Orientador: José Fernando Garcia / Banca: Joaquim Mansano Garcia / Banca: Adriana Santana do Carmo / Resumo: A pecuária bovina de corte da atualidade conta com o auxílio significativo dos programas de melhoramento genético animal para seu sucesso. O desenvolvimento de distintos métodos para realizar avaliações fenotípicas e genotípicas, tem o intuito de selecionar os rebanhos e obter animais geneticamente superiores com produção padronizada. A padronização produtiva de um rebanho deve ser resultante de acasalamentos dirigidos, que podem levar ao aumento da ocorrência de alelos homozigotos no genoma dos animais. Esse aumento da autozigosidade na população, isto é, o aumento do número de animais com alelos idênticos por descendência (IBD), provém do acasalamento entre indivíduos aparentados. Nesse contexto, a ferramenta mais robusta para identificar os fragmentos do genoma animal que são idênticos por descendência é a estimação do coeficiente de endogamia baseado nas corridas de homozigosidade (ROH), que é denominado (FROH). Eventos evolutivos, tais como: o processo de seleção natural, a deriva genética ou aleatória, e o gargalo populacional, podem ter contribuído com o aumento da autozigosidade e da ocorrência de alelos IBD no genoma de uma população resultante da reprodução entre indivíduos aparentados. Essa dissertação revisou o estado da arte do que concerne o estudo da endogamia determinada por análises genômicas (Capítulo 1), e aplicou tais conhecimentos na análise da distribuição dos níveis de autozigosidade baseado em corridas de homozigosidade (ROH) em 1.278 fêmeas da raça Nelore genotipadas para mais de 777 mil SNPs, e identificou regiões autozigotas possivelmente associadas à seleção natural, domesticação, fertilidade, evolução e adaptação dos bovinos (Capítulo 2). O presente estudo abre perspectivas para a realização de análises detalhadas que permitam a mensuração da influência da autozigosidade genômica causada pela pressão seletiva sobre alelos específicos em bovinos ... / Abstract: The current beef cattle chain has had significant help of animal breeding programs to its success. The development of different methods to perform phenotypic and genotypic evaluation has the objective of selecting flocks and producing genetically superior animals with standardized production. The productive standardization of a herd must be the result of directed matings, which can lead to increased incidence of homozygous alleles in the genome of animals. The increase of autozygosity in the population, i.e., increasing the number of animals with alleles identical by descent (IBD), is derived from the mating of related individuals. In this context, the most robust tool to identifies the animal's genome fragments that are identical by descent is the estimation of the inbreeding coefficient based on runs of homozygosity (ROH), which is called (FROH). Evolutionary events, such as the process of natural selection, random or genetic drift, and population bottleneck, may have contributed towards increasing the autozygosity and occurrence of IBD alleles in the genome of a population resulting crosses of related individuals. This thesis reviewed the state of the art with respect to the study of inbreeding determined by genomic analysis (Chapter 1), and applied this knowledge in the analysis of the distribution of autozygosity levels based on runs of homozygosity (ROH) in 1,278 Nelore females genotyped to more than 777,000 SNPs, and identified autozygote regions possibly associated with natural selection, domestication, fertility, evolution and adaptation of cattle (Chapter 2). This study open prospects for conducting detailed analysis on the influence of genomic autozygosity caused by selective pressure on specific alleles in Nelore cattle / Mestre

Orientador: Antonio Ismael Inácio Cardoso / Banca: Noberto da Silva / Banca: Cyro Paulino da Costa / Abstract: The objective of this work was evaluate the inbreeding depression with successive generations of self-pollination in a cucumber "caipira" population (S0, S1, S2, S3; S4 e S5), obtained by crossing Safira x Hatem hybrids. Two experiments were accomplished: one to evaluate immature fruits production and another to analyze the mature fruits production, seed quality and yield. The experimental design of both experiments were randomized blocks, in the first with seven treatments (different generations of self pollination - S0 to S5 and the hybrid Safira), six replicates and five plants per plot and in the second the same seven treatments, four replicates and five plants per plot. In the first experiment (immature fruits) was number of leaves, length of the main stem, number and weight of fruits, total and commercial, number of nodes and vines percentage were evaluated. In the