Thesis (MScAgric)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: The application of assisted reproductive biotechnologies in sheep flocks is hampered by the susceptability of ovine sperm to cryodamage. There is still considerable scope in the improvement of cryopreservation protocols for ovine sperm to minimize the degree of damage to sperm during the cryopreservation process. Pre-cryopreservation processing has a definite effect on the survivability, motility, and fertilizing ability of sperm. Little information is however available on the potential contribution of the genetic make-up of rams, divergently selected for fecundity, on the ability of sperm to offer resistance to the damage caused by cooling, cryopreservation and thawing. The study aimed to investigate the influence of genetic selection for prolificacy (i.e. High Merino Line and Low Merino Line in terms of fecundity) on the ability of ovine sperm to offer resistance to cryodamage. The study investigated the effect of pre-cryopreservation processing by comparing motility and morphometry traits recorded for fresh- and post-thaw Merino ejaculated and epididymal sperm samples obtained form the High and Low lines, respectively. The effect of different sperm concentrations, equilibration periods and the addition or omission of seminal plasma from cryopreserved samples on the viability and morphometrical traits were also investigated. Ejaculate samples were collected by means of the artificial vagina (AV) method from 8 High Line rams and 7 Low Line rams. Epididymal samples were collected from 6 rams of each of the High and Low lines respectively, by recovering the epididymal sperm via aspiration from the cauda epididymides post mortem. Ejaculate samples were subjected to macroscopic and microscopic evaluation, and epididymal samples only to microscopic evaluation, for which the Sperm Class Analyzer® program was used for the evaluation of motility and morphometric measurements. Sperm motility recordings were captured at 100 frames per second. From findings of the study, it was concluded that genotype had no positive influence on the conception rate of the ewes mated to the High or Low Line rams, even though the rams from the two lines differed significantly in terms of their serving capacity. When sperm morphometry was evaluated for fresh ejaculate samples, the two lines differed significantly in terms of the morphometric traits elongation and ellipticity. Epididymal and ejaculated sperm obtained from Low Line rams had broader and rounder heads, compared to sperm obtained from High Line rams. When morphometry was assessed for sperm samples between the two methods of sperm recovery (collected with an AV or recovery via aspiration from the cauda epididymides of sacrificed rams), no morphometrical differences were observed. Significant differences were reported for the majority of the sperm motility traits (i.e. percentage motile, rapid-, medium-, slow swimming, curvilinear velocity (VCL), straight line velocity (VSL), average path velocity (VAP), and amplitude of the lateral head displacement (ALH)) recorded for ejaculated and epididymal sperm. The motility traits ALH and beat-cross frequency (BCF) analysed for epididymal sperm differed significantly between the two lines. When epididymal sperm were evaluated post-thaw, it became evident that the sperm obtained from the High Line rams had a larger acrosome surface cover when compared to that of the Low Line ram sperm. The addition of seminal plasma to epididymal samples did not result in an improvement of the preservation of sperm motility. It is known from the literature that cryopreservation causes a decrease in sperm head size. Head width was unaffected by cryopreservation with the addition of seminal plasma in this study, indicating a potential benefit with the use of seminal plasma in the cryopreservation protocol of epididymal ram sperm. The study compared two pre-processing techniques, i.e. the more time consuming swim-up technique (SUT) with a more time-efficient ‘flush technique’ (FT) to optimize the pre-processing protocol for motility assessment of sperm samples before cryopreservation of ram sperm. Comparison of the SUT and FT indicated that almost all of the motility parameters measured using the FT compared favourably with those obtained using the SUT. The results indicated that the FT can be used a more time-efficient technique to use for determining the motility of a sperm sample prior to cryopreservation. In conclusion, line differences associated with reproduction were observed in terms of the serving capacity of the rams, with selection for fecundity influencing the morphometric traits elongation and ellipticity for sperm obtained from the two lines. Future studies should be aimed at investigating morphometric traits of ovine sperm, to correlate it with fertilizing ability of sperm post-thaw and ensure optimal cryopreservation processing. / AFRIKAANSE OPSOMMING: Die toepassing van ondersteunende reproduksie tegnieke in skaaptroppe word bemoeilik deur die onvermoë van ram sperme om weerstand teen bevriesingskade te bied. Daar is nog baie ruimte vir die verbetering van die bevriesingsprotokolle vir skaap sperm om die omvang van bevriesingskade te verminder. Voor-bevriesing verwerking het dan 'n besliste uitwerking op die oorlewing, beweeglikheid en bevrugtingsvermoë, van skaap sperme. Min inligting is beskikbaar oor die potensiële bydrae van die genetiese samestelling van ramme wat uiteenlopend op grond van vrugbaarheid geselekteer is, op die vermoë van skaap sperme om weerstand te bied teen die skade wat deur verkoeling, diepbevriesing en ontdooiing, veroorsaak word. Die doelwit van die studie was om die invloed van genetiese seleksie vir fekunditeit (d.i. Hoë