The consequences of complications during calving are currently costing the UK dairy cattle industry approximately £110 for a calving of moderate difficulty and £400 for one that is severe. With incidences of difficult first calvings reaching 24% and 4% for a moderate and severe difficult calving respectively, reducing calving complications would be of great benefit to the UK dairy cattle industry. This PhD evaluates (i) the importance, (ii) the most optimal way, and (iii) the potential consequences of genetically selecting for two main traits associated with calving complications, calving ease (CE) and stillbirth (SB). For this, approximately 50.000 first parity and 300.000 later parity national calving data records were kindly provided by two major milk recording organisations in the UK. The work carried out shows that detrimental effects following a difficult first calving are long-lasting as subsequent performance of both the dam and the calf involved is worsened. Fertility of the dam is negatively affected by a difficult calving resulting in an increased calving interval and decreased ability to conceive. A reduction in milk production of a veterinary assisted dam, compared to a non-assisted dam, was detected in the first part of lactation. Veterinary assisted born calves showed a significantly lower milk yield, compared to farmer assisted calves, throughout their first lactation as adult heifers suggesting that the physiological effects, or causes underlying a difficult birth, are long lived. The study advises that genetic parameters of calving traits are to be estimated with an extended sire multi-trait model (accuracy vs. practicality). On average, direct and maternal heritabilities for calving traits are low. A highly heritable indicator trait such as gestation length (GL) can aid in the estimation of genetic parameters for CE and SB although genetic correlations of these traits with GL are moderate. A significant negative genetic direct-maternal correlation was found for CE in first parity recommending farmers to consider both direct and maternal genetic merit for CE when making a selection decision. CE and SB are highly positively correlated traits. GL is maternally correlated to SB in first parity and directly to CE in later parities, both correlations are positive. Estimated genetic correlations with other important traits in dairy cattle breeding show that CE and GL are both directly and maternally related to important selection traits which need to be taken into account if implementation into breeding indices occurs. Results advise limiting the use of GL to benefit the prediction of parameters for low heritable calving traits rather than selecting on GL itself. Genetic correlations suggest that individuals born easily are genetically prone to high milk yield and have reduced fertility in first lactation. Difficult calving heifers are likely to be associated with being wide and deep and high producing animals with a reduced ability to subsequently conceive. Individuals that are born relatively early are associated with good genetic merit for milk production. And finally, individuals carrying their young longer are genetically associated with being wide and large animals that were born relatively early themselves. Lastly, an extension of the current univariate genomic model to a bivariate model, which allows for a possible genetic direct-maternal covariance, shows that improvement in accuracy of genomic breeding values can be gained from use of a bivariate genomic model for maternal traits such as CE. Further development of the model is however recommended prior to the publication of genomic proofs for CE or any other maternal trait. Genetic selection can serve as a tool in the reduction of difficult calvings. The results of this thesis serve to let this happen in a controlled and sustainable manner.

Genetic evaluations for sport horses are performed by many Northern European studbooks, and estimated breeding values - which aid the selection of horses for breeding progeny with good competing ability - are routinely published. Either competition data or young horse evaluation data, or frequently a combination of both is used. Genetic evaluations are not yet performed in GB, and to date the only research conducted has been for the sport of eventing. The aims of this thesis were to: i) perform genetic evaluations for performance in dressage, including considering the effect of breed, ii) perform genetic evaluations for eventing, extending previous work, by using and comparing different methods of producing large (co)variance matrices and using a larger dataset, iii) characterise for the first time data recorded in the recently established young horse evaluation scheme, and if possible perform genetic evaluations and iv) investigate the suitability of international performance data for genetic evaluations for showjumping. Competition data was obtained from the national competition bodies and young horse evaluation data from the British Equestrian Federation. Pedigree was sourced from both. Appropriate mixed effects models were developed; animal models were used where pedigree data was sufficient, and sire models otherwise. Variance components were estimated using residual maximum likelihood and estimated breeding values were predicted using best linear unbiased prediction. Eventing comprises 3 disciplines, each with 4 grades i.e. 12 traits. For the evaluation, multivariate variance component