second experiment (mature fruit) the following traits were evaluated characteristic: seed number and weight per plant and per fruit and seed quality (germination test, first counted of seeds, index of germination speed and weight of 100 seeds). The averages were compared by the Tukey test (5%) and the evaluation of the inbreeding depression was made with regression analysis. In the experiment 1 smaller production of fruits was observed (total and commercial) starting from population S2, demonstrating possible vigor loss. The populations S0 and S1 were similar or superiors for the characteristics number of total fruits, total weight per plant and commercial weight per plant when compared to the hybrid Safira, demonstrating the potencial of this population to obtain a new cultivar or hybrid of the "caipira" type. The experiment two there was no statistical difference for all the appraised characteristics, showing that the inbreeding didn't affect the production and quality of the seeds in this population. / Mestre

In order to establish a method of assessing the degree of inbreeding within herds of cattle, we constructed a calibration index relating kinship and the degree of DNA band sharing in DNA fingerprints. Firstly, chickens were used as a model system to test the possibility of using microsatellite DNA as a probe for DNA fingerprinting in inbreeding analysis. Six genetic groups of chickens with estimated coefficients of inbreeding ranging from 0.026 to $>$ 0.98 (pedigree analysis) were fingerprinted using the minisatellite probe derived from M13 and the microsatellite probe (CAC)$ sb5$. The degree of band sharing using either probe increased in concert with the known amount of inbreeding and was described by the equation Y = 0.56X ($ pm$0.06) + 0.42 ($ pm$0.03); r = 0.998. Since in-gel hybridization using the microsatellite probes was faster and less labour intensive than using the minisatellite probe, it was used in the subsequent studies. Pedigree analysis in Holstein dairy cattle allowed for the empirical calibration of the association of band sharing with the coefficient of relatedness, (r), defined as the expected proportion of genes in 2 individuals that are identical by descent (i.e. for monozygous twins r = 1; for first order relatives r = 0.5; for half sibs r = 0.25 etc.). The average band sharing between pairs (6 pairs at each r value) of individuals within each class formed the basis for calibration. DNA was digested using RsaI. The relationship between band sharing and relatedness was well represented by a linear approximation Y = 0.51X ($ pm$0.09) + 0.50 ($ pm$0.04); r = 0.992. Using this calibration curve, random samples of animals within herds can be tested to establish the herd variability and to minimize inbreeding.

Submitted by Ana Cristina Herrera Rios (anacristinah@gmail.com) on 2018-09-06T21:12:03Z No. of bitstreams: 1 Herrera_a_ma_jabo.pdf: 1549720 bytes, checksum: cc3a9f221086386bf628813bbc967443 (MD5) / Approved for entry into archive by Neli Silvia Pereira null (nelisps@fcav.unesp.br) on 2018-09-10T16:57:12Z (GMT) No. of bitstreams: 1 herrerarios_ac_dr_jabo.pdf: 1549720 bytes, checksum: cc3a9f221086386bf628813bbc967443 (MD5) / Made available in DSpace on 2018-09-10T16:57:12Z (GMT). No. of bitstreams: 1 herrerarios_ac_dr_jabo.pdf: 1549720 bytes, checksum: cc3a9f221086386bf628813bbc967443 (MD5) Previous issue date: 2018-07-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O uso intensivo de biotecnologias reprodutivas tem feito com que se eleve a taxa de nascimento de progênies com maior grau de parentesco (maior taxa de nascimento de meio-irmãos e irmãos completos). Assim, o conhecimento sobre o coeficiente da endogamia média do rebanho torna-se relevante para a eficiência do sistema de produção. Com o advento da genômica, o coeficiente de endogamia (F) pode ser estimado com base na informação de milhares de marcadores do tipo polimorfismos de base única (SNPs), espalhados por todo o genoma. No presente estudo, informações de 3.785 animais da raça Nelore (1,760 machos e 2,025 fêmeas) genotipados para 777.962 SNPs do BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) foram utilizadas com o objetivo de avaliar a taxa de endogamia em rebanhos comerciais da raça Nelore, bem como investigar o seu efeito (depressão endogâmica) sobre a expressão fenotípica de características reprodutivas (idade ao primeiro parto (IPP), ocorrência de prenhez precoce (OPP) e reconcepcão de novilhas (REC)). A estimativa do valor de F, bem como da depressão endogâmica, foi feita utilizando diferentes metodologias: (i) matriz de parentesco genômica com frequências alélicas obtidas da população base (FG); (ii) matriz de parentesco genômica com frequências alélicas fixadas em 0,5 (FGRM); (iii) com base no