Merino Lyn en Lae Merino Lyn in terme van fekunditeit) op die vermoë van skaap sperme om weerstand teen bevriesingskade te bied, te ondersoek. Die studie het getoets wat die bevriesing proses se effek op epididimale sperme is, deur sperm motiliteit en -morfometrie te vergelyk tussen vars gekollekteerde sperme en sperm monsters na ontdooiing. Die effek van verskillende sperm konsentrasies, ekwilibrasie tydperke en die byvoeging of uitsluiting van seminale plasma op die lewensvatbaarheid en morfometriese eienskappe van Merino ramsperme is ondersoek in die studie. Geëjakuleerde monsters is versamel met behulp van 'n kunsmatige vagina (AV) van 8 Hoë Lyn en 7 Lae Lyn ramme. Epididimale monsters is verkry van 6 ramme van elk van die Hoë en Lae Lyne, deur middel van aspirasie van die sperme uit die cauda epididimii nadoods. Geëjakuleerde sperm monsters is met behulp van makroskopiese en mikroskopiese metodes geëvalueer, en epididimale sperm monsters slegs mikroskopies geëvalueer, met behulp van die Sperm Class Analyzer® program wat vir die evaluasie van beweeglikheid en morfometriese afmetings gebruik is. Sperm beweeglikheids opnames is opgeneem teen 100 raampies per sekonde. Die resultate van die studie het aangedui dat genotipe geen effek het op besetting van die ooie gepaar met die Hoë of Lae Lyn ramme gehad het nie, terwyl die dekvermoë aansienlik tussen ramme van die twee lyne verskil het. Wanneer die morfometriese eienskappe van vars geëjakuleerde sperme vergelyk was, het die lyne beduidend in terme van die morfometriese eienskappe van verlenging (elongation) en elliptisiteit verskil het. Die epididimale en geëjakuleerde sperme verkry vanaf die Lae Lyn ramme het ʼn breër en ronder kopvorm getoon as sperme wat verkry is van die Hoë Lyn ramme. Wanneer die morfometriese eienskappe van sperme versamel met die twee verskillende metodes (d.i. kunsmatige vagina of aspirasie vanuit die cauda epididimides) vergelyk was, is geen morfometriese verskille waargeneem nie. Die meeste sperm beweeglikheidseienskappe (d.i. persentasie beweeglike, vinnig-, medium- en stadig-swemmende sperme, VCL, VSL, VAP en ALH) van geëjakuleerde en epididimale sperme het verskil. Die beweeglikheidseienskappe amplitude van die laterale verplasing van die spermkop (ALH) en frekwensie waarmee sperm sy eie pad kruis (BCF), soos bepaal vir epididimale sperme, het beduidend tussen die twee lyne verskil. Met die evaluering van epididimale sperme na ontdooiing was dit duidelik dat sperme verkry van die Hoë Lyn ramme 'n groter mate van akrosoom-oppervlak gehad het, in vergelyking met sperme van die Lae Lyn ramme. Die byvoeging van seminale plasma by epididimale monsters het nie bygedra tot 'n verbetering van spermbeweeglikheid nie. Bestaande literatuur dui aan dat diepbevriesing 'n afname in die kopgrootte van sperme veroorsaak. In hierdie studie het die byvoeging van seminale plasma ʼn verandering in kopgrootte voorkom, wat dui op ʼn potensiële voordeel om seminale plasma in die bevriesingsprotokol van epididimale ramsperme in te sluit. Die studie het twee beweeglikheid bepalingstegnieke vergelyk om te bepaal of die tydrowende “opswem” tegniek (SUT) vervang kan word met 'n meer tyd-doeltreffende "spoel tegniek” (FT) in die voorbevriesing verwerking protokolle van ram sperme. Vergelyking van die twee tegnieke het aangedui dat die meeste van die kinematiese eienskappe van die FT gunstig met die waardes soos verkry met die SUT, vergelyk het. Resultate het getoon dat die FT parameters goed vergelyk met die beweeglikheid parameters van die SUT, dus kan dit aangeneem word dat die FT ʼn meer tyd-doeltreffende tegniek is wat vergelykbare sperm beweeglikheidsinligting oor skaap sperm monsters voor bevriesing sal verskaf. In samevatting is verskille in terme van die dekvermoë en op morfometriese vlak, meer spesifiek die eienskappe van verlenging (elongation) en elliptisiteit, tussen die twee lyne waargeneem. In toekomstige studies moet die morfometriese eienskappe van skaapsperme verder bestudeer word, asook die korrelasie daarvan met die bevrugtingsvermoë na ontdooiing bepaal om sodoende die diepbevriesing protokolle van skaapsperme te optimaliseer.

This investigation explored the utility of mean osteon area, perimeter, and circularity as parameters for distinguishing between human and non-human bone. Although species of origin can be readily ascribed to undamaged remains, this evaluation can become difficult, if not impossible, when bone macrostructure has been obscured through taphonomic processes such as thermal alteration or extreme fragmentation. If mature Ovis aries, domestic sheep, and human osteon metrics area are significantly different, then osteon metrics can be useful parameters for distinguishing between these tissues and, thus, determining the species of origin for a bone sample of unknown provenience. This investigation consisted of histological analysis of cortical bone from 35 O. aries rib samples. O. aries samples were acquired from Riverslea Farm in Epping, New Hampshire (n = 30) and Cedar Ledge Farm in Somers, Connecticut (n = 5). Mean osteon area, perimeter, and circularity were assessed by manually tracing calibrated digital images of rib cross-sections using the ImageJ software from the National Institute of Health (NIH, Bethesda, MD). The results presented here indicate (1) that there are statistically significant histomorphometric differences between species, specifically goat and sheep, (2) that there are significant histomorphometric differences based on the anatomical, intra-rib sampling location, and (3) that the osteon metrics discussed here are may be poor parameters by which to ascribe the species of origin for remains with no known provenience, based on comparisons with findings from other publications.

