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A method was developed and tested to estimate challenge load due to disease outbreaks and other challenges in sows using reproduction records. The method was based on reproduction records from a farm with known disease outbreaks. It was assumed that the reduction in weekly reproductive output within a farm is proportional to the magnitude of the challenge. As the challenge increases beyond certain threshold, it is manifested as an outbreak. The reproduction records were divided into 3 datasets. The first dataset called the Training dataset consisted of 57,135 reproduction records from 10,901 sows from 1 farm in Canada with several outbreaks of porcine reproductive and respiratory syndrome (PRRS). The known disease status of sows was regressed on the traits number born alive, number of losses as a combination of still birth and mummified piglets, and number of weaned piglets. The regression coefficients from this analysis were then used as weighting factors for derivation of an index measure called challenge load indicator. These weighting factors were derived with i) a two-step approach using residuals or year-week solutions estimated from a previous step, and ii) a single-step approach using the trait values directly. Two types of models were used for each approach: a logistic regression model and a general additive model. The estimates of challenge load indicator were then compared based on their ability to detect PRRS outbreaks in a Test dataset consisting of records from 65,826 sows from 15 farms in the Netherlands. These farms differed from the Canadian farm with respect to PRRS virus strains, severity and frequency of outbreaks. The single-step approach using a general additive model was best and detected 14 out of the 15 outbreaks. This approach was then further validated using the third dataset consisting of reproduction records of 831,855 sows in 431 farms located in different countries in Europe and America. A total of 41 out of 48 outbreaks detected using data analysis were confirmed based on diagnostic information received from the farms. Among these, 30 outbreaks were due to PRRS while 11 were due to other diseases and challenging conditions. The results suggest that proposed method could be useful for estimation of challenge load and detection of challenge phases such as disease outbreaks.

Production traits such as growth rate may depend on the social interactions between group members. These social interactions might be partly heritable and are referred to as indirect genetic effects (IGE), social-, associative-, or competitive genetic effects. IGE may contribute to heritable variation in traits, and can thus be used to increase the response to selection. This, however, has hardly been tested by selection experiments. Our objective was to determine the effects of one generation of selection on IGE for growth (IGEg) in pigs on ADG, BW, ADFI, feed efficiency, and post-mortem measurements. Sires (n=24) and dams (n=64) were selected to create a high vs. low contrast for IGEg in the offspring (n=480). The IGE difference was 2.8 g ADG per pen mate, corresponding to 14 g higher ADG in high IGEg offspring compared to low IGEg offspring when housed in groups of 6 (i.e. (6-1)×2.8 = 14). Male (barrows) and female (gilts) offspring were housed in groups of 6 of the same IGEg classification, in either barren concrete pens or pen enriched with straw and wood shavings (n=80 pens). Pigs were followed from birth to slaughter. Data were analyzed in a mixed model with pen as random factor. There was no difference in ADG between high and low IGEg pigs during the finishing period (wk 10 to 23). Opposite to expectations, high IGEg tended to have a 17 g lower ADG from weaning to slaughter (P=0.08), which was caused by a higher BW of low IGEg pigs in wk 5 (P=0.008). This led to a 2.3 kg lower carcass weight (P=0.02) and 2.2 mm less muscle depth for high IGEg pigs (P=0.03). High IGEg pigs had a higher stomach wall damage score (P=0.01). Pigs on straw had a 25 g lower ADG during finishing (P=0.03), and less stomach wall damage (P

This paper focuses on how farmers can reduce damaging behaviour in livestock farming by using robustness strategies. We suggest focusing not only on breeding and improvement of early life, but also on supporting adaptation to the environment by offering a suitable housing environment. First, we describe the theoretical background to robustness. Three different robustness strategies are then related to one external and two internal aspects of system vulnerability, namely, exposure, resistance and resilience. Subsequently, we investigate the extent to which robustness can contribute to the reduction of damaging behaviour.

Grain yield in wheat is influenced directly and indirectly by other plant characteristics. One of the main goals in wheat breeding programs is increase of grain yield. Considering the role of crop rotation in increasing grain yield, and in order to study the difference between crop rotations for wheat yield and yield components (Darya cultivar), an experiment was conducted with six rotation treatments (wheat-chickpea-wheat, wheat-cotton-wheat, wheat-watermelon-wheat, wheat-wheat-wheat, wheat-canola-wheat and wheat-sunflower-wheat), as a randomized complete blocks design with six replications, at Research Farm of Agricultural Research Station of Gonbad Kavous, Iran, during 2004 to 2008. Results showed that number of spikes per m-2, number of kernels per spike and mean kernel weight were important traits in all rotations. Also, selection of different traits could be changed depending on the experiment’s conditions, as in the wheat-wheat-wheat, wheat-watermelon-wheat and wheat-sunflower-wheat rotations the kernel weight, grain filling period and vegetative growth period are useful for indirect selection of breeding strategy while in wheat-canola-wheat and wheat-chickpea-wheat rotations the number of kernels per spike, number of spikes per m2, grain filling period and vegetative growth period are more important.

Se colectaron en diferentes regiones de Cuba semillas de las accesiones de papayo Tallo Morado de Nava, Amarilla de Duaba, Amarilla de Nava y Sapote de Pilón. Estas se plantaron en condiciones de campo en Jagüey Grande, Matanzas - Cuba, donde se evaluó la presencia e intensidad de síntomas de mancha anular, siguiendo una escala graduada del 1 al 5. Los resultados mostraron un incremento temporal de la proporción de plantas afectadas en todas las accesiones. La accesión Amarilla de Duaba mostró los síntomas a los dos meses después de la primera evaluación (MDPE), mientras que el resto lo hizo a los cinco MDPE, aunque con proporciones que variaron entre ellas. A los siete MDPE las accesiones Amarilla de Duaba y Amarilla de Nava mostraron proporciones idénticas de plantas enfermas, mientras que Tallo morado de Nava y Sapote de Pilón mostraron proporciones inferiores. La intensidad de los síntomas se incrementó en los diferentes órganos siguiendo el siguiente orden: tallo (1,7 a 2,66), pecíolos (2,21 a 3,03) y follaje (3,44-4,03). En los frutos la intensidad de los síntomas observados fue inferior a 2,5, considerados como leves de acuerdo a su intensidad y distribución. Se ofrecen los primeros resultados sobre la susceptibilidad a la mancha anular de estas accesiones, siendo de gran utilidad para los productores, así como para los programas de mejoramiento genético en el país.Os acessos de mamão Tallo morado de Nava, Amarilla de Duaba, Amarilla de Nava e Sapote de Pilón foram coletados em diferentes regiões de Cuba e plantados em condições de campo em Jagüey Grande, Matanzas - Cuba. Nestas plantas foram avaliadas a presença e intensidade dos sintomas de mancha anelar, usando uma escala graduada de 1-5. Os resultados mostraram um aumento, com o tempo, na proporção de plantas afetadas em todos os acessos. O acesso Amarilla de Duaba apresentou sintomas dois meses após a primeira avaliação (MDPE), enquanto para os restantes foram observados sintomas após cinco MDPE, contudo em proporções diferentes entre eles. Aos sete MDPE os acessos Amarilla de Duaba e Amarilla de Nava, apresentaram proporções iguais de plantas doentes, enquanto Tallo morado de Nava e Sapote de Pilon apresentaram menores proporções. O aumento da intensidade dos sintomas foi diferente nos órgãos da planta na seguinte ordem: caule (1,7-2,66), pecíolos (2,21-3,03) e folhagens (3,44-4,03). Nos frutos a intensidade dos sintomas observados foi inferior a 2,5, considerada leve em função da sua intensidade e distribuição. Estes são os primeiros resultados sobre a susceptibilidade a mancha anelar destes acessos, sendo muito úteis para os produtores, bem como para os programas de melhoramento do país.The papaya accessions "Tallo morado de Nava", "Amarilla de Duaba", "Amarilla de Nava" and "Sapote de Pilón" were collected from different regions of Cuba and planted under field conditions in Jagüey Grande, Matanzas - Cuba. These plants were assessed for the presence and intensity of ringspot symptoms, using a graduated scale of 1-5. Results showed an increase, with time, in the proportion of affected plants for all accessions. The accession "Amarilla de Duaba" had symptoms two months after the first assessment (MAFA), while for the remaining accessions, symptoms were noted after only five MAFA but at proportions that differed among them. At seven MAFA, the accessions "Amarilla de Duaba" and "Amarilla de Nava" had proportions equal to those of diseased plants, while "Tallo morado de Nava" and "Sapote de Pilon" showed lower proportions. The increase in symptom intensity was different for the plant organs in the following order: stem (1.7-2.66), petioles (2.21-3.03) and leaves (3.44-4.03). For fruits, the intensity of the observed symptoms was inferior to 2.5, considered light based on their intensity and distributions. These are the first results about ringspot susceptibility for these accessions, which are highly useful for farmers, as well as for breeding programs in the country.