excesso de SNPs em homozigose (FSNP); e (iv) corrida de homosigose (FROH). Os resultados da corrida de homosigose também foram utilizados para identificar os padrões (tamanho e distribuição) dos segmentos ROH na raça Nelore bem como para identificar ilhas de homosigose (segmentos ROH compartilhados por mais de 50% da população). Foram identificados 210.636 segmentos ROH distribuídos nos 29 autossomos e cinco ilhas de homozigose localizadas nos cromossomos 5, 7, 12, 21 e 26, nas quais 43 genes foram identificados. Alguns destes genes (INHBE, INHBC, STAT6, FGF8 e DPCD) foram previamente associados com caracteristicas reproductivas, de crescimento, resposta inmume e adaptabilidade em bovinos. As médias para o coeficiente de endogamia calculado com base nas diferentes abordagens foram: -0,0006 (FG), 0,4376 (FGRM), 0,5500 (FSNP) e 0,0590 (FROH). As correlações foram ente baixas FG-FSNP (-0,28), FG-FGRM (-0,20), FG-FROH (0,21), a moderadas FROH-FSNP (0,68), FROH-FGRM (0,72) e fortemente alta para FSNP-FGRM (0,99). O valor médio de F variou de acordo com a metodologia utilizada. O valor extremamente alto do FSNP denota que este método tende a superestimar as taxas de endogamia. Independentemente do método utilizado para obter os valores de F, foi verificado que o aumento de 1% no coeficiente de endogamia médio do rebanho influenciou desfavoravelmente a média das características reprodutivas avaliadas. / The intensive use of reproductive biotechnologies has increased the birth rate of progenies with high degree of relationships (higher birth rate of half- and full-sibs). Thus, the control of herd inbreeding becomes relevant for the efficiency of the production system. With genomics, the inbreeding coefficient can be estimated using thousands of single nucleotide polymorphisms (SNPs), spread throughout the genome. In the present study, information of 3,785 Nelore animals (1,760 males and 2,025 females) genotyped with 777,962 SNP markers of BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) was used with the objective of evaluating the inbreeding rates of Nelore commercial herds, as well as to investigate the effects of inbreeding (inbreeding depression) on the phenotypic expression of reproductive traits (age at first calving (AFC), heifer early pregnancy (EP), and heifer rebreeding (HR)). The inbreeding coefficient (F) and inbreeding depression were estimated based on (i) genomic relationship matrix considering allele frequencies estimated from the base population (FG); (ii) genomic relationship matrix considering allele frequencies fixed at 0.5 (FGRM); (iii) excess of homozygous SNPs (FSNP); and (iv) runs of homozygosity (FROH). The runs of homozygosity results were also used to identify the pattern (size and distribution) of ROH segments as well as to identify ROH islands (ROH segments shared by more than 50% of the population). In total, there were identified 210,636 ROH segments and five ROH Islands located on the chromosomes 5, 7, 12, 21 and 26, in which 43 annotated genes were identified. Some of these genes (INHBE, INHBC, STAT6, FGF8 and DPCD) were previously associated with reproduction and growth traits, inmume response and adaptability in cattle. The average inbreeding calculated based on different approaches were -0.0006 (FG), 0.4376 (FGRM), 0.5500 (FSNP) e 0.0590 (FROH). These correlations ranged from low FG-FSNP (-0.28), FG-FGRM (-0.20), FG-FROH (0.21), to moderated FROH-FSNP (0.68), FROH-FGRM (0.72) and extremely high FSNP-FGRM (0.99). The average population inbreeding coefficient ranged according to the method used. The extremely high value of FSNP indicates that this approach tend to overestimate the inbreeding rates. Independently of the method used to obtain the F values, it was verified that the increase of 1% in the average herd inbreeding unfavorably influenced the mean value of the evaluated reproductive traits. / FAPESP#2009/16118-5

A switch from hunting to beginnings of farming and agriculture was a crucial step for humans and for developing civilization. This period was suitable for domestication processes. Dogs were the first domesticated animals at all. Their breeding was connected with settlement and cattle protection and they were used as shepherd and hunting dogs. In some cultures they are even used as food source. Recent trends lead to breeding of new breeds and division of original gene pool into smaller closed groups which lead to an increase of homozygosity and to display recessively inherited diseases. These effects are mostly visible in small local breeds that have a small population size. Global protection of genetic diversity in cattle, poultry and pigs was already addressed in many studies, probably because of the high economic value of these animals. Impact of domesticated