Herbivory is one major force accelerating aspen decline in North America, but it is unclear why herbivores prefer certain aspen stands over others, or over other plant species in the understory. In this dissertation, I determined the influence of nutrients and plant secondary compounds (PSC), physiological state, chemical composition, and prior experience on aspen preference by sheep in controlled pen experiments. In addition, I explored the relationship between herbivory, regeneration, recruitment, and other landscape elements for specific aspen stands within Wolf Creek Ranch in northern Utah using biomass and chemical composition of the understory and chemical defenses of juvenile aspen trees (i.e., the foodscape). Aspen intake was enhanced when lamb diets contained a high crude protein to energy ratio or when the basal diet contained a low density of energy. Intake was depressed as concentrations of PG (phenolic glycosides) increased in aspen leaves or when lambs were fed a high energy to protein ratio. The effects of nutrients on aspen intake were greater when phenolic glycosides in aspen were present at low concentrations. However, when given a choice between aspen leaves of high or low PG content, lamb preference depended more on aspen nutrient and mineral availability, or on prior diet, than on defense chemistry. On the landscape, I found that stands at low elevations with low abundance of nutrients in the understory are more likely to experience less regeneration and recruitment than those growing within nutrient-rich sites. Aspen browsing was negatively correlated with PG content in aspen stands, and elk presence (measured via fecal pellets) was negatively correlated with abundance of understory protein. In conclusion, aspen herbivory appears to be controlled by the interplay between types and amounts of nutrients offered by the landscape and the chemical composition of aspen stands. A clear assessment of these variables on the landscape, i.e., the foodscape, will aid in the development of novel management strategies aimed at providing nutrients (e.g., through supplements, introduced forages) at strategic locations in order to reduce aspen herbivory within at-risk aspen stands.

Merino sheep are the most numerous domestic livestock in Australia and feral goats are wide-spread and locally abundant in many of the regions where sheep are grazed. Foot and mouth disease (FMD) is a disease of ungulates that causes severe economic hardship to countries where outbreaks occur or where it has become endemic. In India, Africa, Greece and recently the United Kingdom and Eire, sheep and goats have been implicated in the spread and maintenance of FMD. In Australia, there are contingency plans (AUSVETPLANS) for dealing with an outbreak of FMD. Included in those plans are strategies for control of the disease in feral ungulates including feral pigs and feral goats. Modelling has provided assistance in developing strategies to combat outbreaks in feral pigs and for controlling outbreaks in domestic livestock. No models have been constructed to aid decisions about controlling FMD in feral goats where they co-occur with merino sheep. In Australia, the greatest densities of free-ranging feral goats and domestic livestock occur in the high rainfall zone (> 500 mm mean annual rainfall) along the eastern tablelands and adjacent slopes of the Great Dividing Range. Previous studies of feral goat biology, population dynamics and behaviour in Australia have concentrated on arid and semi-arid zones or on islands. Interactions between free ranging feral goats and merino sheep have not previously been studied in the high rainfall zone. My study investigated the ecological and behavioural characteristics of feral goats and their interactions with sympatric merino sheep at a high rainfall site in central eastern New South Wales. The population dynamics, biological and behavioural parameters of feral goats and sheep were then used to model FMD in such an environment. Deterministic temporal models and a new spatial stochastic model were used. Of particular interest were the rates of contact within and between subgroups of feral goats (termed herds and mobs), within and between subgroups of merino sheep (termed flocks and mobs), and between subgroups of the two species. Feral goats at the study site were found to be numerous (mean density = 34.94 goats km-2, from aerial surveys), in good condition, fecund and had high adult survival and low annual adult mortality (survival= 0.81�1.00) in the absence of harvesting and hunting. They had an observed instantaneous rate of increase of 0.112 per year. Annual rate of increase was similar to other sites in Australia without sustained harvesting pressure. Home ranges were small for both males (3.754 km², s.e. = 0.232, n = 116 goats) and females (2.369 km², s.e. = 0.088, n = 241 goats). From this and other Australasian studies, an inverse power function was found to be an excellent descriptor of the relationship between mean annual rainfall and female home range size. A resource selection function was fitted in a geographic information system to observational data of feral goats. The habitat selection of feral goats included a preference for wooded vegetation on eastern and north eastern aspects at higher elevations. The resource selection function was also used to set the probabilities of occurrence of feral goats in 1 ha areas of the landscape and these probabilities were used to generate heterogeneity in a spatial model of foot and mouth disease virus (FMDV) transmission. Daily per capita contact rates were estimated from observed contacts in the field where a contact between individuals was recognised when one approached within 1 body length ([approx] 1m) of another. The contacts between feral goats within herds were frequent and occurred at a rate of 6.96 (s.e. = 1.27) goat�goat contacts day-1. Sheep to sheep contacts were slightly less frequent (4.22 sheep�sheep contacts day-1, s.e. = 0.65) but both estimates were most likely negatively biased because of observer errors in estimating the number of individual animals coming in contact with observation subject (focal) animals. Contacts between herds of feral goats were not common and those between adjacent populations were fewer than 1 per year. In sheep, flock to flock contact was largely governed by husbandry practices and occurred at a mean daily rate of 0.0014 flock�flock contacts. Contacts between sheep and feral goats were less frequent but nonetheless common (2.82 goat�sheep contacts day-1, s.e. = 0.40). In feral goats the size of the mob in which focal goats were observed was found to be the most important factor in determining contact rates between individuals and a counter-intuitive inverse relationship was identified. Contacts were heterogeneous and density was not an important determinant of contact rates implying that, because of the uniformly high densities at the site, saturation had occurred. The temporal models of FMDV transmission showed that the rate of contact within and between species was such that FMD was predicted to spread rapidly throughout an infected herd or flock. Control strategies of intense culling of feral goats at the population level were predicted to allow the disease to persist at low prevalence, with a small peak corresponding to the annual lambing pulse in sheep. However, the same level of control (>90% reduction) at the herd level was predicted to eliminate FMD and allow the safe reintroduction of sheep. Extreme control that left very small groups (<3 individuals) may be counter productive because such small groups are likely to join the reintroduced sheep in an effort by the goats to meet gregarious urges. The spatial model was more reassuring. It predicted that FMD would die out in a mixed sheep and feral goat population in less than 90 days because of the low rate of herd to herd contact and herd to flock contact. For similar environments, the contingency planning consequences are that an outbreak of FMD introduced into feral goats from sympatric sheep is likely to be containable by removing all the sheep, determining the extent and likely range of the feral goats, then removing a substantial proportion of or eradicating each herd. Feral goats, being relatively sedentary, are unlikely to spread to adjacent populations and the disease will die out through lack of contact between herds and populations. Because feral goat home ranges overlap and are centred on one or two small catchments, a containment ring of feral goat control, set to encompass the home range of a target herd and that of adjacent herds, should be adequate to limit spread of FMD.