Spain is among the main seafood consumer countries in the world and an important aquaculture industry has been developed to satisfy its demands. Rearing facilities of aquatic species exist in Spain since Roman times, and in the Middle Age more sophisticated hatcheries were developed in Monasteries and Abbeys for freshwater species. Galicia (NW Spain) is the main productive region due to the special characteristics of its coasts. Different fish and mollusk species are produced in intensive or semi-extensive systems in this region. The leader species of Spanish aquaculture is the Mediterranean mussel (Mytillus galloprovincialis), and within fish, sea bream (Sparus aurata), sea bass (Dicentrarchus labrax), rainbow trout (Oncorhynchus mykiss) and turbot (Scopthalmus maximus). Breeding programs started in the 90's in turbot, currently in the fifth generation of selection, and more recently in sea bass and sea bream. Microsatellite traceability tools have been developed to assist breeding programs and to estimate heritabilities for potential selective traits in fish and, to a minor extent, in mollusks. Genomic resources and tools arrive to Spanish aquaculture through flatfish (turbot and Senegalese sole, Solea senegalensis) and later, this know-how has been transferred to other fish and mollusk species. The first transcriptomic databases, microarrays and genetic maps were developed in turbot and Senegalese sole. The last main achievement has been the whole assembling of turbot genome, which is being used as reference for new genotyping (RAD-seq) and gene expression (RNA-seq) methodologies. It is time to apply the huge amount of information accumulated in broad multidisciplinary research consortia to boost production to a higher level in collaboration with industry. Statement of relevance Main genomics advances for boosting Spanish aquaculture.

Downy mildew is a fungal disease caused by Plasmopara halstedii and leads to loss of yield up to 100% in sunflower. Disease control is performed mostly through chemical seed treatment and breeding. Due to the time consuming nature of conventional breeding, it is supported by biotechnological approaches. Marker-assisted selection (MAS) is a strategic approach in molecular breeding using molecular markers. Single nucleotide polymorphisms (SNPs) such as insertions, deletions, and base-pair substitutions are more advantageous than other molecular markers. The abundance and biallelic nature of SNPs in a genome provide flexibility in the choosing of SNPs at the desired loci. Competitive allele-specific PCR (KASP) is a genotyping technology for screening of trait-specific SNP markers. In this study, SNP markers (NSA002867, NSA006138; NSA000052, NSA000354; NSA002220, NSA002251) linked with the downy mildew resistance genes Pl(arg), Pl(13) and Pl(8), respectively, were analyzed via KASP in three parental crosses (RHA-419 x Coiombi, RHA-419 x P64LC53, RHA-419 x Oliva) for Pl(arg) one parental cross (HA-R5 x P64LC53) for Pl(13), one parental cross (P64LC53 x HA-89) for Pl(8), and 140 F-2 individuals. According to the allelic discrimination results, NSA002867 and NSA006138 markers were discriminative in all crosses for PIarg, NSA000354 marker was discriminative for Pl(13), and NSA002220 and NSA002251 markers were discriminative for PI8. This study has revealed the potential use of SNP markers in combination with KASP assay for MAS studies, particularly downy mildew resistance in sunflower.

Objectives of this study were to determine the combined market share of breeding companies in aquaculture production in Europe, to describe the main characteristics of breeding companies and their programs, and to provide per species estimates on cumulative genetic gain in growth performance. Surveys were conducted among breeding companies of five major species cultured in Europe: Atlantic salmon, rainbow trout, European seabass, gilthead seabream, and turbot. The market share was estimated as the combined egg or juvenile production of breeding companies relative to the total egg or juvenile production in Europe for each species in 2012. Cumulative genetic gain was estimated from the number of selected generations in current breeding programs, combined with genetic trends, reported selection responses in literature, and phenotypic differences. The combined market share of breeding companies ranged from 43–56% for seabass to 100% for turbot. The total volume of fish production in Europe that originated from selective breeding was 1653–1706 thousand tonnes, corresponding to 80–83% of the total aquaculture production. Over species, there were 37 breeding programs of which the majority performed family selection. Growth performance was universally selected upon. Cumulative genetic gain in growth performance varied from + 65% for turbot to + 900% for trout in terms of harvest weight, and from + 25% for turbot to + 200% for trout in terms of thermal growth coefficient. It is concluded that selective breeding has a major impact on European aquaculture and will contribute to future growth of the sector. Statement of relevance This manuscript helps to understand the impact of selective breeding on European aquaculture. It shows that the adoption of selective breeding is much higher in Europe than globally. It demonstrates that selective breeding has led to major improvements. Forecasts of industry trends are made and the importance of selective breeding to future growth of aquaculture production is illustrated.

Rainbow trout is a globally important fish species for aquaculture. However, fish for most farms worldwide are produced by only a few breeding companies. Selection based solely on fish performance recorded at a nucleus may lead to lower-than-expected genetic gains in other production environments when genotype-by-environment (G × E) interaction exists. The aim was to quantify the magnitude of G × E interaction of growth traits (tagging weight; BWT, harvest weight; BWH, and growth rate; TGC) measured across 4 environments, located in 3 different continents, by estimating genetic correlations between environments. A total of 100 families, of at least 25 in size, were produced from the mating 58 sires and 100 dams. In total, 13,806 offspring were reared at the nucleus (selection environment) in Washington State (NUC) and in 3 other environments: a recirculating aquaculture system in Freshwater Institute (FI), West Virginia; a high-altitude farm in Peru (PE), and a cold-water farm in Germany (GER). To account for selection bias due to selective mortality, a multitrait multienvironment animal mixed model was applied to analyze the performance data in different environments as different traits. Genetic correlation (rg) of a trait measured in different environments and rg of different traits measured in different environments were estimated. The results show that heterogeneity of additive genetic variances was mainly found for BWH measured in FI and PE. Additive genetic coefficient of variation for BWH in NUC, FI, PE, and GER were 7.63, 8.36, 8.64, and 9.75, respectively. Genetic correlations between the same trait in different environments were low, indicating strong reranking (BWT: rg = 0.15 to 0.37, BWH: rg = 0.19 to 0.48, TGC: rg = 0.31 to 0.36) across environments. The rg between BWT in NUC and BWH in both FI (0.31) and GER (0.36) were positive, which was also found between BWT in NUC and TGC in both FI (0.10) and GER (0.20). However, rg were negative between BWT in NUC and both BWH (–0.06) and TGC (–0.20) in PE. Correction for selection bias resulted in higher additive genetic variances. In conclusion, strong G × E interaction was found for BWT, BWH, and TGC. Accounting for G × E interaction in the breeding program, either by using sib information from testing stations or environment-specific breeding programs, would increase genetic gains for environments that differ significantly from NUC.