carnivores to humans is comparable and due to the growing market in veterinary services it is needed to protect sufficient genetic variability of various unique races. The aim of this work is to compare selected local breeds of dogs from different regions of origin, to evaluate their overall genetic diversity, to determine the occurrence of candidate types of diseases and to compare the frequency of these diseases in selected breeds. Main output is to recommend appropriate methods to protect the gene pool of these unique races. Central European breed (e.g. Český Fousek), subtropical breed (e.g. Sarplaninec), tropical continental breed (eg. Basenji), tropical island breed (e.g. The New Guinea Singing Dog) will be selected. The material will be collected at exhibitions and in cooperation with local farmers. The samples will be processed by classical methods of population genetics in the laboratory of molecular genetics FTZ ČZU.

Made available in DSpace on 2015-06-17T19:34:01Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-12-18. Added 1 bitstream(s) on 2015-06-18T12:47:35Z : No. of bitstreams: 1 000830516.pdf: 435277 bytes, checksum: f6acf506d25f52c5bef6c02d3894fa15 (MD5) / A pecuária bovina de corte da atualidade conta com o auxílio significativo dos programas de melhoramento genético animal para seu sucesso. O desenvolvimento de distintos métodos para realizar avaliações fenotípicas e genotípicas, tem o intuito de selecionar os rebanhos e obter animais geneticamente superiores com produção padronizada. A padronização produtiva de um rebanho deve ser resultante de acasalamentos dirigidos, que podem levar ao aumento da ocorrência de alelos homozigotos no genoma dos animais. Esse aumento da autozigosidade na população, isto é, o aumento do número de animais com alelos idênticos por descendência (IBD), provém do acasalamento entre indivíduos aparentados. Nesse contexto, a ferramenta mais robusta para identificar os fragmentos do genoma animal que são idênticos por descendência é a estimação do coeficiente de endogamia baseado nas corridas de homozigosidade (ROH), que é denominado (FROH). Eventos evolutivos, tais como: o processo de seleção natural, a deriva genética ou aleatória, e o gargalo populacional, podem ter contribuído com o aumento da autozigosidade e da ocorrência de alelos IBD no genoma de uma população resultante da reprodução entre indivíduos aparentados. Essa dissertação revisou o estado da arte do que concerne o estudo da endogamia determinada por análises genômicas (Capítulo 1), e aplicou tais conhecimentos na análise da distribuição dos níveis de autozigosidade baseado em corridas de homozigosidade (ROH) em 1.278 fêmeas da raça Nelore genotipadas para mais de 777 mil SNPs, e identificou regiões autozigotas possivelmente associadas à seleção natural, domesticação, fertilidade, evolução e adaptação dos bovinos (Capítulo 2). O presente estudo abre perspectivas para a realização de análises detalhadas que permitam a mensuração da influência da autozigosidade genômica causada pela pressão seletiva sobre alelos específicos em bovinos ... / The current beef cattle chain has had significant help of animal breeding programs to its success. The development of different methods to perform phenotypic and genotypic evaluation has the objective of selecting flocks and producing genetically superior animals with standardized production. The productive standardization of a herd must be the result of directed matings, which can lead to increased incidence of homozygous alleles in the genome of animals. The increase of autozygosity in the population, i.e., increasing the number of animals with alleles identical by descent (IBD), is derived from the mating of related individuals. In this context, the most robust tool to identifies the animal's genome fragments that are identical by descent is the estimation of the inbreeding coefficient based on runs of homozygosity (ROH), which is called (FROH). Evolutionary events, such as the process of natural selection, random or genetic drift, and population bottleneck, may have contributed towards increasing the autozygosity and occurrence of IBD alleles in the genome of a population resulting crosses of related individuals. This thesis reviewed the state of the art with respect to the study of inbreeding determined by genomic analysis (Chapter 1), and applied this knowledge in the analysis of the distribution of autozygosity levels based on runs of homozygosity (ROH) in 1,278 Nelore females genotyped to more than 777,000 SNPs, and identified autozygote regions possibly associated with natural selection, domestication, fertility, evolution and adaptation of cattle (Chapter 2). This study open prospects for conducting detailed analysis on the influence of genomic autozygosity caused by selective pressure on specific alleles in Nelore cattle