Submitted by Marco Antônio de Ramos Chagas (mchagas@ufv.br) on 2017-06-06T11:18:38Z No. of bitstreams: 1 texto completo.pdf: 909512 bytes, checksum: 95d360795ba1a42ae10b3949c99caca0 (MD5) / Made available in DSpace on 2017-06-06T11:18:38Z (GMT). No. of bitstreams: 1 texto completo.pdf: 909512 bytes, checksum: 95d360795ba1a42ae10b3949c99caca0 (MD5) Previous issue date: 2005-12-14 / Fundação de Amparo a Pesquisa do Estado de Minas Gerais / Os ovinos foram introduzidos no Brasil principalmente pelos portugueses e espanhóis durante o processo de colonização. Por motivos sócio-culturais, a criação desses animais foi considerada no Brasil uma atividade de categoria inferior, de modo que foram criados somente para subsistência. Esse descaso fez com que os produtos derivados de ovinos (lã, carne, pele) perdessem competitividade frente aos produtores de outros países. Para que ocorra uma mudança desse cenário, é necessária uma profunda modificação logística de todas as classes envolvidas na produção de ovinos, visto que os ovinos representam, principalmente nas regiões Sul e Nordeste, uma fonte de recursos importante do ponto de vista social, cultural e histórico. O objetivo desse trabalho foi realizar um conjunto de técnicas moleculares que permitam a caracterização genética das principais raças e/ou estoques de ovinos naturalizados do Brasil de modo a.oferecer subsídios para a elaboração de programas estratégicos de conservação e melhoramento desta espécie. Foram utilizadas quatro classes de marcadores moleculares (RAPD, microssatélites, sequenciamento do DNA mitocondrial e do cromossomo Y) em até 11 raças de ovinos naturalizadas e comerciais existentes no Brasil. Os resultados permitiram identificar padrões de estruturação genética existentes nessa espécie no Brasil, bem como demonstraram a viabilidade de aplicação de marcadores moleculares para: 1) monitoramento genético de rebanhos; 2) testes de exclusão de paternidade para controle de pedigrees; 3) origem geográfica de raças ou populações; 4) inferências filogenéticas intra- específicas. / In Brazil, sheep breeds were introduced during the colonization process by Spanish and Portuguese settlers. Social and cultural factors determined that sheep rearing was considered a low-status activity, and therefore, sheep were raised only to meet subsistence goals. The outcome of this is that products derived from sheep such as wool, meat and hides are non competitive in the international market. A change of this scenario requires a profound logistic alteration involving all sheep production-related groups, particularly in the northern and southern regions in the country, where sheep are of high cultural, social and historical relevance. The objective of this work was to characterize the main naturalized Brazilian sheep breeds using molecular markers. Our results will be a baseline for the development of management and conservation programs. Four kinds of molecular markers were used (RAPD, microsatellites, and sequences of mtDNA and Y chromosome) and were applied on 11 breeds of naturalized and commercial breeds. Results identified the genetic structure of the species in the Country and demonstrated the efficiency of molecular markers for 1) herd genetic monitoring, 2) paternity (exclusion) analyses, 3) for determining the geographic origin of breeds and populations, and 4) for investigating within-species phylogenies.

GOUVEIA, João José de Simoni. Análise genômica das principais raças de ovinos brasileiras. 2013. 155 f. Tese (doutorado em zootecnia)- Universidade Federal do Ceará, Fortaleza-CE, 2013. / Submitted by Elineudson Ribeiro (elineudsonr@gmail.com) on 2016-04-08T19:00:28Z No. of bitstreams: 1 2013_tese_jjsgouveia.pdf: 3082019 bytes, checksum: 5a0196089265679f1847c82925a8a7c1 (MD5) / Approved for entry into archive by José Jairo Viana de Sousa (jairo@ufc.br) on 2016-05-25T21:39:11Z (GMT) No. of bitstreams: 1 2013_tese_jjsgouveia.pdf: 3082019 bytes, checksum: 5a0196089265679f1847c82925a8a7c1 (MD5) / Made available in DSpace on 2016-05-25T21:39:11Z (GMT). No. of bitstreams: 1 2013_tese_jjsgouveia.pdf: 3082019 bytes, checksum: 5a0196089265679f1847c82925a8a7c1 (MD5) Previous issue date: 2013 / The Brazilian locally adapted sheep breeds, also known as native and creole, are descendant from animals brought during the settlement period and, since then, are been subjected to evolutive (both systematic and non systematic) processes, what resulted in the formation of highly adapted genotypes to the diverse environmental Brazilian conditions. Although these breeds don’t posses the same productive potential when compared with the exotic improved breeds, they are considered extremely important from a social and cultural point of view. Moreover, the locally adapted breeds are essential for the maintenance of traditional production systems. The optimization of the utilization of naturalized genetic resources depends on a deep knowledge of these populations, and then, the morphological, productive and molecular