To support breeding programs of pear tree, on the selection of cultivars to subtropical area in Brazil, the objective of this research was to adjust the growth medium basic to pollen grain germination. The pollen grains of 'D'Água' cultivar were spread on the surface of Petri dishes containing 20 ml of culture medium in accordance with the following sequential experiments: 1) ágar (4; 6; 8 and 10 g L-1) and pH (3,5; 4,5; 5,5 and 6,5); 2) sucrose (0; 30; 60 and 90 g L-1); 3) calcium nitrate (0; 200; 400 and 800 mg L-1); 4) boric acid (0; 400; 800 and 1200 mg L-1); 5) temperature of incubation (15; 20; 25 e 30 ºC) and 6) emission time of the pollen tube (0; 1; 2; 3; 4; 5 and 6 hours after inoculation). After incubation, the germination rate of pollen grains of nine pear cultivars ('Rocha', 'Abate Fetel', 'Packham's Triumph', 'Atago', 'Hosui', 'Primorosa', 'Triunfo', 'Seleta' and 'D'Água') was evaluated, and number of stamens, the number of pollen grains per anther and per flower. The protocol for germination of pollen grains of pear tree consist in the culture medium have to be solidified with 10 g L-1 ágar, being the pH measured to 5,2 , added with 90 g L-1 sucrose, 145 mg L-1 calcium nitrate and 700 mg L-1 boric acid, with incubation temperature of 23 ºC. The readings germination percentage should be performed after five hours of incubation. The pollen grain 'Rocha' cultivar showed higher germination percentage. RESUMO Visando dar suporte aos trabalhos de melhoramento da pereira, para seleção de cultivares para regiões subtropicais, objetivou-se ajustar o meio de cultura para a germinação de grãos de pólen. Os grãos de pólen da cultivar 'D'Água' foram espalhados sobre placas de Petri contendo 20 mL de meio, de acordo com os experimentos sequenciais: 1) ágar (4; 6; 8 e 10 g L-1) e pH (3,5; 4,5; 5,5 e 6,5); 2) sacarose (0; 30; 60 e 90 g L-1); 3) nitrato de cálcio (0; 200; 400 e 800 mg L-1); 4) ácido bórico (0; 400; 800 e 1200 mg L-1); 5) temperatura de incubação (15; 20; 25 e 30 ºC) e 6) tempo de emissão do tubo polínico (0; 1; 2; 3; 4; 5 e 6 horas após a inoculação). Após a inoculação avaliou-se a germinação dos grãos de pólen de nove cultivares ('Rocha', 'Abate Fetel', 'Packham's Triumph', 'Atago', 'Hosui', 'Primorosa', 'Triunfo', 'Seleta' e 'D'Água'), além do número de anteras, número de grãos de pólen por antera e por flor. O protocolo para germinação de grãos de pólen de pereira consiste no meio de cultura ser solidificado com 10 g L-1 de ágar, com pH ideal de 5,2, acrescido de 90 g L-1 de sacarose, 145 mg L-1 de nitrato de cálcio e 700 mg L-1 de ácido bórico, com temperatura de incubação de 23,7 ºC. As análises de germinação devem ser realizadas após 5h de incubação. Os grãos de pólen da cultivar 'Rocha' apresentaram maior porcentagem de germinação.

Doutoramento em Biologia Slash Pine (Pinus elliottii var. elliottii) and the hybrid (Pinus elliottii var. elliottii x Pinus caribaea var. hondurensis) have a great economic value due to their high growth ratio and resin production. Therefore, it is important to achieve a strategy to propagate this species and the hybrid more rapidly maintaining their characteristics. This project aims to preserve/enlarge the Pinus germplasm collection, provided by the company KLÓN, Innovative Technologies from Cloning, by micropropagation and cryopreservation techniques and analyze the putative changes (genetic stability) in micropropagated plants by flow cytometry, to study plant survival rates, growth and photosynthetic performance after acclimatization. In Chapter I, general aspects of the species and hybrid under study are presented, as well as a brief description of the breeding programs in Pinus spp. and the contribution that innovative techniques of in vitro propagation can give, leading to decades of anticipation on the breeding programs results. It was also described some major aspects to the different micropropagation and cryopreservation techniques, always presenting a review of current knowledge on the use of these techniques in the genus Pinus. Finally, the research objectives of this thesis are presented. Chapter II is dedicated to the application of a micropropagation protocol by proliferation of axillary shoots in the specie Pinus elliottii var. elliottii. This Chapter was divided in two sections. In section II.1 a protocol was optimized for large-scale P. elliottii micropropagation, which describes all the steps from disinfection and seed germination to the production of seedlings in vitro, which were used as explants for shoot induction. Various conditions for induction, shoot elongation and rooting were tested, and a protocol enabling the production of micropropagated plantlets 20 to 22 weeks after germination in vitro has been established. In section II.2 was performed the genetic and physiological characterization of P.elliottii plants micropropagated by the methodology developed in the previous section, in comparison with seedlings. The physiological performance of the plants was evaluated by determination of various parameters associated with photosynthesis and carbon metabolism, such as: chlorophyll a fluorescence; relative water content; gas exchange; pigment and carbohydrate contents. In turn, the genetic characterization was performed by analysis by flow cytometry of putative alterations in DNA content, ploidy level and in cell cycle dynamics. The results indicate that the developed micropropagation protocol for P. elliottii did not induce significative changes, both at physiological and genetic level, in the plants. Chapter III focuses on the optimization of a somatic embryogenesis process for the hybrid Pinus elliottii var. elliottii x Pinus caribaea var. hondurensis, from the initiation to the plants regeneration produced from somatic embryos. For initiation of embryogenic cultures of this hybrid, immature megagametophytes obtained from five open-pollinated plus trees were used as explants. To optimize the process, the effect of genotype in both the initiation and maturation, as the influence of different formulations of basal media and growth regulators in the various stages of the process were evaluated. Throughout the process was assessed the genetic stability of embryogenic masses with different time in culture, and at the end of the produced emblings, in comparison with the mother-trees needles. This protocol allows the production of emblings from somatic embryos not having been detected variability in the DNA content and ploidy level. Chapter IV is dedicated to the preservation of germplasm bank produced for the hybrid under study. Cryopreservation of embryogenic masses is beneficial not only for the preservation of germplasm during the breeding programs development, as well as to avoid the loss of the potential of the embryogenic masses. For the optimization of an embryogenic masses cryopreservation protocol using the slow freezing method, different variations were tested in pretreatments and in the duration of slow freezing step. Pretreatments to which the embryogenic tissue was subjected, did not compromise the maturation capacity of cryopreserved masses. On the contrary, cryopreservation had in some genotypes a beneficial effect. The optimized protocol allowed the regeneration of plants from cryopreserved masses and the process did not induce major genetic changes (embryogenic masses cryo and non cryopreserved were analyzed by flow cytometric). Finally, Chapter V presents the final conclusions of this PhD thesis, gathering the results of this thesis on the propagation and preservation methodologies for the species and hybrid in study and discussion this contribution to the state of art in this field. Future challenges for further research in these areas are presented in this Chapter. Pinus elliottii var. elliottii e o híbrido, Pinus elliottii var. elliottii x Pinus caribaea var. hondurensis, têm um grande valor económico, devido à sua elevada taxa de crescimento e produção de resina. Surge assim a necessidade de desenvolver estratégias de propagação mais eficientes desta espécie e do híbrido, mantendo as suas características. Este estudo tem como objetivos preservar / aumentar o banco de germoplasma de Pinus, fornecido pela empresa KLÓN, Innovative Technologies from Cloning, utilizando técnicas de micropropagação e de criopreservação, analisar possíveis alterações na estabilidade genética das plantas micropropagadas através de citometria de fluxo, estudar a taxa de sobrevivência de plantas, crescimento e desempenho fotossintético após aclimatização. No Capítulo I foram abordados aspetos gerais da espécie e híbrido em estudo, assim como uma breve descrição dos programas de melhoramento em Pinus spp. e da contribuição que técnicas inovadoras de propagação in vitro podem dar levando a décadas de antecipação dos resultados dos respectivos programas de melhoramento. Foram também descritos alguns aspetos mais importantes relativos às diferentes técnicas de micropropagação e criopreservação existentes, apresentando sempre uma revisão do conhecimento atual sobre o uso destas técnicas no género Pinus. Para finalizar este capítulo, os objetivos de investigação desta Tese são apresentados. O Capítulo II é dedicado à aplicação de uma metodologia de micropropagação (por proliferação de rebentos axilares) da espécie Pinus elliottii var. elliottii. Este capítulo foi dividido em duas secções. Na secção II.1 foi otimizado um protocolo para micropropagação em larga escala de P. elliottii desde a desinfecção e germinação de sementes para a produção de plântulas in vitro. Estas por sua vez são utilizadas como explantes para a indução de rebentos. Foram testadas várias condições para a indução, alongamento e enraizamento de rebentos, tendo sido estabelecido um protocolo que permite a produção de plântulas micropropagadas 20 a 22 semanas após germinação in vitro. Na secção II.2 foi realizada a caracterização genética e fisiológica de plantas de P. elliottii micropropagadas pela metodologia desenvolvida na secção anterior, em comparação com plantas provenientes de sementeira. O desempenho fisiológico das plantas foi avaliado pela determinação de diversos parâmetros relacionados com a fotossíntese e o metabolismo de carbono, tais como a fluorescência de clorofila a, o teor relativo em água, as trocas gasosas, o teor de pigmentos e de carbohidratos. Por sua vez a caracterização genética foi realizada pela análise do conteúdo em DNA e nível de ploidia, e ainda as dinâmicas do ciclo célular, com recurso à citometria de fluxo. Os resultados obtidos indicam que o protocolo de micropropagação desenvolvido para P. elliottii não provoca alterações significativas tanto a nível fisiológico como genético nas plantas. O Capítulo III centra-se na otimização de um processo de embriogénese somática para o híbrido Pinus elliottii var. elliottii x Pinus caribaea var. hondurensis, desde a iniciação até à regeneração de plantas produzidas a partir de embriões somáticos. Para a iniciação de culturas embriogénicas deste híbrido foram utilizados como explantes megagametófitos imaturos obtidos a partir de polinização aberta de cinco árvores plus. Para a otimização do processo foi avaliado o efeito do genótipo tanto na iniciação como na maturação, tal como o influência de diferentes formulações de meios basais e reguladores de crescimento nas diversas fases do processo. Ao longo do processo foi avaliada a estabilidade genética das massas embriogénicas com diferentes tempos de cultura, e no final das plântulas produzidas, em comparação com as agulhas das árvores-mãe, concluindo-se que foi desenvolvido um protocolo que permite a produção de plantas provenientes de embriões somáticos não tendo sido detectada variabilidade ao nível de conteúdo em DNA e nível de ploidia. O Capítulo IV é dedicado à preservação do banco de germoplasma produzido para o híbrido em estudo. A criopreservação de massas embriogénicas é benéfica não só para a preservação de germoplasma durante o desenvolvimento de programas de melhoramento, como para evitar a perda do potencial embriogénico das massas. Para a otimização de um protocolo de criopreservação de massas embriogénicas pelo método de congelamento lento, foram testadas diferentes variações nos pré-tratamentos e na duração do passo de congelação lenta. Os pré-tratamentos a que o tecido embriogénico foi submetido não influenciaram negativamente a capacidade de maturação das massas criopreservadas, apresentando-se a criopreservação até em alguns genótipos com um efeito benéfico. O protocolo otimizado permitiu a regeneração de plantas a partir de massas criopreservadas, para as quais se comprovou que o processo não provocou alterações genéticas, através da análise por citometria de fluxo de massas embriogénicas crio e não criopreservadas. Finalmente, no Capítulo V são apresentadas as conclusões finais da Tese de Doutoramento, onde são realçados os avanços realizados como resultado desta tese nas metodologias de propagação e preservação para a espécie e híbrido em estudo. Neste capítulo são também apresentados os desafios futuros para a continuação da investigação nas áreas de propagação e preservação de Pinus.

