelic markers and 7,000 QTLs randomly distributed over 29 BTA. It was assumed that QTLs explained 100% of the genetic variance. For QTL, the amount of alleles per loci ranged randomly from two to four. Uncertain paternity scenarios using 0%, 25%, 50%, 75%, and 100% were studied. Four ways of scaling the mean of the genomic matrix (G) to match the mean of the pedigree relationship matrix among genotyped animals (A22) were tested. Accuracy, bias and inflation were investigated for five groups of animals: ALL = all animals; BULL = only bulls; GEN = genotyped animals; FEM = females; YOUNG = young males. The use of genomic information in the model (ssGBLUP) provided more accurated prediction (ranging from 0.31 to 0.97) than traditional BLUP (ranging from 0.05 to 0.97), especially in the YOUNG group. In real data, all models included contemporary groups and age at calving in classes as fixed effects. The accuracy of the estimated breeding value (EBV/GEBV) prediction was calculated in each scenario with eight groups of animals: ALL = all animals in the population, BULL = only bulls with ten or more progenies; GEN = genotyped animals, GENwithPHEN = genotyped animals with phenotypes, GENwithoutPHEN = genotyped animals without phenotypes, YOUNG = male and female young animals without phenotypes, YwithoutGEN = young animals without phenotypes and genotypes, and YwithGEN = young animals without phenotypes and with genotypes. Accuracies of EBV (BLUP method) ranged from 0.02 to 0.46 for W450 and 0.04 to 0.18 for AFC, while the accuracies of GEBV (ssGBLUP) ranged from 0.13 to 0.48 for W450 and 0.16 to 0.33 for AFC. The results obtained in simulated and real data showed that EBV and GEBV accuracy decreased as the proportion of MS increased. Additionally, the use of genomic information in the genetic evaluation by ssGBLUP increases the accuracy of evaluation, especially for animals with few number of information, such as young animals. / FAPESP: 2013/25910-0

Anolis carolinensis has been a model organism for ecology and evolutionary biology since the seventies, yet there are still understudied aspects of their ecology. A five-year study has provided microsatellite genotypes to be used in building a pedigree and assess relatedness, enabling us to evaluate the spatial distribution of an urban population of A. carolinensis. Results indicate no correlation between a male’s size and the distance others keep from it; however, males belonging in the heavyweight morph are dictating the spatial distribution in this population. In addition, juvenile dispersal of male offspring and partial philopatry of female offspring are key in this dynamic, where a single heavyweight male will actively defend a small area that contains multiple females, some of which are be daughters, and multiple unrelated males, most likely sneaker males.

In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within < 50 kb indicating that > 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.

This thesis is an investigation into the possible genetic background underlying the liability of Standardbred racehorses (Std) to atrial fibrillation (AF). Pedigrees of 204 affected Std admitted to the Ontario Veterinary College Teaching Hospital (OVCTH) for treatment of AF born from 1978 to 2007 and of 1,017 randomly selected racing contemporaries (5 for each Std admitted). Estimates of heritability of AF were obtained using a linear threshold animal model. Marginal genetic contributions of ancestors to affected and control cohorts were determined and differences were tested. The estimate of heritability of AF in the Std was 14% on the observed scale. Eleven ancestors had significantly higher contributions to affected cohorts than to controls. Many of these ancestors appeared multiple times in the five-generation pedigrees of affected horses. Results strongly indicate a genetic predisposition to AF in the Std, with the arrhythmia particularly prevalent in one popular sire line.

The objective of this thesis was to investigate the genomic changes that have occurred due to the effects of long-term artificial selection applied by soybean breeders. A total of 42 cultivars from six different breeding programs, comprising the multi-generational pedigree of OAC Bayfield were genotyped with molecular markers and chromosomal inheritance was tracked throughout the pedigree. The graphical genotype profile of the 20 chromosomes revealed substantial allelic structure that has been built up in certain chromosomes, in the form of specific linkage blocks, which have been conservatively inherited. A selective sweep analysis using microsatellite markers was performed using the members of OAC Bayfield’s pedigree to identify genomic regions that have retained a molecular selective signature through OAC Bayfield in the varieties derived from it. Overall, there was a high level of agreement between the identified quantitative trait loci (QTL) and the phenotypic traits that would have been expected to be under breeders’ selection.

Thesis (Ph. D.)--University of Washington, 1997. / Vita. Includes bibliographical references (leaves [110]-123).