characterizations are essential to the success of conservation and utilization of these locally adapted genotypes. Therefore, the principal aim of this thesis was to deepen molecular the knowledge of the three main locally adapted Brazilian sheep breeds: Brazilian Creole, Morada Nova and Santa Ines. Thus, Chapter I entitled "Identification of selection signatures in livestock species" is a literature review that is proposed to describe the main effects of natural/artificial selection in the genomes of species of farm animals, present the main methods of signature selection analysis and discuss recent advances in this area of study. Two studies were conducted and resulted in the chapters II and III of this thesis. The chapter II, entitled “Identification of selection signatures in brazilian locally adapted sheep breeds”, aimed the identification and characterization of putative genomic regions that underwent selection and the identification of candidate genes related to productive/adaptative differences between these breeds. The identification of signatures of selection was performed through two approaches: population differentiation (FST) and linkage disequilibrium (iHS and Rsb). Seventy eight genes, related to functions as: immune response, nervous system development, sensorial perception and wool/hair development were identified. The chapter III, entitled “Identification of population substructure in brazilian locally adapted sheep breeds”, aimed the identification and characterization of of genetic substructure within the three main locally adapted Brazilian sheep breeds: Brazilian Creole, Morada Nova and Santa Ines. The level of genetic differentiation between herds of the same breeds was, in general, high. Both in the Brazilian Creole and in the Santa Ines breeds the presence of distinct groups on animals could be observed, what suggests the occurrence of different ecotypes/lineages within these breeds. / As raças de ovinos localmente adaptadas brasileiras, também conhecidas como nativas ou crioulas, descendem de animais trazidos durante o período colonial e, desde aquela época, vêm sendo submetidas a processos evolutivos sistemáticos e não sistemáticos., o que resultou na formação de genótipos altamente adaptados às mais diversas condições ambientais brasileiras. Embora estas raças não possuam o mesmo potencial produtivo das raças exóticas melhoradas, elas são consideradas extremamente importantes devido às relações sociais e culturais que guardam com as populações do campo. Além disso, as raças localmente adaptadas possuem características adaptativas importantíssimas para a manutenção de sistemas produtivos tradicionais. A otimização da utilização dos recursos genéticos naturalizados depende de um conhecimento profundo destas populações e, portanto, a caracterização morfológica, produtiva e molecular são ferramentas imprescindíveis para o sucesso da conservação e utilização deste recurso genético. Com base nisso, o objetivo desta tese foi aprofundar os estudos de caracterização molecular das principais raças de ovinos localmente adaptadas brasileiras: Crioula Lanada, Morada Nova e Santa Inês. Assim, o capítulo I intitulado “Identificação de assinaturas de seleção em animais de produção” consiste em uma revisão cujo objetivo é descrever os principais efeitos da seleção natural/artificial nos genomas das espécies de animais de produção, apresentar os principais métodos de análise de assinaturas de seleção e discutir os recentes avanços nesta área de estudo. Foram realizados dois estudos que resultaram nos capítulos II e III desta tese. O capítulo II, intitulado “Identificação de assinaturas de seleção em ovinos de raças localmente adaptadas brasileiras”, teve como objetivo a identificação e caracterização de regiões genômicas prováveis de estar sob seleção nas três principais raças brasileiras localmente adaptadas de ovinos e caracterizar estar regiões com a finalidade de identificar genes envolvidos com diferenças produtivas/adaptativas entre estas raças. A identificação das regiões sujeitas à seleção foi feita com base em dois tipos de metodologia: diferenciação entre populações (FST) e desequilíbrio de ligação (iHS e Rsb). Foram identificados 78 genes candidatos envolvidos com funções como: resposta imune, desenvolvimento do sistema nervoso, percepção sensorial e desenvolvimento de pelos/lã. O capítulo III, intitulado: “Identificação de subestrutura de populações em ovinos de raças localmente adaptadas brasileiras”, teve como objetivos identificar e caracterizar a presença de subestruturação genética dentro das três principais raças brasileiras localmente adaptadas de ovinos. Foi observada, de uma forma geral, a presença de diferenciação genética bastante considerável ao comparar os rebanhos de cada raça analisada. Além disso, tanto na raça Crioula Lanada quanto na raça Santa Inês, pode ser observada a presença de grupos bem distintos de indivíduos, sugerindo a efetiva presença de diferentes ecótipos/linhagens dentro destas raças.