Doutoramento em Biologia Submitted by Alexandra Bastos (alexandrabastos@ua.pt) on 2016-12-13T18:53:22Z No. of bitstreams: 1 tese.pdf: 60532906 bytes, checksum: fc5742c6a5fee74a8015abb3472a607a (MD5) Made available in DSpace on 2016-12-13T18:53:22Z (GMT). No. of bitstreams: 1 tese.pdf: 60532906 bytes, checksum: fc5742c6a5fee74a8015abb3472a607a (MD5) Previous issue date: 2016-03-14

O Brasil é um dos maiores produtores de milho do mundo e possui grande potencial para a produção de milho verde. Além de agregar valor ao produto, a comercialização de milho verde cresceu muito nos últimos anos. Há escassez de informações sobre a avaliação e a obtenção de cultivares destinadas à produção de milho-verde e também sobre estudos genéticos das características envolvidas nessa produção. Objetivou-se, neste trabalho, estimar parâmetros genéticos e fenotípicos, a correlação genética, classificar e identificar híbridos de milho verde promissores ao mercado consumidor e avaliar a eficiência dos pesos econômicos atribuídos. Os resultados determinaram que a seleção terá sucesso, para as diferentes características de milho-verde, pois, a herdabilidade foi de alta magnitude para as características avaliadas. A avaliação da produtividade de espigas empalhadas (PEE) é suficiente para definir quais os híbridos apresentam o melhor desempenho para a produtividade de espigas comerciais (PEC), diâmetro (DIAM) e comprimento de espigas (COMP). Isso indica que as características PEC, DIAM e COMP podem ser descartadas da avaliação em programas de melhoramento de milho-verde. Os híbridos HS48, HS27, HS24, HS25, HS12 e HS45 acumularam um maior número de características desejadas em um único genótipo, com base no índice de seleção baseado na soma de postos, sendo os mais promissores para a produção de milho-verde. Os pesos econômicos utilizados foram capazes de distinguir e identificar os híbridos mais promissores para a produção de milho- verde e podem ser utilizados como critério de seleção em programas de melhoramento de milho-verde. Brazil is one of the largest producers of corn of the world and it possesses great potential for vegetable corn production. Besides adding value to the product, the commercialization of vegetable corn increased in the last years. There is shortage of information about the evaluation and the acquisition of genotypes destined to the production of vegetable corn and also on genetic studies of the traits involved in this production. The objective of this work was to estimate the genetic and phenotypic parameters, and the genetic correlation, and to classify and identify hybrids of promising vegetable corn to the consumer market and to evaluate the efficiency of the attributed economical weights. The results determined that the selection will succeed, for the different traits of vegetable corn, because the heritability was of high magnitude to the appraised traits. Evaluation of husked ears yield (PEE) was enough to define which hybrid presents better commercial ear productivity, diameter and corn ear length. This indicates that those traits could be discarded in the selection process of genotypes of breeding programs for vegetable corn production. The hybrids HS48, HS27, HS24, HS25 and HS12 accumulated the largest number of desirable traits in a single genotype based on the sum of rank index. The used economical weights were efficient to distinguish and identify the most promising hybrid for vegetable corn production and they can be used as a selection criterion in programs of breeding of vegetable corn.

It is well known that breeding is based on phenotypic and behavioural performance assessed at the level of each honeybee colony. By selection, the genes responsible for the desired characters have to be favoured, by evaluation and classification of all colonies involved in a breeding program. Generally, in the beekeeping practice, the most applied method of selection is the mass selection regarding the main objective- honey production. Some more elaborated programs use selection simultaneous selection on several characters. Until now, a standard method for honey bees evaluation and selection on several characters could not be generalized, every breeder establishing the selection method depending on proposed goals which could be different especially when we speak about different races and environmental conditions. Taking into account the selection objectives in Romania it was conceived a standardized methodology for the selection on several characters in Romanian condition.

In recent years, an increasing number of papers has been published on the genetic diversity trends in crop cultivars released in the last century using a variety of molecular techniques. No clear general trends in diversity have emerged from these studies. Meta analytical techniques, using a study weight adapted for use with diversity indices, were applied to analyze these studies. In the meta analysis, 44 published papers were used, addressing diversity trends in released crop varieties in the twentieth century for eight different field crops, wheat being the most represented. The meta analysis demonstrated that overall in the long run no substantial reduction in the regional diversity of crop varieties released by plant breeders has taken place. A significant reduction of 6% in diversity in the 1960s as compared with the diversity in the 1950s was observed. Indications are that after the 1960s and 1970s breeders have been able to again increase the diversity in released varieties. Thus, a gradual narrowing of the genetic base of the varieties released by breeders could not be observed. Separate analyses for wheat and the group of other field crops and separate analyses on the basis of regions all showed similar trends in diversity.