analysis was performed, using and comparing three different methods of estimating the large 12 by 12 (co)variance matrices required for breeding value prediction. Significant, but low, heritabilities were found for dressage (0.07 – 0.09) and showjumping (0.09 – 0.16), and in the lower grades of cross-country (0.01), indicating that genetic progress for competition performance can be made by selection, particularly in showjumping. Genetic correlations within dressage and showjumping were high whereas those across disciplines were generally low and only significant for some of the lower grades, particularly between dressage and showjumping. Twelve breeding values were predicted for each horse. The methods based on combining covariance matrices from bivariate analyses were found to be the most reliable. In the dressage evaluations, significant heritabilites of 0.15 without accounting for breed effects and 0.11 when accounting for breed were found. Breed had a significant effect on competition performance, with warmbloods performing better than other breed groups. The model including breed was found to be the most appropriate for genetic evaluations in GB, although not currently implementable in practice due to limited recording of the breed identifier. In the young horse scheme, owners select which discipline (dressage, showjumping or eventing) their horse will enter. Traits are then recorded within the intended discipline. For the analyses, a genetic correlation of 1.0 was assumed between the same trait recorded in different disciplines. Significant, moderate, heritabilites were found for all five traits – veterinary (0.25), type and temperament (0.42), athleticism (0.20), conformation (0.29) and correctness of paces (0.30). The young horse scheme appears to be successful in establishment and uptake. Evaluations were performed for showjumping using international competition data. The small size of the dataset (approximately 6239 records on 479 horses) and large degree of selection limited the study. A larger dataset, including national data, needs to be made available to perform more accurate evaluations. However, an upper limit on the heritability was estimated to be 0.09 (standard error 0.012). This study explored the use of competition and young horse data for genetic evaluations. The eventing evaluations were the most reliable, and breeding values have been estimated which are ready for publication. However, there are certain limitations to all the competition data sources; there was selection in the data available for dressage and showjumping that biases the analyses. In addition, there were general limitations in the recording of competing horses, and in pedigree recording that limit the accuracy of the analysis. The young horse data represents a very valuable data source for genetic evaluations, although the scheme is still in its early stages. Ultimately, the most appropriate genetic evaluations will likely use a combination of young horse data and adult competition data. Further work can now perform multi-trait genetic evaluations using multiple data sources, such as combining young horse and competition data, or multiple competition disciplines.

The reliability of genetic evaluations across separate management units (e.g. flocks) depends on the extent of genetic links or connections among animals in these units. Where poor connectedness exists, comparisons of estimated breeding values (EBV) across units may be biased. The objectives of this study were to identify breeding strategies to increase connectedness among units, to evaluate statistics that may reflect the reduction in bias as connectedness increases in such strategies, and to assess levels of connectedness in Suffolk and Targhee flocks participating in the National Sheep Improvement Program. Expectations of bias when production units have different genetic means were derived for a simple sire model. These expectations were applied to data involving two flocks of animals with three different types of connections: sharing of a common reference sire or use of either a full- or half-sibling sire in each flock. Bias decreased as numbers of progeny in each flock increased for all methods. Linking through a reference sire was most effective and was the only method that eliminated bias as progeny numbers became infinite. Pedigree and performance data on a single trait with heritability 0.25 were then simulated for 15 flocks with 40 to 140 ewes per flock. Each flock was simulated with a different founder genetic mean to introduce bias into the genetic evaluation. Flocks participated in sire referencing schemes by artificial insemination, with varying levels of participation, or by natural service. With sire referencing genetic gain was higher and inbreeding was lower than without, and bias was rapidly reduced to near-zero levels. Discontinuing the schemes led to lower genetic gain, but bias was not reintroduced. The prediction error correlation of flock genetic means was proposed as a connectedness measure because it was strongly associated with bias. Benchmarks of 0.05 and 0.10 for "good" and "superior" connectedness were established. Targhee flocks have increased connectedness across the breed by actively exchanging rams over 15 yr. In the Suffolk breed, connectedness has only improved within segregated clusters of flocks. Suffolk breeders need to engage in active ram exchange to decrease risk of biased across-flock EBV comparisons. / Ph. D.