Submitted by Vanessa Zirondi Longhini null (vanessa92274@aluno.feis.unesp.br) on 2016-02-16T23:39:57Z No. of bitstreams: 1 Dissertação_Vanessa Longhini.pdf: 813017 bytes, checksum: f100d3205cc5149beda7724df1a9c5fa (MD5) / Approved for entry into archive by Sandra Manzano de Almeida (smanzano@marilia.unesp.br) on 2016-02-17T11:55:34Z (GMT) No. of bitstreams: 1 longhini_vz_me_bot.pdf: 813017 bytes, checksum: f100d3205cc5149beda7724df1a9c5fa (MD5) / Made available in DSpace on 2016-02-17T11:55:34Z (GMT). No. of bitstreams: 1 longhini_vz_me_bot.pdf: 813017 bytes, checksum: f100d3205cc5149beda7724df1a9c5fa (MD5) Previous issue date: 2016-02-04 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O objetivo foi avaliar o efeito do consórcio da cultura do milho com capim-marandu com ou sem feijão guandu para ensilagem, com posterior sobressemeadura de aveia preta em linha e a lanço sobre a disponibilidade e altura de forragem para pastejo, o comportamento ingestivo, o desempenho e as características da carcaça de cordeiros suplementados com essas silagens em semi-confinamento. O delineamento experimental foi inteiramente casualizado, os tratamentos avaliados foram combinados em arranjo fatorial 2 x 2, em esquema de parcelas subdivididas, sendo dois tipos de silagem (S): de milho com capim-marandu e feijão guandu (C/G) e sem feijão guandu (S/G), duas modalidades de sobressemeadura da aveia preta (AV): em linha (Li) ou a lanço (La). Foram utilizados 48 cordeiros machos em ambos os anos. As características de carcaça não foram influenciadas pela interação entre os fatores (P > 0,05), no entanto, os fatores S x AV e S x C influenciaram as variáveis disponibilidade de forragem (DF), consumo de massa seca de suplemento (CMS, % do Peso Corporal – PC) e pastejo (P). O ganho médio diário (GMD) e ócio diário (OD) foram influenciadas apenas pela interação S x AV. A inclusão do feijão guandu no sistema de produção em consócio com milho e capim-marandu e a sobressemeadura da aveia em linha aumentou (P ≤ 0,05) a DF, influenciando no aumento do tempo de P e no menor CMS de suplemento (% do PC). Conclui-se, portanto, que o consórcio do milho com capim-marandu e feijão guandu cultivados para silagem no verão/outono aumenta a disponibilidade de pastagem. No inverno/primavera a modalidade de sobressemeadura da aveia em linha apresenta maior disponibilidade de forragem para pastejo em relação a lanço. O consórcio tríplice é uma alternativa a ser utilizado em sistemas integrados de produção agropecuária, em condições tropicais. Em semi-confinamento, o tempo de pastejo aumenta quando há maior disponibilidade de forragem. A silagem de milho em consórcio com capim-marandu e feijão guandu não interfere no desempenho e características de carcaça de cordeiros semi-confinados. / The objective was to evaluate the effect of maize intercropped with palisadegrass with or without pigeonpea for silage, with subsequent overseeded oat line and broadcasted on the availability and height of forage for grazing, ingestive behavior, performance and carcass characteristics of lambs supplemented with such silage in semi-feedlot. The experimental design was completely randomized, the treatments were combined in a factorial arrangement 2 x 2, in a split-plot, two types of silage (S): corn with palisadegrass and pigeonpea (C / G) and without pigeonpea (S / G), two mode overseeded of oat (AV): in line (Li) or broadcast (La). Were used 48 lambs males. Carcass characteristics were not influenced by the interaction between the factors (P > 0,05), however, the interaction factors S x AV and S x C, influenced the variables availability of forage (DF), dry matter intake of supplement (CMS ,% Body Weight - PC) and grazing time (P). The average daily gain (GMD) and daily idling time (OD) were influenced only by S x AV interaction. The inclusion of pigeonpea in the production system in intercropped with corn and palisadegrass and overseeded oat in line increased (P ≤ 0,05) DF, influencing the increase in the time of P and lower CMS of supplement (% PC). It can be conclued, therefore, that the intercropped of corn with palisadegrass and pigeonpea for silage in the summer/fall increases the forage availability of pasture. In winter/spring the mode overseeded of oat in line provided greater forage availability for grazing than broadcast. The triple intercropped is an alternative to be used in integrated agricultural production systems in tropical conditions. In semi-confinement, grazing time increases when there is greater availability of forage. Corn silage in intercropped with palisadegrass and pigeonpea does not interfere with performance and carcass characteristics of semi-lambs. / FAPESP: 2014/12950-6

Submitted by Luara Afonso de Freitas null (luaraa.freitas@gmail.com) on 2018-02-28T12:52:28Z No. of bitstreams: 1 FREITAS_2018.pdf: 2467849 bytes, checksum: d131127bf0cf93ad3b5bfccd0626241b (MD5) / Approved for entry into archive by Alexandra Maria Donadon Lusser Segali null (alexmar@fcav.unesp.br) on 2018-02-28T13:18:49Z (GMT) No. of bitstreams: 1 freitas_la_me_jabo.pdf: 2467849 bytes, checksum: d131127bf0cf93ad3b5bfccd0626241b (MD5) / Made available in DSpace on 2018-02-28T13:18:49Z (GMT). No. of bitstreams: 1 freitas_la_me_jabo.pdf: 2467849 bytes, checksum: d131127bf0cf93ad3b5bfccd0626241b (MD5) Previous issue date: 2018-02-21 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O uso de raças ou animais resistentes aos endoparasitas dentro do sistema de produção de ovinos de carne é uma das alternativas mais eficientes para se obter maior produção. O controle dos acasalamentos entre animais aparentados é de grande importância para reduzir perdas na produção pelo aumento da homozigose de alelos deletérios. O peso corporal é uma das características de maior importância econômica em ovinos e pode ser registrado ao longo da vida de um mesmo animal. Os modelos de regressão aleatória na avaliação genética de medidas longitudinais são geralmente recomendados para estimar parâmetros genéticos de dados longitudinais. As análises multivariadas são um conjunto de métodos estatísticos que torna possível a análise simultânea de medidas múltiplas para cada indivíduo ou fenômeno observado. Este trabalho teve como objetivos: (1) analisar a estrutura populacional e verificar o efeito da endogamia sobre características fenotípicas de crescimento e resistência a verminose, (2) comparar estruturas (homogeneidade e heterogeneidade de variâncias) para modelar a variância residual em modelos de regressão aleatória, (3) avaliar a influência