Recent genomic evaluation studies using real data and predicting genetic gain by modeling breeding programs have reported moderate expected benefits from the replacement of classic selection schemes by genomic selection (GS) in small ruminants. The objectives of this study were to compare the cost, monetary genetic gain and economic efficiency of classic selection and GS schemes in the meat sheep industry. Deterministic methods were used to model selection based on multi-trait indices from a sheep meat breeding program. Decisional variables related to male selection candidates and progeny testing were optimized to maximize the annual monetary genetic gain (AMGG), that is, a weighted sum of meat and maternal traits annual genetic gains. For GS, a reference population of 2000 individuals was assumed and genomic information was available for evaluation of male candidates only. In the classic selection scheme, males breeding values were estimated from own and offspring phenotypes. In GS, different scenarios were considered, differing by the information used to select males (genomic only, genomic+own performance, genomic+offspring phenotypes). The results showed that all GS scenarios were associated with higher total variable costs than classic selection (if the cost of genotyping was 123 euros/animal). In terms of AMGG and economic returns, GS scenarios were found to be superior to classic selection only if genomic information was combined with their own meat phenotypes (GS-Pheno) or with their progeny test information. The predicted economic efficiency, defined as returns (proportional to number of expressions of AMGG in the nucleus and commercial flocks) minus total variable costs, showed that the best GS scenario (GS-Pheno) was up to 15% more efficient than classic selection. For all selection scenarios, optimization increased the overall AMGG, returns and economic efficiency. As a conclusion, our study shows that some forms of GS strategies are more advantageous than classic selection, provided that GS is already initiated (i.e. the initial reference population is available). Optimizing decisional variables of the classic selection scheme could be of greater benefit than including genomic information in optimized designs.

Following our recent Review article (Gonzalez-Recio et al., 2015), we received correspondence by Steele (2016). We thank Dr. Steele for his comments, which provide a thorough review of his work on human immunology, which has persuaded him that “hard types of soma-to-germline transfer are ongoing at very high frequency in human immune system germlines.” His and other researchers' studies on reverse transcriptase (RT) based feedback mechanisms showed that RNA could be retrotranscripted to DNA, and it can be inserted into the mammalian germline, and therefore be transferred to the progeny.

Background Transmissible spongiform encephalopathies (TSE) are fatal neurodegenerative diseases of several mammalian species, including humans. In Italy, the active surveillance through rapid tests on brain stem from small ruminants started in 2002 on randomly selected samples of healthy slaughtered animals. Sampling number was proportionally related to the regional small ruminant population. Of the twenty Italian regions, Sicily has the second largest population of small ruminants which is mainly constituted by crossbreed animals (>70 %). Sicily contains also three native sheep breeds Pinzirita, Comisana and Valle del Belice. Native goat breeds are Girgentana, Messinese, Argentata dell’Etna, Maltese and Rossa Mediterranea. The polymorphisms of prion protein gene (PRNP) may influence disease susceptibility and breeding programs for genetic TSE resistance are being applied in sheep. Protective alleles have been recently reported for goats also. These differ from those in sheep and may allow breeding programs in the near future. In this paper the data of active surveillance for scrapie control in general population of small ruminants in Sicily are reported together with the analysis on the polymorphism of PRNP in a number of Sicilian autochthonous breeds. The evaluation of the frequency of protective alleles is fundamental for the implementation of a TSE resistance breeding program. Results TSE surveillance in small ruminants in Sicily showed a of total fifty seven scrapie outbreaks from 1997 to 2014 involving mainly crossbreed animals. The PRNP polymorphism analysis in autochthonous breeds showed protective allele frequencies of 30–40 % ARR in sheep and 12–18 % K222 in three of the four goat breeds; these breeds are distributed over limited areas of the island. Conclusion The study on PRNP polymorphisms in Sicilian small ruminant population showed higher frequency of the protective alleles compared to most other European breeds. Our results suggest that PRNP genetic variety in Sicilian sheep and goats can be a resource for TSE resistance breeding programmes while maintaining the conservation of endangered breeds and valorisation of their typical food products. Electronic supplementary material The online version of this article (doi:10.1186/s12917-016-0766-9) contains supplementary material, which is available to authorized users.

Katlanmış haploid (KH) teknolojisi son yıllarda gelişmiş ıslah programlarında yaygın olarak kullanılan bir araç haline gelmiştir. In vivo haploid indirgemenin mısır da paternal (androgenetic) ve maternal (gynogenetic) haploidler olarak bilinen iki metodu vardır. Bu çalışmada maternal haploid indirgeme metodu uygulanmıştır. RWS, RWK-76, RWS x RWK-76 ve WS14 indirgeyici materyalleri tozlayıcı olarak kullanılmıştır. Mısır Araştırma Enstitüsünde 2010-2013 yılları arasında yürütülen çalışmada 30 tek melez kaynak materyal olarak kullanılmıştır. Kaynak materyaller FAO 650-700 olum grubundadır. Kaynak materyal ile indirgeyici genotipler arasında yapılan indükleme melezlemesinden 15911 adet tohum elde edilmiştir. R1-nj renk markörü dikkate alınarak seleksiyon yapılmış ve 3012 adet haploid kabul edilen tohum seçilmiştir. Yönteme göre her bir indirgeyici hattın Sakarya koşullarında haploid indükleme oranı (HİO) belirlenmiştir. En yüksek HİO, RWK-76 indirgeyici hattında %20.42 bulunmuştur. En düşük HİO ise WS14 hattında %17.75 olarak hesaplanmıştır. Haploid embriyoya sahip tohumlar 23 oC'de karanlıkta iklim odasında çimlendirilmiştir. Çimlendirilmiş materyalde koleoptil ve kök kısaltılmıştır. Kromozom katlaması için %0.06 colchicine+%0.5 dimethylsulfoxide (DMSO) çözeltisi 20 oC'de 12 saat uygulanmıştır. Daha sonra su ile yıkanarak viyollere dikimi yapılmıştır. KH0 bitkileri 3-4 yapraklı olana kadar iklim odasında büyütülmüştür. Tarlaya dikimi yapılan KH0 bitkilerinde çiçeklenme döneminde fertil olanlarda kendileme yapılmıştır. Haploid kabul edilen 3012 tohumdan çimlendirme ve kromozom katlaması sonrası tarlaya dikilen 2178 fideden %89'u canlı bitki, canlı bitkilerin %57'si fertil bitki, fertil bitkilerin %31.23'ü kendileme yapılabilecek bitki ve kendileme yapılan bitkilerden %7.8'i kendileme yapılarak tohum alınan bitki olmuştur. Tez çalışması sonucunda 27 adet katlanmış haploid hat elde edilmiştir. The double haploid (DH) technology has become widely used tool of modern maize breeding programs in recent years. There are two methods in vivo haploid induction in maize which are paternal (androgenetic) haploid and maternal (gynogenetic) haploid induction. In this study, the maternal haploid induction method was applied. RWS, RWK-76, RWS x RWK-76 and WS14 inducer genotypes were used as pollinator. This study was conducted through 2010-2013 years and 30 single cross were used as source material. The source materials are in 650-700 FAO maturity groups. Seeds of 15911 number were obtained by crossing inducer lines with source materials. Putative haploid seeds of 3012 number were selected as using R1-nj coloration marker gene. According to the method, haploid induction rate (HIR) was determined in each inducer line on Sakarya location. Highest HIR were established as 20.42% in RWK-76 inducer line. The lowest HIR was calculated as 17.75% in the WS14. Putative haploid seeds were germinated at 23 °C in a growth chamber. Coleoptile and root of seedlings were reduced and treated with 0.06% colchicine+0.5% dimethylsulfoxide (DMSO) solution for 12 hours at 20 °C to seedlings. Seedlings were planted viols after washing with water and DH0 plants were grown untill reaching 3-4 leaves in growth chamber. Following planting in the field, inbreeding were conducted for the fertile DH0 plants during the flowering period. Seedling of 2178 was formed from putative haploid seeds of 3012 numbers. Live plants were from 89% of 2178 seedlings which are planted the field. Fertile plants were formed 57% of live plants. Inbreeding were able to made on 31.23% of fertile plants and seeds have been taken from 7.8% of inbreeding plants. At the end of the study, 27 doubled haploid lines were obtained. 125

This article reviews the concept of Lamarckian inheritance and the use of the term epigenetics in the field of animal genetics. Epigenetics was first coined by Conrad Hal Waddington (1905-1975), who derived the term from the Aristotelian word epigenesis. There exists some controversy around the word epigenetics and its broad definition. It includes any modification of the expression of genes due to factors other than mutation in the DNA sequence. This involves DNA methylation, post-translational modification of histones, but also linked to regulation of gene expression by non-coding RNAs, genome instabilities or any other force that could modify a phenotype. There is little evidence of the existence of transgenerational epigenetic inheritance in mammals, which may commonly be confounded with environmental forces acting simultaneously on an individual, her developing fetus and the germ cell lines of the latter, although it could have an important role in the cellular energetic status of cells. Finally, we review some of the scarce literature on the use of epigenetics in animal breeding programs. © 2015 González-Recio, Toro and Bach.