Sport horse genetic evaluations are used throughout Europe to inform breeding practices. In England specifically, British Equestrian Federation Futurity evaluations are used to assess horse potential and to inform British breeding. Futurity premium scores are allocated to represent performance potential based on horse’s component traits (primarily conformation and locomotion). This study demonstrated that over half (61/106) questionnaire respondents believe that Futurity premium scores influence horse training decisions and monetary value. This is highly relevant to the industry as premium scores can therefore have economic and welfare implications. Therefore horse premiums must be reliable and indicative of future competition performance. Retrospective Futurity premiums (n=566) were investigated for reliability using the MiniTab™ v17 statistical package. Regression analysis of premium scores versus test variables demonstrated that whilst horse age and colour significantly correlated with Futurity premiums (P=0.017 and P=0.027 respectively); sex and test location did not (P >0.05). Regression analysis of components of horse competition records (lifetime points, placings, winnings, percentage scores and penalty points) versus Futurity premiums demonstrated limited correlations. British Eventing penalty point scores correlated with the majority of Futurity scores, BD percentage scores correlated with one and British Showjumping, none. British Eventing penalty point scores appear the most appropriate measure of performance as this method evaluates each phase of the individual’s competition, unlike points/placings. Futurity component scores demonstrated mixed results. A high Futurity score did not necessarily predict a high performance score. A key issue with the data was the fact that the horses examined were relatively young. Average horse age was 7 years and therefore these horses may not have been old enough to have developed their abilities towards their mature potential, limiting competition results therefore their records and consequently affecting analysis outcomes. Furthermore, industry practitioners have highlighted judge subjectivity as a limitation, however results suggest that test location (representing the judging panel) is not influential in scoring. As the Futurity develops, a larger dataset of older horses will become available which will provide further insight into the tests usefulness.

Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Improvement and selection of superior animals for longevity is a viable complimentary strategy for increasing functional longevity of Holstein dairy cattle. Genetic evaluation of animals for functional longevity is a prerequisite for improvement of the trait. This study was carried out to determine non-genetic factors that influence functional longevity in South African Holstein cattle, as well as to estimate genetic parameters for functional longevity, estimate sire breeding values, and to establish the contribution of conformation traits to the risk of cows being culled from dairy herds. Analyses were carried out using records of 166 222 daughters of 2 051 sires from 1 545 herds in six regions of South Africa. The regions were the Western Cape, Eastern Cape, Northern Cape, Free State, Kwa-Zulu Natal and the combined Gauteng & North Western Provinces. Data were analysed using a piecewise Weibull sire-maternal grandsire model in which the baseline hazard was assumed to change at 270 and 380 days in milk as well as at drying-off. The fixed effects model comprised of the time-independent effect of age at first calving, the combined time-dependent effects of region x year of calving, number of lactations x within-herd milk production class, year of calving x within-herd protein and year of calving x fat percentage production class. Model also had the combined time-dependent effect of herd size x annual herd size change. The random herd-year and sire effects were later included in the model for the estimation of sire and herd-year variance components. Analyses indicated a decline in the survival function, an indicator of functional longevity, among cows that calved for the first time in 2000, 2004 and 2008. Cows that delivered their first calf in 2000 had better survival functions that those that calved for the first time in 2004 and 2008. All fitted effects significantly contributed to the risk of a cow being culled from a herd. Within-herd milk production made the largest contribution to the risk of a cow being culled from a herd. Survival was best in the Northern Cape and worst in Eastern Cape. The risk of being culled was the highest for cows in the second stage of lactation (271- 380 days), when the entire lactation period was considered. High producing cows were more likely not to be culled from a herd than