desta modelagem na estimação de parâmetros genéticos a fim de determinar o modelo mais apropriado para estudar o crescimento e a resistência à verminose e (4) avaliar a associação genética e explorar o perfil genético da produção de carne e resistência à verminose em ovinos da raça Santa Inês. O banco de dados fenotípico conteve 2.159 registros de peso corporal oriundos de 753 animais, 1.468 registros de volume globular provenientes de 476 animais e 981 registros de contagem de ovos por grama de fezes oriundos de 375 animais entre 30 a 900 dias de idade medidos mensalmente e registros de pedigree de 2.410 animais da raça Santa Inês. Os animais foram divididos em 10 classes de idade (CI90 = 30 a 90 dias de idade CI180= 91 a 180 dias de idade, CI270= 181 a 270 dias de idade, CI360= 271 a 360 dias de idade, CI450= 361 a 450 dias de idade, CI540= 451 a 540 dias de idade, CI630= 541 a 630 dias de idade, CI720= 631 a 720 dias de idade, CI810= 721 a 810 dias de idade, CI900= 811 a 900 dias de idade). A estrutura do pedigree foi analisada utilizando o programa Endog 4.8. As análises de estimação dos componentes de variância foram realizadas por meio de modelo animal unicaracterística de regressão aleatória pelo método de máxima verossimilhança restrita utilizando polinômios de Legendre. O critério da informação bayesiana foi utilizado para selecionar o melhor modelo. A análise de componentes principais foi realizado no software STATISTIC e a analise de agrupamento hierárquico e não hierárquico no software R. Foi observado aumento no coeficiente de endogamia até a 6ª geração máxima, aumento do parentesco médio e da porcentagem de animais endogâmicos até a 7ª geração máxima. O polinômio de Legendre de ordem 3 (intercepto, linear e quadrático) proporcionou o melhor ajuste dos dados para peso corporal, volume globular e contagem de ovos por grama de fezes. A seleção dos animais poderia ser feita com base no peso corporal a partir de 271 dias de idade, pois a estimativa de herdabilidade foi de 0,23 (0,03) e foram altas as correlações genéticas do peso corporal nesta idade com a maioria dos pesos corporais nas demais idades, exceto com peso corporal medida entre 30 a 90 dias de idade. A seleção destes animais para resistência a verminose se realizada poderá ser pouco eficiente devido às baixas estimativas de herdabilidade para volume globular (0,09±0,01 a 0,18±0,02) e contagem de ovos por grama de fezes (0,01±0,02 a 0,17±0,03), portanto, o ganho genético será a longo prazo. A seleção para peso corporal poderia trazer ganhos genético favoráveis para a característica volume globular devido à proximidade das características no eixo do componente principal um. Nas análises de agrupamento apenas um dos três grupos genéticos identificados apresentou perfil genético indicado para a seleção para peso corporal e volume globular. / The use of resistant animals to gastrointestinal nematode parasites within the meat production system is one of the most efficient alternatives to increase meat yield in sheep. The control of mating between related animals is of great importance to reduce losses in meat production by increasing the homozygosity of deleterious alleles. Application of Random regression models in the genetic evaluation of longitudinal measurements is generally recommended to adjust growth curves and to estimate genetic parameters of longitudinal data. The multivariate analyzes are a set of statistical methods that make possible the simultaneous analysis of multiple measures for each individual or observed phenomena. The aims of this study were: (1) to analyze the population structure and verify the effect of inbreeding on phenotypic traits of growth and resistance to gastrointestinal nematode parasites, (2) to compare structures (homogeneity and heterogeneity of variances) to model residual variance in random regression models, (3) to study the influence of this modeling in the estimation of genetic parameters in order to determine the most appropriate model to study the growth and resistance to gastrointestinal nematode parasites curves, and (4) evaluate the genetic association and explore the genetic profile of meat production and resistance to gastrointestinal nematode parasites in Santa Inês sheep. The data contained 2,159 body weight records from 753 animals, 1,468 mean corpuscular volume records from 476 animals and 981 records of fecal egg counts from 375 animals and pedigree information from 2,410 in Santa Ines sheep. The animals were divided into 10 age classes (CI90 = 30 to 90 days of age CI180 = 91 to 180 days of age, CI270 = 181 to 270 days of age, CI360 = 271 to 360 days of age, CI450 = 361 to 450, CI540 = 451 to 540 days of age, CI630 = 541 to 630 days of age, CI720 = 631 to 720 days of age, CI810 = 721 to 810 days of age, CI900 = 811 to 900 days of age). The structure of the pedigree was analyzed using the program Endog 4.8. Analyzes of the variance component estimates were performed using a one-trait model of random regression using the restricted maximum likelihood method. The Bayesian information criterion was used to select the best model. The principal component analysis was performed in STATISTIC software and hierarchical and non-hierarchical analysis grouping was performed in the software R. There was an increase in the inbreeding coefficient up to the 6th maximum generation and also an increase in the average relatedness and in the percentage of inbred animals up to the 7th maximum generation. Genetic correlation estimates for all traits in the age classes presented values close to the unit at close weighings, with a reduction in the magnitude of the correlations as the time interval between weighings increased. The Legendre polynomial of order 3 (intercept, linear and quadratic) provided the best fit of the data for body weight, mean corpuscular volume, and fecal egg counts. The selection of the animals could be made based on body weight from 271 days of age, as the heritability estimate was moderate, 0.23 (0.03), and showed high genetic correlations with most body weights, except with body weight from 30 to 90 days of age. Selection of these animals for resistance to gastrointestinal nematode parasites if carried out may result in low efficiency due to the low estimates of heritability for the mean corpuscular volume (0.09 ± 0.01 to 0.18 ± 0.02) and fecal egg counts (0.01 ± 0.02 to 0.17 ± 0.03), therefore, the genetic gain will be low and in the long term. The selection of body weight could bring favorable genetic gains to the mean corpuscular volume due to the proximity of the traits in the axis of the main component one. In cluster analysis, only one of the three genetic groups identified has a genetic profile indicated for selection for the studied traits. / 2016/10583-1