In a recent manuscript published by our group we analyzed the reproductive biology of the grass Paspalum malacophyllum by using traditional embryological techniques combined with current cytological and molecular methods. Our findings confirmed apparent contradictions regarding the reproductive behavior of P. malacophyllum from six independently published reports over the past six decades. Herein we summarize the main findings, conclusions, and validations of all previous studies, highlighting the need for multiple approaches to characterize reproductive systems when using apomictic plants in a breeding program. Fil: Hojsgaard, Diego Hernan. Universitat of Gottingen; Alemania Fil: Burson, B. L.. United States Department of Agriculture; Argentina. Texas A&M University; Estados Unidos Fil: Quarin, Camilo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Nordeste. Instituto de Botánica del Nordeste (i); Argentina. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias; Argentina Fil: Martínez, Eric Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Nordeste. Instituto de Botánica del Nordeste (i); Argentina. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias; Argentina

O objetivo do trabalho foi estabelecer meio de cultura e avaliar a germinação de grãos de pólen in vitro e após a aplicação de boro na panícula em cultivares de nespereira. Foi determinado o meio de cultura ideal para germinação dos grãos de pólen e avaliada a porcentagem de germinação utilizando pólen da cultivar Mizauto. Também avaliou-se o melhor estágio de desenvolvimento floral e horário do dia para coleta do pólen, bem como o tempo de incubação para sua germinação. Após estabelecido o meio, foi determinada a germinação de nove cultivares: Mizauto, Mizuho, Fukuhara, Parmogi, Centenária, Kurisaki, Néctar de Cristal, Mizumo e Precoce de Campinas. Em campo, avaliou-se a aplicação de ácido bórico em panículas de nespereiras Mizauto, nas concentrações 600 mg L–1, 1.200 mg L–1 e 1.800 mg L–1, além do controle sem aplicação. O meio de cultura estabelecido foi de 200 g L–1 de sacarose, 1.200 mg L–1 de ácido bórico, solidificado com 10 g L–1 de agar e pH 6, incubado por sete horas. O melhor estágio do botão floral foi na pré-antese, coletado entre 14 e 18 horas. A aplicação de 900 mg L–1 de ácido bórico em campo elevou a germinação dos grãos de pólen para 57,68%. This study aimed to establish a culture media and evaluate pollen grains germination in vitro and after boron applying in the panicles of Loquat cultivars. Was established an appropriate culture media for pollen grains germination and evaluated the germination percentage in Mizauto cultivar. Was also evaluated the best stage of floral growth and the best period of the day to collect the pollen, beyond the evaluation of incubation time for their germination. After established the appropriate culture media, it was determined the germination of 9 cultivars: Mizauto, Mizuho, Fukuhara, Parmogi, Centenária, Kurisaki, Néctar de Cristal, Mizumo and Precoce de Campinas. On the field, was evaluated the applying of boric acid with different concentrations 600, 1200 and 1800 mg L–1 and without applying on the panicles of Mizauto cultivar. The culture media established was composed by 200 g L–1 of sucrose, 1200 mg L–1 of boric acid, solidified with 10 g L–1 of Agar and pH 6, and incubated during seven hours. The best stage of floral bud was in pre-anthesis, collected between two and six pm. The applying of 900 mg L–1 of boric acid on field raised the pollen grain germination to 57.68%.

The annual production from global aquaculture has increased rapidly from 2.6 million tons or 3.9% of the total supply of fish, shellfish and mollusks in 1970, to 66.7 million tons or 42.2% in 2012, while capture fisheries have more or less leveled out at about 90 million tons per year since the turn of the century. Consequently, the future seafood supply is likely to depend on a further increase of aquaculture production. Unlike terrestrial animal farming, less than 10% of the aquaculture production comes from domesticated and selectively bred farm stocks. This situation has substantial consequences in terms of poorer resource efficiency, poorer product quality and poorer animal welfare. The history of biological and technical challenges when establishing selective breeding programs for aquaculture is discussed, and it is concluded that most aquaculture species may now be domesticated and improved by selection. However, the adoption of selective breeding in aquaculture is progressing slowly. This paper reports on a study carried out in 2012 to identify key issues to address in promoting the development of genetically improved aquaculture stocks. The study involved semi structured interviews of 34 respondents from different sectors of the aquaculture society in East and Southeast Asia, where 76% of the global aquaculture production is located. Based on the interviews and literature review, three key factors are identified: (i) long-term public commitment is often needed for financial support of the breeding nucleus operation (at least during the first five to ten generations of selection), (ii) training at all levels (from government officers and university staff to breeding nucleus and hatchery operators, as well as farmers), and (iii) development of appropriate business models for benefit sharing between the breeding, multiplier and grow-out operators (whether being public, cooperative or private operations). The public support should be invested in efforts of selective breeding on the most important and highest volume species, which may not be a priority for investment by private breeders due to, for instance, long generation intervals and delays in return to investment.

Utilizando-se simulação determinística, foram avaliados seis esquemas de melhoramento, com diferentes grupos de informações: (1) somente características de crescimento, (2) somente características leiteiras, (3) características de crescimento e reprodutivas, (4) características leiteiras e reprodutivas, (5) características de crescimento e leiteiras e (6) características de crescimento, leiteiras e reprodutivas. Avaliaram-se também a resposta à variação no uso de touros provados por meio do teste de progênie, a resposta sem a realização do teste de progênie no estrato de vacas de corte da população e a resposta à variação no valor econômico do peso ao abate. Em todos os esquemas avaliados, foram verificados altos ganhos genéticos e lucros decorrentes do programa. Os esquemas que consideraram as características leiteiras foram mais eficientes pela seleção para maior produção de leite e menor peso de vaca adulta. As características de fertilidade foram mais importantes para os esquemas de corte. A resposta econômica à seleção foi maior com o aumento no uso de touros provados, embora não proporcionalmente. A contribuição das características de corte para o lucro genético somente superou a das leiteiras quando o valor econômico do peso ao abate superou em 14 vezes o da produção de leite. Foi demonstrado não haver necessidade da realização do teste de progênie com as vacas de corte para o sistema de dupla aptidão estudado. A deterministic simulation was used to compare six breeding schemes based on different levels of performance recording: (1) only body weights, (2) only dairy traits, (3) body weights and reproductive traits, (4) dairy and reproductive traits, (5) body weights and dairy traits and (6) body weights, reproductive and dairy traits. Other factors were also studied, as the level of usage of proven sires, variations in the economic value of slaughter weight and eliminating progeny testing in the beef herd tier of the population. Genetic gains and returns were high in all schemes. Dairy schemes were superior, mainly due to responses in lowering mature cow weight and increasing milk yield. Reproductive traits were more important in the beef schemes. Returns increased with higher usage of proven sires, although not proportionally. The contribution of beef traits to genetic profit was higher than that of dairy traits only when the economic value of slaughter weight exceeded 14 times the economic value of milk yield. The exclusion of progeny testing in the beef cows tier had little effect on the genetic or economic results.