poor producing cows. Cows were more likely to be culled for low protein production percentage than within-herd fat production percentage. The risk of being culled was low for heifers calving at 20 to 25 months of age. The higher risk of culling among cows with multiple lactations indicated the culling policy of dairy farmers to retain a higher number of younger cows than older cows in herds. A decrease in herd size was indicative of a high culling rate. Effective heritability was 0.109. Breeding values ranged from 2.12 for the best cows to -4.80 for the worst cows. This implied that the best and the worst cows were 2.12 times and 4.80 more likely to be culled from herds than the average cow respectively. Genetic trends for functional longevity indicated a marginal decline in sire estimated breeding values. This corresponded with the phenotypic decline in the survivor function observed in cows that calved in 200, 2004 and 2008. All udder, rump, body, feet and leg type traits, with the exception of rear leg side, significantly influenced functional longevity. Farmers culled cows mainly of extremely poor type with a tendency to retain animals with poor to very good structure. Udder traits contributed the most to the risk of a cow being culled. Cows were more likely to be culled for poor scores received for rear teat placement, rear udder height and fore udder attachment, than for any of the other conformation type traits. The contribution of angularity to the risk of being culled was also high, indicating a preference for highly angular bodied cows. Conformation type traits can therefore be used as indicator traits for functional longevity in Holstein cattle, especially when selection and culling is done based on very poor scores for udder traits. The study indicated that genetic improvement in functional longevity can be achieved with the evaluation and selection of dairy sires. There is therefore a wide scope for including functional longevity in the selection objectives for South African Holstein cattle. There is a need to develop appropriate models to ensure that the national dairy industry can benefit from using a Weibull piecewise model. / AFRIKAANSE OPSOMMING: Die verbetering en seleksie van voortreflike diere vir langlewendheid is 'n lewensvatbare en aanvullende strategie vir die verhoging van die funksionele langlewendheid van Holstein melkbeeste. Die genetiese evaluasie van melkproduserende diere ten opsigte van hierdie eienskap is ʼn voorvereiste om verbetering in die eienskap moontlik te maak. Die studie is uitgevoer om nie-genetiese faktore wat die funksionele langlewendheid van Suid-Afrikaanse Holsteins beïnvloed te bepaal, om genetiese parameters vir langlewendheid en vaar teeltwaardes vir dié eienskap te bepaal en ook om die bydrae van bouvorm eienskappe tot die waarskynlikheid van koeie om uitgeskot te word, te bepaal. ʼn Databasis bestaande uit rekords van 166 222 dogters van 2 051 vaars, wat in ses streke in Suid-Afrika (Wes-Kaap, Oos-Kaap, Noord-Kaap, Vrystaat, KwaZulu-Natal en die gekombineerde Gauteng en Noord-Wes Provinsies) voorgekom het, is vir die studie gebruik. Data is ontleed met behulp van 'n stuksgewyse Weibull vader-moeder grootvader model, waarin die basislyn risiko aanvaar is om te verander op 270, 380 dae na kalwing en by afdroog van die melkkoeie. Die vaste effek model het die tyd-onafhanklike effek van ouderdom met eerste kalwing en die tyd-afhanklike effekte van streek en jaar van kalwing, aantal laktasies en binne-kudde melkproduksie klas, binne-kudde proteïen en vet persent produksie klasse volgens jaar van kalwing, asook die gekombineerde tyd-afhanklike effek van kuddegrootte en jaarlikse verandering in kudde grootte, ingesluit. Die ewekansige trop-jaar en vaar effekte is later opgeneem in die model vir bepaling van die vaar- en kudde-jaar variansie komponente. Ontledings het aangedui dat daar 'n algemene afname in die oorlewingsfunksie, wat ʼn aanduiding van funksionele langlewendheid is, was in koeie wat vir die eerste keer in 2000, 2004 en 2008 gekalf het. Koeie wat vir die eerste keer in 2000 gekalf het, het ʼn hoër waarde vir die oorlewingsfunksie gehad as koeie wat onderskeidelik in 2004 en 2008 gekalf het. Alle vaste effekte het betekenisvol tot die waarskynlikheid van ʼn koei om uitgeskot te word, bygedra. Binne-kudde melkproduksie het die grootste bydrae tot die waarskynlikheid van ʼn koei om uitgeskot te word, gemaak. Wanneer die totale laktasieperiode in ag geneem is, was daar gevind dat koeie wat in die tweede fase van laktasie (271-380 dae) die hoogste risiko ervaar het om uitgeskot te word. Hoë produseerders, wanneer hulle met lae produseerders vergelyk is, was minder geneig om uitgeskot te word. Koeie was meer geneig om uitgeskot te word vir lae proteïen produksie persentasie as binne-kudde vet produksie