Abstract The evolution of microsatellites was studied within and between the pine species. Sequences showed that microsatellites do not necessarily mutate in a stepwise fashion and that size homoplasy is common due to flanking sequence and repeat area changes within and between the species. Thus, some assumptions of statistical methods based on changes in repeat numbers may not hold. Sequences from cross-species amplifications revealed evidence of duplications of microsatellite loci in pines. On two independent occasions, the repeat area of the microsatellite had undergone a rapid expansion during the last 10-25 million of years. Microsatellite markers were used together with other molecular markers (allozymes, RFLPs, RAPDs, rDNA RFLPs) and an adaptive trait (date of bud set) to study patterns of genetic variation in Scots pine (Pinus sylvestris) in Finland. All molecular markers showed high level of within population variation, while differentiation among populations was low (FST = 0.02). Of the total variation in bud set, 36.4 % was found among the populations which experience a steep climatic gradient. Thus, the markers applied were poor predictors of population differentiation of the quantitative trait studied The distribution of genetic variation was studied in five natural populations of radiata pine (Pinus radiata), species which has gone through bottlenecks in the past. Null allele frequencies were estimated and used in later analyses. Microsatellites showed high level of variability within populations (He = 0.68-0.77). Allele length distributions and average number of alleles per locus showed some traces of bottlenecks. Instead, comparison of observed genetic diversities and expected diversities suggested post-bottleneck expansion of populations. Genetic differentiation (FST and RST) among populations was over 10 %, reflecting situation in the isolated radiata pine populations. Using microsatellites and a newly developed Bayesian method, individual inbreeding coefficients were estimated in five populations of radiata pine. Most individuals were outbred while some were selfed. Presumably, in ancestral radiata pine populations the recessive deleterious alleles have been eliminated after bottlenecks and the mating system has changed as a consequence.

No description available.

Intensive selection for increased milk production over many generations has led to growing genetic similarity and increased relationships in dairy population. In the current study, inbreeding depression was estimated for number of days to first service, summit milk, conception by 70 days non-return, and calving rate with a linear mixed model (LMM) approach and for calving difficulty, calf mortality with a Bayesian threshold model (BTM) for categorical traits. Effectiveness of classical and unknown parentage group procedures to estimate inbreeding coefficients was evaluated depending on completeness of a 5-generation pedigree. A novel method derived from the classical formula to estimate inbreeding was utilized to evaluate completeness of pedigrees. Two different estimates of maternal inbreeding were fitted in separate models as a linear covariate in combined LMM analyses (Holstein registered and grade cows and Jersey cows) or separate analyses (registered Holstein cows) by parity (1-4) with fetal inbreeding. Impact of inbreeding type, model, data structure, and treatment of herd-year-season (HYS) on magnitude and size of inbreeding depression were assessed. Grade Holstein datasets were sampled and analyzed by percentage of pedigree present (0-30%, 30-70% and 70-100%). BTM analyses (sire-mgs) were performed using Gibbs sampling for parities 1, 2 and 3 fitting maternal inbreeding only. In LMM analyses of grade data, the least pedigree and diagonal A matrix performed the worst. Significant inbreeding effects were obtained in most traits in cows of parity 1. Fetal inbreeding depression was mostly lower than that from maternal inbreeding. Inbreeding depression in binary traits was the most difficult to evaluate. Analyses with non-additive effects included in LMM, for data by inbreeding level and by age group should be preferred to estimate inbreeding depression. In BTM inbreeding effects were strongly related to dam parity and calf sex. Largest effects were obtained from parity 1 cows giving birth to male calves (0.417% and 0.252% for dystocia and calf mortality) and then births to female calves (0.300% and 0.203% for dystocia and calf mortality). Female calves from mature cows were the least affected (0.131% and 0.005% for dystocia and calf mortality). Data structure was found to be a very important factor to attainment of convergence in distribution. / Ph. D.