Utilizando-se simulação determinística, foram avaliados seis esquemas de melhoramento, com diferentes grupos de informações: (1) somente características de crescimento, (2) somente características leiteiras, (3) características de crescimento e reprodutivas, (4) características leiteiras e reprodutivas, (5) características de crescimento e leiteiras e (6) características de crescimento, leiteiras e reprodutivas. Avaliaram-se também a resposta à variação no uso de touros provados por meio do teste de progênie, a resposta sem a realização do teste de progênie no estrato de vacas de corte da população e a resposta à variação no valor econômico do peso ao abate. Em todos os esquemas avaliados, foram verificados altos ganhos genéticos e lucros decorrentes do programa. Os esquemas que consideraram as características leiteiras foram mais eficientes pela seleção para maior produção de leite e menor peso de vaca adulta. As características de fertilidade foram mais importantes para os esquemas de corte. A resposta econômica à seleção foi maior com o aumento no uso de touros provados, embora não proporcionalmente. A contribuição das características de corte para o lucro genético somente superou a das leiteiras quando o valor econômico do peso ao abate superou em 14 vezes o da produção de leite. Foi demonstrado não haver necessidade da realização do teste de progênie com as vacas de corte para o sistema de dupla aptidão estudado.A deterministic simulation was used to compare six breeding schemes based on different levels of performance recording: (1) only body weights, (2) only dairy traits, (3) body weights and reproductive traits, (4) dairy and reproductive traits, (5) body weights and dairy traits and (6) body weights, reproductive and dairy traits. Other factors were also studied, as the level of usage of proven sires, variations in the economic value of slaughter weight and eliminating progeny testing in the beef herd tier of the population. Genetic gains and returns were high in all schemes. Dairy schemes were superior, mainly due to responses in lowering mature cow weight and increasing milk yield. Reproductive traits were more important in the beef schemes. Returns increased with higher usage of proven sires, although not proportionally. The contribution of beef traits to genetic profit was higher than that of dairy traits only when the economic value of slaughter weight exceeded 14 times the economic value of milk yield. The exclusion of progeny testing in the beef cows tier had little effect on the genetic or economic results.

Implementing genomic selection (GS) in small ruminant breeding programs is still at the research and development level. This new way of selection in animals and plants was made possible thanks to the development of low costs, high density SNP chips. It proved to be highly beneficial in dairy cattle breeding programs. The French small ruminant industries are strongly interested in evaluating the efficiency of this tool in their situation. However, they are also very cautious given the inherent differences in terms of capacity and functionalities between dairy cattle and small ruminant breeding programs. This study is part of bigger efforts mobilized to evaluate the use and management of genomic information in sheep and goats breeding programs.The PhD work examined (1) the impact of genomic selection on genetic gain of small ruminant breeding programs; (2) the economic efficiency of genomic selection in small ruminant, through an example of a meat sheep breeding program; (3) the benefits of optimizing the use of decision variables on genetic gain; and (4) contributed some ideas on how to optimize the choice of individuals in the reference population. The modeling parts were done by deterministic methods and the examples focused on the existing breeding programs (dairy sheep, meat sheep and dairy goats) with medium to small size breeding units. The results of this study suggest that adopting genomic selection can be more profitable than classic selection in terms of genetic gain, provided that, at least, a medium size reference population is available (around 2,000 individuals). They show, especially in dairy breeds, that the GS potentials of reducing generation interval could greatly increase the genetic gain. In meat sheep breeding program, exploring the possibility of combining genomic information and meat phenotypes gave higher genetic gain than classic or pure genomic selection. In terms of economic impacts, results of the meat sheep breeding program we modeled show that all genomic selection strategies are more expensive than classic selection. However, the contribution margins (total revenues minus total variable costs) of some GS variants were slightly higher than benefits from classic selection. The study also shows, across breeds and selection strategies, that optimizing the use of decision variables could greatly increase the genetic gain and benefits, compared to the current situation. With this thesis we can conclude that adopting genomic selection in small ruminant breeding programs is possible and could be more beneficial than classic selection in some cases. However, there are more obstacles compared to dairy cattle, especially,construction of reliable reference populations and high costs of genotypes relative to the 7 value of selection candidates. These might delay implementation in general or prevent it in some breeds.

Production traits such as growth rate may depend on the social interactions between group members. These social interactions might be partly heritable and are referred to as indirect genetic effects (IGE), social-, associative-, or competitive genetic effects. IGE may contribute to heritable variation in traits, and can thus be used to increase the response to selection. This, however, has hardly been tested by selection experiments. Our objective was to determine the effects of one generation of selection on IGE for growth (IGEg) in pigs on ADG, BW, ADFI, feed efficiency, and post-mortem measurements. Sires (n=24) and dams (n=64) were selected to create a high vs. low contrast for IGEg in the offspring (n=480). The IGE difference was 2.8 g ADG per pen mate, corresponding to 14 g higher ADG in high IGEg offspring compared to low IGEg offspring when housed in groups of 6 (i.e. (6-1)×2.8 = 14). Male (barrows) and female (gilts) offspring were housed in groups of 6 of the same IGEg classification, in either barren concrete pens or pen enriched with straw and wood shavings (n=80 pens). Pigs were followed from birth to slaughter. Data were analyzed in a mixed model with pen as random factor. There was no difference in ADG between high and low IGEg pigs during the finishing period (wk 10 to 23). Opposite to expectations, high IGEg tended to have a 17 g lower ADG from weaning to slaughter (P=0.08), which was caused by a higher BW of low IGEg pigs in wk 5 (P=0.008). This led to a 2.3 kg lower carcass weight (P=0.02) and 2.2 mm less muscle depth for high IGEg pigs (P=0.03). High IGEg pigs had a higher stomach wall damage score (P=0.01). Pigs on straw had a 25 g lower ADG during finishing (P=0.03), and less stomach wall damage (P

International audience; Background Identifying the relevant environmental variables that cause GxE interaction is often difficult when they cannot be experimentally manipulated. Two statistical approaches can be applied to address this question. When data on candidate environmental variables are available, GxE interaction can be quantified as a function of specific environmental variables using a reaction norm model. Alternatively, a factor analytic model can be used to identify the latent common factor that explains GxE interaction. This factor can be correlated with known environmental variables to identify those that are relevant. Previously, we reported a significant GxE interaction for body weight at harvest in rainbow trout reared on three continents. Here we explore their possible causes.MethodsReaction norm and factor analytic models were used to identify which environmental variables (age at harvest, water temperature, oxygen, and photoperiod) may have caused the observed GxE interaction. Data on body weight at harvest was recorded on 8976 offspring reared in various locations: (1) a breeding environment in the USA (nucleus), (2) a recirculating aquaculture system in the Freshwater Institute in West Virginia, USA, (3) a high-altitude farm in Peru, and (4) a low-water temperature farm in Germany. Akaike and Bayesian information criteria were used to compare models.ResultsThe combination of days to harvest multiplied with daily temperature (Day*Degree) and photoperiod were identified by the reaction norm model as the environmental variables responsible for the GxE interaction. The latent common factor that was identified by the factor analytic model showed the highest correlation with Day*Degree. Day*Degree and photoperiod were the environmental variables that differed most between Peru and other environments. Akaike and Bayesian information criteria indicated that the factor analytical model was more parsimonious than the reaction norm model.ConclusionsDay*Degree and photoperiod were identified as environmental variables responsible for the strong GxE interaction for body weight at harvest in rainbow trout across four environments. Both the reaction norm and the factor analytic models can help identify the environmental variables responsible for GxE interaction. A factor analytic model is preferred over a reaction norm model when limited information on differences in environmental variables between farms is available.

Solomon Abegaz Guangul Zsfassung in dt. Sprache Wien, Univ. für Bodenkultur, Diss., 2014 OeBB

Nuña beans (Phaseolus vulgaris L.), an ancient and pre-ceramic landrace native to Andean region, possess the property of popping and a high content of proteins and carbohydrates, which makes it an alternative nutritious snack. Knowledge on the genetic bases of popping ability is relevant for common bean improvement. Progenies derived from two nuña bean crosses were used in a generation mean based mating design to determine the inheritance and gene action for five popping related traits: length of popped seeds (PSL), popping dimension index (PDI), percentage of un-popped seeds (PUS), popping percentage average (PPA) and expansion coefficient (EC). Significant additive gene effects were found for all traits, and was the only source of the observed variation for PSL, while dominance and higher-order interactions among loci contributed to the genetic divergence for the other traits. The dominance of the cultivated over nuña alleles for PDI, PPA, EC and PUS, was confirmed by high mid-parent heterosis values and generation mean comparisons. The [d] and [dd] gene effects were in opposite direction for PPA and EC, indicating duplicate epistasis. Therefore, epistasis is likely to be an important explanation for the heterosis in both traits. For PDI and PUS, the opposite signs for [aa] and [dd] gene effects indicated that the genes for increasing popping are dispersed between the parents. Generation means and variances of BC1P2 indicated advantages of the backcross breeding procedure to improve the adaptation of the exotic germplasm and at the same time, transfer part of the desired donor genes to cultivated common bean. The backcross to the nuña parent could be an alternative to maintain/recover the favorable epistatic gene combinations found for PDI, PPA, EC and PUS traits. © 2013 Springer Science+Business Media Dordrecht., MICINN (AGL2011-25562); EU-FEDER; Junta de Andalucía (Grant No. P10-AGR-06931); Campus de Excelencia Internacional Agroalimentario-CeiA3