persentasie. Die waarskynlikheid om uitgeskot te word, was laag vir verse wat op ʼn ouderdom van 20 tot 25 maande gekalf het. Die hoër risiko van uitskot van koeie met veelvuldige laktasies het aangedui dat melkboere geneig was om meer jonger koeie te behou en ouer koeie uit te skot. ʼn Afname in kuddegrootte was aanduidend van ʼn hoë uitskotpersentasie. Die effektiewe oorerflikheid was 0.109, met teelwaardes wat van 2.12 vir die hoogste produserende koeie tot -4.80 vir die laagste produserende koeie, gewissel het. Hierdie waardes het dus aangedui dat hoë produseerders en swak produseerders onderskeidelik ʼn 2.12 en 4.80 groter kans gehad het om uitgeskot te kan word. Genetiese tendense vir funksionele langlewendheid het aangedui dat daar 'n marginale afname in vaar beraamde teelwaardes vir funksionele langlewendheid was. Dit het ooreengestem met die waargenome fenotipiese afname in die oorlewingsfunksie wat in 2000, 2004 en 2008 gekalf het. Alle bou-tipe eienskappe (uier, agterkwart, liggaam, voet en been), met die uitsondering van die agterbeen kant, het funksionele langlewendheid betekenisvol beïnvloed. Boere het koeie hoofsaaklik op uiters swak boutipe uitgeskot, met 'n neiging om diere wat as ʼn swak tot uiters goeie bouvorm geklassifiseer is, te behou. Uier eienskappe het die meeste tot die waarskynlikheid van ʼn koei om uitgeskot te word, bygedra. Koeie met ʼn lae gradering vir agterste speen plasing, agter-uier hoogte en voor-uier aanhegting se waarskynlikheid om uitgeskot te word, was groter. Die bydrae van hoekigheid tot die waarskynlikheid van ʼn koei om uitgeskot te word was hoog, wat ʼn aanduiding van ʼn voorkeur vir 'n baie growwe hoekigheid was. Bouvorm tipe eienskappe kan dus gebruik word as indikator eienskappe vir funksionele langlewendheid in Holstein melkbeeste, veral wanneer in ag geneem word dat die meeste melkboere seleksie op grond van swak gradering van uier eienskappe doen. Die studie het aangedui dat genetiese verbetering in funksionele langlewendheid teweeg gebring kan word met die evaluering en seleksie van Holstein vaars. Daar is dus ʼn geleentheid vir die insluiting van funksionele langlewendheid in die seleksie doelwitte vir Suid-Afrikaanse Holstein beeste. Daar is ʼn behoefte om toepaslike modelle te ontwikkel wat met die toepassing daarvan, sal verseker dat die plaaslike melkbedryf sal kan voordeel trek deur die gebruik van 'n stuksgewyse Weibull model benadering.

Made available in DSpace on 2016-08-10T10:44:43Z (GMT). No. of bitstreams: 1 BRUNO FRAUZINO RIBEIRO CAMILO.pdf: 1862817 bytes, checksum: ba7c8b48dadf912fb820375d1be59050 (MD5) Previous issue date: 2014-12-15 / The objective was to study the effects on the ordering of the animals by their genetic value of the inclusion of direct maternal additive genetic covariance models of prediction of breeding values for weaning weight in beef cattle using simulated data. The data were simulated considering three different values of maternal direct additive genetic correlation (-0.25, -0.50 and +0.25) and three reasons direct additive variance and maternal additive (1: 1, 1: 2 and 2: 1), making a total of nine scenarios. In each scenario, the breeding values were predicted including whether or not the covariance in the model. The values of the Spearman correlation between animal clinics, considering the predicted genetic value, the scenarios of direct maternal additive genetic correlation -0.50 in the ratios of variances 1: 1 and 2: 1 were equal to 0.84 and 0, 85, respectively; -0.25 scenario the correlation variance in the ratios 1: 1, 1: 2 and 2: 1 were 0.96, 0.95 and 0.97 respectively, and the positive correlation scenario in +0.25 Variance ratios 1: 1, 1: 2 and 2: 1 with values of 0.92, 0.91 and 0.96 respectively. The values were high and significant, suggesting greater consistency between the animal merit orders. The average value for the Spearman correlation estimated in scenario - 0.50 1: 2 was equal to 0.46 indicating lesser proximity between merit orders of individuals in this scenario. The results indicate include the covariance in prediction models for the classification of animals are closer to real. / Objetivou-se estudar os efeitos, sobre a ordenação dos animais por seu valor genético, da inclusão da covariância genética aditiva direta maternal nos modelos de predição dos valores genéticos de peso a desmama de bovinos de corte utilizando dados simulados. Os dados foram simulados considerando-se três valores diferentes de correlação genética aditiva direta maternal (-0,25, -0,50 e +0,25) e três razões de variância aditiva direta e aditiva maternal (1:1, 1:2 e 2:1), perfazendo um total de nove cenários. Em cada cenário, os valores genéticos foram preditos incluindo-se ou não a covariância no modelo. Os valores da correlação de Spearman entre os postos dos animais, considerando o