Orientador: Ciniro Costa / Resumo: O objetivo foi avaliar o efeito do consórcio da cultura do milho com capim-marandu com ou sem feijão guandu para ensilagem, com posterior sobressemeadura de aveia preta em linha e a lanço sobre a disponibilidade e altura de forragem para pastejo, o comportamento ingestivo, o desempenho e as características da carcaça de cordeiros suplementados com essas silagens em semi-confinamento. O delineamento experimental foi inteiramente casualizado, os tratamentos avaliados foram combinados em arranjo fatorial 2 x 2, em esquema de parcelas subdivididas, sendo dois tipos de silagem (S): de milho com capim-marandu e feijão guandu (C/G) e sem feijão guandu (S/G), duas modalidades de sobressemeadura da aveia preta (AV): em linha (Li) ou a lanço (La). Foram utilizados 48 cordeiros machos em ambos os anos. As características de carcaça não foram influenciadas pela interação entre os fatores (P > 0,05), no entanto, os fatores S x AV e S x C influenciaram as variáveis disponibilidade de forragem (DF), consumo de massa seca de suplemento (CMS, % do Peso Corporal – PC) e pastejo (P). O ganho médio diário (GMD) e ócio diário (OD) foram influenciadas apenas pela interação S x AV. A inclusão do feijão guandu no sistema de produção em consócio com milho e capim-marandu e a sobressemeadura da aveia em linha aumentou (P ≤ 0,05) a DF, influenciando no aumento do tempo de P e no menor CMS de suplemento (% do PC). Conclui-se, portanto, que o consórcio do milho com capim-marandu e feijão guandu cultivado... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The objective was to evaluate the effect of maize intercropped with palisadegrass with or without pigeonpea for silage, with subsequent overseeded oat line and broadcasted on the availability and height of forage for grazing, ingestive behavior, performance and carcass characteristics of lambs supplemented with such silage in semi-feedlot. The experimental design was completely randomized, the treatments were combined in a factorial arrangement 2 x 2, in a split-plot, two types of silage (S): corn with palisadegrass and pigeonpea (C / G) and without pigeonpea (S / G), two mode overseeded of oat (AV): in line (Li) or broadcast (La). Were used 48 lambs males. Carcass characteristics were not influenced by the interaction between the factors (P > 0,05), however, the interaction factors S x AV and S x C, influenced the variables availability of forage (DF), dry matter intake of supplement (CMS ,% Body Weight - PC) and grazing time (P). The average daily gain (GMD) and daily idling time (OD) were influenced only by S x AV interaction. The inclusion of pigeonpea in the production system in intercropped with corn and palisadegrass and overseeded oat in line increased (P ≤ 0,05) DF, influencing the increase in the time of P and lower CMS of supplement (% PC). It can be conclued, therefore, that the intercropped of corn with palisadegrass and pigeonpea for silage in the summer/fall increases the forage availability of pasture. In winter/spring the mode overseeded of oat in line provid... (Complete abstract click electronic access below) / Mestre

In seasonal mammals the duration of nocturnal melatonin secretion accurately reflects the environmental photoperiod. The endocrine rhythm is decoded by a specialised portion of the pituitary gland (the pars tuberalis, PT) which then relays this information to the pars distalis and hypothalamus, precipitating huge annual changes in physiology and behaviour. However how the PT decodes the melatonin signal is currently unknown. Melatonin influences gene transcription in the ovine PT at its onset and offset, and the phase relationship of these two groups is believed to form the underlying mechanism by which the PT integrates seasonal time. The transcripts induced at melatonin offset are understood to be under the control of a seasonally gated cAMP mechanism. Conversely processes involved in melatonin-mediated gene induction are currently not understood.The work in this thesis ultimately aims to reveal how the seasonal melatonin signal is decoded by the PT. To this end melatonin-mediated gene induction has been characterised through RNAseq, the highly displaced cohorts submitted to bioinformatic promoter analysis and the paradigm tested though in vitro modelling techniques.In this study a 1.5 h infusion with melatonin acutely regulated 219 transcripts in the ovine PT (115 induced, 104 repressed, >1.5 fold change), confirming previous association of several genes (including Cry1, MT1, Gadd45g, Nampt and Npas4) to rapid melatonin control. Gross promoter analysis of these groups indicated that the induced gene cohort was significantly enriched for GC content and CpG islands suggesting the involvement of epigenetic mechanisms of transcriptional control. Further bioinformatic analysis specifically implicated the importance of transcription factors ZFP161 and PAX5 in melatonin-mediated gene induction in the PT. Several immortalised cell lines were screened for the presence of a functional melatonin receptor. Two strains (MCF7 oMT1 and NES2Y) exhibited significant attenuation of forskolin-mediated cAMP accumulation when co-treated with melatonin, a hallmark of melatonin Gαi-coupled protein receptor signalling. These lines were subsequently evaluated as models of melatonin-mediated gene induction of the sheep PT through ovine promoter reporter assays of Cry1, Nampt, NeuroD1 and Npas4. However, treatment with melatonin failed to evoke a reporter response suggesting that the cell line models were inadequately equipped to reflect PT biology. Subsequently a protocol was established to culture ovine PT explants culture which faithfully recapitulated melatonin mediated transcriptional dynamics in vitro, providing a possible tool for the future investigation of the PT. Lastly, previous work has shown the transcriptional profile of Npas4 to peak highly and transiently, pre-empting the expression of other melatonin-induced genes. Using a COS7 cell line model, heterologously-expressed NPAS4 was shown to form functional heterodimeric partnerships with ARNT and ARNTL and transactivate both Cry1 and Nampt promoter reporters through novel binding sites. Collectively these data indicated NPAS4 to act as an immediate activator of melatonin regulated circuits