O monitoramento da endogamia é fundamental para o estabelecimento de um programa de melhoramento animal. Os coeficientes de endogamia foram estimados a partir de segmentos de homozigose (FROH), matriz de parentesco genômico com frequências alélicas derivadas dos dados (FGRM), frequências alélicas ajustadas a 0,5 (FGRM05), excesso de homozigose (FHOM) e informação de pedigree (FPED) em bovinos Nelore e ovelhas Santa Inês. Os dados genotípicos para a população Nelore foram obtidos de 2.569 animais utilizando um painel de 725,293 polimorfismos de nucleotídeo único e um pedigree composto por 15.846 indivíduos. Para a população de ovinos Santa Inês, 576 animais foram genotipados para 47.033 polimorfismos de nucleotídeo único, juntamente com dados de pedigree de 32.266 indivíduos. Picos notáveis nos cromossomos 7, 12 e 21 dos bovinos e no cromossomo 16 das ovelhas, representavam ilhas de ROH (> 47%), destacando regiões possivelmente afetadas pela pressão seletiva. Os valores médios para FPED, FROH, FGRM e FGRM05 foram 0,005, 0,058, -0,007 e 0,40, respectivamente no caso do Nelore, enquanto valores medias de 0,32, 0,049, 0,015, 0,287 e 0,015 para FPED, FROH, FGRM, FGRM05 e FHOM, respectivamente no caso das ovelhas. Esses coeficientes de endogamia foram associados negativamente com peso ao nascer, peso à desmama, ganho de peso pós-desmame, escore de muscularidade, precocidade, conformação e circunferência escrotal em bovinos Nelore e para todas as características analisadas em Santa Inês. Também foi encontrada uma correlação negativa entre depressão endogâmica e estimativas de variâncias genômicas de dominância variando de -0,35 a -0,98 para Nelore e -0,89 a -0,91 para ovinos Santa Inês. Nós afirmamos que as descobertas relatadas podem ser usadas para manter a diversidade genética em bovinos Nelore e ovelhas Santa Inês sob uma perspectiva genômica. / Monitoring inbreeding is critical for establishing a sustainable breeding program. Inbreeding coefficients were estimated from runs of homozygosity (FROH), genomic relationship matrices coupled with allele frequencies derived from data (FGRM), allele frequencies set to 0.5 (FGRM05), excess of homozygosity (FHOM), and pedigree information (FPED) from Nellore cattle and Santa Ines populations. Genotypic data for the Nellore population were obtained from 2,803 animals using a panel of 725, 293 single-nucleotide polymorphisms and a pedigree consisting of 15,846 individuals. For the Santa Ines sheep population 576 animals were genotyped for 47,033 single-nucleotide polymorphisms along with pedigree data of 32,266 individuals. In cattle noticeable peaks on chromosome 7, 12, and 21, and in sheep on chromosome 16, represented hotspots of autozygosity (> 47%), highlighting putative regions affected by selective pressure. The mean values for FPED, FROH, FGRM, and FGRM05 were 0.005, 0.058, -0.007, and 0.40, respectively for Nellore, while for Santa Ines were 0.32, 0.049, 0.015, 0.287 and 0.015 for FPED, FROH, FGRM, FGRM05 and FHOM, respectively. These inbreeding coefficients were negatively associated with birth weight, weaning weight, post-weaning weight gain, muscularity score, finishing score, conformation score, and scrotal circumference on Nellore and for all traits analyzed on Santa Ines. Also, a negative correlation was found between inbreeding depression and estimates of dominance genomic variances ranging from -0.35 to -0.98 for Nellore and -0.89 to -0.91 for Santa Ines sheep. We contend that the findings reported here can be used to maintain genetic diversity in Nellore cattle and Santa Ines sheep from a genomic perspective.