valor genético predito, nos cenários de correlação genética aditiva direta maternal -0,50 nas razões de variâncias 1:1 e 2:1 foram iguais a 0,84 e 0,85, respectivamente; no cenário de correlação -0,25 nas razões de variâncias 1:1, 1:2, e 2:1 foram iguais a 0,96, 0,95 e 0,97 respectivamente e no cenário de correlação positiva +0,25 nas razões de variâncias 1:1, 1:2 e 2:1 com valores de 0,92, 0,91 e 0,96 respectivamente. Os valores foram altos e significativos, o que sugere maior concordância entre as ordens de mérito dos animais. O valor médio para a correlação de Spearman estimados no cenário -0,50 1:2 foi igual a 0,46 indicando menor proximidade entre as ordens de mérito dos indivíduos neste cenário. Os resultados indicam incluir a covariância nos modelos de predição para que as classificações dos animais estejam mais próximas do real.

Made available in DSpace on 2014-06-11T19:26:07Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-02-16Bitstream added on 2014-06-13T18:29:30Z : No. of bitstreams: 1 guidolin_dgf_me_jabo.pdf: 239613 bytes, checksum: 25503ca97d099f8707e7f0c6cd325324 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A identificação de interação genótipo-ambiente em bovinos de corte pode auxiliar o processo de seleção, aumentando a eficiência da avaliação genética de reprodutores submetidos à ambientes distintos. Características medidas pós-desmame estão mais sujeitas aos efeitos da interação genótipoambiente do que na fase pré-desmame. Assim, o objetivo deste trabalho foi verificar a existência do efeito da interação genótipo-ambiente sobre os pesos corporais aos 365 (P365), 450 (P450) e aos 550 (P550) dias de idade de bovinos Nelore criados nos estados de Goiás, Mato Grosso, Mato Grosso do Sul, Minas Gerais, Pará e São Paulo. Os componentes de (co)variância, parâmetros genéticos e os valores genéticos preditos foram estimados para cada característica, por estado e para o conjunto total de dados, pelo método da máxima verossimilhança restrita. Correlações de Spearman entre as classificações dos touros por estado quanto ao valor genético para cada característica ou considerando cada estado individualmente e em conjunto (todos os estados), assim como a correlação genética entre observações da mesma característica, medida em dois estados distintos foram utilizadas para avaliar o efeito da interação genótipo-ambiente sobre as características estudadas. Correlações de Spearman não significativas indicaram mudança de posição na classificação de touros e conseqüente existência de interação genótipo-ambiente. A ocorrência desta interação também foi constatada em algumas ocasiões por estimativas de correlação genética entre observações da mesma característica em estados diferentes, para P365 foi observada indícios de interação entre SP e GO (0,71), SP e MT (0,68) e também entre SP e PA (-0,11), para P450, MT e MG (-0,28), GO e PA (0,62) e SP e PA (0,66), para a característica P550, MT e MG (-0,38), MG e PA (0,73), MG e SP (-0,34) e para... / The properly identification of genotype-environment interaction in beef cattle herds can help the selection process and improve genetic evaluation of sires submitted in different environments. Post weaning traits may be more influenced by the genotype-environment interactions than others. So, this paper objective was verify genotype-environment interaction in, beef cattle, body weight at 365 (P365), 450 (P450) and 550 (P550) days of age in herds distributed in six Brazilian states, Goiás (GO), Mato Grosso (MT), Mato Grosso do Sul (MS), Minas Gerais (MG), Pará (PA) and São Paulo (SP). Genetic parameters, (co)variance components and genetic values were estimated for each trait, each state and for all states together, using maximum restricted likelihood method. Spearman correlations among sire’s classifications due to its genetic value, for each trait, by state individually or in group (using data from all states), genetic correlation between the same trait measured in two different states were used to evaluate genetic-environment interaction over the traits studied. Non significant Spearman’s correlation indicated position changes at sires classification and consequently genotype-environment interaction. This interaction occurrence was also observed between genetic correlations of the same trait measured in two different states. Genetic correlation for P365, between SP and GO states were (0, 71), SP and MT (0, 68) and also between SP and PA (-0, 11). For P450, MT and MG (-0, 28), GO and PA (0, 62) and SP and PA (0, 66). P550, MT and MG (-0, 38), MG and PA (0, 73), MG and SP (-0, 34) and SP and PA (-0, 86). There so, selection conduced considering data obtained in one state could be different than one based in others. Beef cattle summary organized by state would be indicated if this one would be economically viable.

Resumo: Objetivou-se estimar parâmetros genéticos e fenotípicos da produção de ovos total e parcial em aves de postura por meio de modelos de dimensão finita e infinita, visando à seleção das aves para a característica produção de ovos. Utilizou-se dados de fêmeas, nascidas a partir de três incubações, provenientes de uma geração de uma linhagem de poedeiras, desenvolvida pela EMBRAPA Suínos e Aves em Concórdia, SC. A produção de ovos foi avaliada individualmente por meio do número de ovos, a partir de 20 até 70 semanas de idade. As produções foram divididas em períodos, sendo que cada período consistiu em três semanas de produção. As características estudadas foram os registros parciais nos períodos e o registro total da produção de ovos (PTOTAL). Para análise em modelo animal uni e bicaracterística, utilizou-se o programa computacional MTDFREML. Maior herdabilidade foi estimada para o período de 20 a 22 semanas de idade (P1) e PTOTAL (0,33 ± 0,07 e 0,23 ± 0,06). Correlações genéticas entre os períodos parciais e PTOTAL variaram de 0,42 ± 0,15 (PTOTAL com P2, de 20 a 22 semanas de idade) até 1,00 (PTOTAL com P9 e P11, de 44 a 46 e 50 a 52 semanas de idade, respectivamente). A correlação de Spearman entre as ordens dos 43 galos quanto aos valores genéticos para produção de P9, P10 (de 47 a 49 semanas de idade) e de P11 com PTOTAL foi significativa (p<0,001) para P9 e P11, igual a 1,00 e para P10 (p<0,0028), igual a 0,99. Concluiu-se que o registro parcial de ovos para os períodos P9, P10 e P11 poderiam ser considerados no processo de seleção visando à produção total de ovos. Porém, devido os mesmos apresentarem baixas estimativas de herdabilidade (0,06; 0,12 e 0,10, respectivamente para P9, P10 e P11) a seleção seria mais eficiente considerando o PTOTAL. Portanto, seria recomendada a seleção baseada na produção total de ovos, pois a mesma... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The aim was to estimate genetic and phenotypic parameters for total and partial records of egg production of laying hens using finite and infinite-dimension models, with a view to selecting birds for egg production. Data on females born from three incubations, from a generation of an egg-laying strain developed by EMBRAPA Suínos e Aves, Concórdia, SC, were used. Egg production was evaluated individually as the number of eggs produced between the ages of 20 and 70 weeks. The production was divided into three-week periods. The traits studied were the partial records for each period (P1 to P17) and the total recorded egg production (PTOTAL). For analysis in one and two-trait animal models, the MTDFREML software was used. Higher heritabilities were estimated for the periods of 20 to 22 weeks of age (P1) (0.33 ± 0.07) and PTOTAL (0.23 ± 0.06). The genetic correlations between the partial periods and PTOTAL ranged from 0.42 ± 0.15 (P1) to 1.00 (for P9 and P11, representing 44-46 and 50-52 weeks of age, respectively). Spearman's correlation between the ranks of the 43 sires, regarding the genetic values for production in P9, P10 (47-49 weeks of age) and P11 in relation to PTOTAL, was significant and equal to 1.00 (P<0.001) for P9 and P11 and equal to 0.99 (P<0.0028) for P10. Although highly correlated with PTOTAL, these periods had low heritability estimates in two-trait analysis (0.06, 0.12 and 0.10, respectively for P9, P10 and P11). Thus, selection based on these partial periods would be inefficient and basing it on total egg production would be recommended, since this presented higher heritability estimates. To estimate the covariance functions using random regression models, the DXMRR option in the DFREML statistical software was used. The most appropriate model regarding goodness-of-fit of the egg production data in these laying hens was the one composed of third-order... (Complete abstract click electronic access below) / Orientador: Danísio Prado Munari / Coorientadora: Lenira El Faro Zadra / Coorientadora: Mônica Côrrea Ledur / Banca: João Ademir de Oliveira / Banca: Claudia Cristina Paro de Paz / Mestre

Resumo: A identificação de interação genótipo-ambiente em bovinos de corte pode auxiliar o processo de seleção, aumentando a eficiência da avaliação genética de reprodutores submetidos à ambientes distintos. Características medidas pós-desmame estão mais sujeitas aos efeitos da interação genótipoambiente do que na fase pré-desmame. Assim, o objetivo deste trabalho foi verificar a existência do efeito da interação genótipo-ambiente sobre os pesos corporais aos 365 (P365), 450 (P450) e aos 550 (P550) dias de idade de bovinos Nelore criados nos estados de Goiás, Mato Grosso, Mato Grosso do Sul, Minas Gerais, Pará e São Paulo. Os componentes de (co)variância, parâmetros genéticos e os valores genéticos preditos foram estimados para cada característica, por estado e para o conjunto total de dados, pelo método da máxima verossimilhança restrita. Correlações de Spearman entre as classificações dos touros por estado quanto ao valor genético para cada característica ou considerando cada estado individualmente e em conjunto (todos os estados), assim como a correlação genética entre observações da mesma característica, medida em dois estados distintos foram utilizadas para avaliar o efeito da interação genótipo-ambiente sobre as características estudadas. Correlações de Spearman não significativas indicaram mudança de posição na classificação de touros e conseqüente existência de interação genótipo-ambiente. A ocorrência desta interação também foi constatada em algumas ocasiões por estimativas de correlação genética entre observações da mesma característica em estados diferentes, para P365 foi observada indícios de interação entre SP e GO (0,71), SP e MT (0,68) e também entre SP e PA (-0,11), para P450, MT e MG (-0,28), GO e PA (0,62) e SP e PA (0,66), para a característica P550, MT e MG (-0,38), MG e PA (0,73), MG e SP (-0,34) e para... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The properly identification of genotype-environment interaction in beef cattle herds can help the selection process and improve genetic evaluation of sires submitted in different environments. Post weaning traits may be more influenced by the genotype-environment interactions than others. So, this paper objective was verify genotype-environment interaction in, beef cattle, body weight at 365 (P365), 450 (P450) and 550 (P550) days of age in herds distributed in six Brazilian states, Goiás (GO), Mato Grosso (MT), Mato Grosso do Sul (MS), Minas Gerais (MG), Pará (PA) and São Paulo (SP). Genetic parameters, (co)variance components and genetic values were estimated for each trait, each state and for all states together, using maximum restricted likelihood method. Spearman correlations among sire's classifications due to its genetic value, for each trait, by state individually or in group (using data from all states), genetic correlation between the same trait measured in two different states were used to evaluate genetic-environment interaction over the traits studied. Non significant Spearman's correlation indicated position changes at sires classification and consequently genotype-environment interaction. This interaction occurrence was also observed between genetic correlations of the same trait measured in two different states. Genetic correlation for P365, between SP and GO states were (0, 71), SP and MT (0, 68) and also between SP and PA (-0, 11). For P450, MT and MG (-0, 28), GO and PA (0, 62) and SP and PA (0, 66). P550, MT and MG (-0, 38), MG and PA (0, 73), MG and SP (-0, 34) and SP and PA (-0, 86). There so, selection conduced considering data obtained in one state could be different than one based in others. Beef cattle summary organized by state would be indicated if this one would be economically viable. / Orientador: João Ademir de Oliveira / Coorientador: Danísio Prado Munari / Coorientadora: Cládudia Cristina Paro de Paz / Banca: Sandra Aidar de Queiroz / Banca: Ruy Alberto Caetano Correa Filho / Mestre

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