A method was developed and tested to estimate challenge load due to disease outbreaks and other challenges in sows using reproduction records. The method was based on reproduction records from a farm with known disease outbreaks. It was assumed that the reduction in weekly reproductive output within a farm is proportional to the magnitude of the challenge. As the challenge increases beyond certain threshold, it is manifested as an outbreak. The reproduction records were divided into 3 datasets. The first dataset called the Training dataset consisted of 57,135 reproduction records from 10,901 sows from 1 farm in Canada with several outbreaks of porcine reproductive and respiratory syndrome (PRRS). The known disease status of sows was regressed on the traits number born alive, number of losses as a combination of still birth and mummified piglets, and number of weaned piglets. The regression coefficients from this analysis were then used as weighting factors for derivation of an index measure called challenge load indicator. These weighting factors were derived with i) a two-step approach using residuals or year-week solutions estimated from a previous step, and ii) a single-step approach using the trait values directly. Two types of models were used for each approach: a logistic regression model and a general additive model. The estimates of challenge load indicator were then compared based on their ability to detect PRRS outbreaks in a Test dataset consisting of records from 65,826 sows from 15 farms in the Netherlands. These farms differed from the Canadian farm with respect to PRRS virus strains, severity and frequency of outbreaks. The single-step approach using a general additive model was best and detected 14 out of the 15 outbreaks. This approach was then further validated using the third dataset consisting of reproduction records of 831,855 sows in 431 farms located in different countries in Europe and America. A total of 41 out of 48 outbreaks detected using data analysis were confirmed based on diagnostic information received from the farms. Among these, 30 outbreaks were due to PRRS while 11 were due to other diseases and challenging conditions. The results suggest that proposed method could be useful for estimation of challenge load and detection of challenge phases such as disease outbreaks.

International audience; Background Feather pecking is a major welfare issue in laying hen industry that leads to mortality. Due to a ban on conventional cages in the EU and on beak trimming in some countries of the EU, feather pecking will become an even bigger problem. Its severity depends both on the victim receiving pecking and on its group mates inflicting pecking (indirect effects), which together determine plumage condition of the victim. Plumage condition may depend, therefore, on both the direct genetic effect of an individual itself and on the indirect genetic effects of its group mates. Here, we present estimated genetic parameters for direct and indirect effects on plumage condition of different body regions in two purebred layer lines, and estimates of genetic correlations between body regions.MethodsFeather condition scores (FCS) were recorded at 40 weeks of age for neck, back, rump and belly and these four scores were added-up into a total FCS. A classical animal model and a direct–indirect effects model were used to estimate genetic parameters for FCS. In addition, a bivariate model with mortality (0/1) was used to account for mortality before recording FCS. Due to mortality during the first 23 weeks of laying, 5363 (for W1) and 5089 (for WB) FCS records were available.ResultsTotal heritable variance for FCS ranged from 1.5% to 9.8% and from 9.8% to 53.6% when estimated respectively with the classical animal and the direct–indirect effects model. The direct–indirect effects model had a significantly higher likelihood. In both lines, 70% to 94% of the estimated total heritable variation in FCS was due to indirect effects. Using bivariate analysis of FCS and mortality did not affect estimates of genetic parameters. Genetic correlations were high between adjacent regions for FCS on neck, back, and rump but moderate to low for belly with other regions.ConclusionOur results show that 70% to 94% of the heritable variation in FCS relates to indirect effects, indicating that methods of genetic selection that include indirect genetic effects offer perspectives to improve plumage condition in laying hens. This, in turn could reduce a major welfare problem.

International audience; Background The use of whole-genome sequence data can lead to higher accuracy in genome-wide association studies and genomic predictions. However, to benefit from whole-genome sequence data, a large dataset of sequenced individuals is needed. Imputation from SNP panels, such as the Illumina BovineSNP50 BeadChip and Illumina BovineHD BeadChip, to whole-genome sequence data is an attractive and less expensive approach to obtain whole-genome sequence genotypes for a large number of individuals than sequencing all individuals. Our objective was to investigate accuracy of imputation from lower density SNP panels to whole-genome sequence data in a typical dataset for cattle.MethodsWhole-genome sequence data of chromosome 1 (1737 471 SNPs) for 114 Holstein Friesian bulls were used. Beagle software was used for imputation from the BovineSNP50 (3132 SNPs) and BovineHD (40 492 SNPs) beadchips. Accuracy was calculated as the correlation between observed and imputed genotypes and assessed by five-fold cross-validation. Three scenarios S40, S60 and S80 with respectively 40%, 60%, and 80% of the individuals as reference individuals were investigated.ResultsMean accuracies of imputation per SNP from the BovineHD panel to sequence data and from the BovineSNP50 panel to sequence data for scenarios S40 and S80 ranged from 0.77 to 0.83 and from 0.37 to 0.46, respectively. Stepwise imputation from the BovineSNP50 to BovineHD panel and then to sequence data for scenario S40 improved accuracy per SNP to 0.65 but it varied considerably between SNPs.ConclusionsAccuracy of imputation to whole-genome sequence data was generally high for imputation from the BovineHD beadchip, but was low from the BovineSNP50 beadchip. Stepwise imputation from the BovineSNP50 to the BovineHD beadchip and then to sequence data substantially improved accuracy of imputation. SNPs with a low minor allele frequency were more difficult to impute correctly and the reliability of imputation varied more. Linkage disequilibrium between an imputed SNP and the SNP on the lower density panel, minor allele frequency of the imputed SNP and size of the reference group affected imputation reliability.

Se colectaron en diferentes regiones de Cuba semillas de las accesiones de papayo Tallo Morado de Nava, Amarilla de Duaba, Amarilla de Nava y Sapote de Pilón. Estas se plantaron en condiciones de campo en Jagüey Grande, Matanzas - Cuba, donde se evaluó la presencia e intensidad de síntomas de mancha anular, siguiendo una escala graduada del 1 al 5. Los resultados mostraron un incremento temporal de la proporción de plantas afectadas en todas las accesiones. La accesión Amarilla de Duaba mostró los síntomas a los dos meses después de la primera evaluación (MDPE), mientras que el resto lo hizo a los cinco MDPE, aunque con proporciones que variaron entre ellas. A los siete MDPE las accesiones Amarilla de Duaba y Amarilla de Nava mostraron proporciones idénticas de plantas enfermas, mientras que Tallo morado de Nava y Sapote de Pilón mostraron proporciones inferiores. La intensidad de los síntomas se incrementó en los diferentes órganos siguiendo el siguiente orden: tallo (1,7 a 2,66), pecíolos (2,21 a 3,03) y follaje (3,44-4,03). En los frutos la intensidad de los síntomas observados fue inferior a 2,5, considerados como leves de acuerdo a su intensidad y distribución. Se ofrecen los primeros resultados sobre la susceptibilidad a la mancha anular de estas accesiones, siendo de gran utilidad para los productores, así como para los programas de mejoramiento genético en el país. Os acessos de mamão Tallo morado de Nava, Amarilla de Duaba, Amarilla de Nava e Sapote de Pilón foram coletados em diferentes regiões de Cuba e plantados em condições de campo em Jagüey Grande, Matanzas - Cuba. Nestas plantas foram avaliadas a presença e intensidade dos sintomas de mancha anelar, usando uma escala graduada de 1-5. Os resultados mostraram um aumento, com o tempo, na proporção de plantas afetadas em todos os acessos. O acesso Amarilla de Duaba apresentou sintomas dois meses após a primeira avaliação (MDPE), enquanto para os restantes foram observados sintomas após cinco MDPE, contudo em proporções diferentes entre eles. Aos sete MDPE os acessos Amarilla de Duaba e Amarilla de Nava, apresentaram proporções iguais de plantas doentes, enquanto Tallo morado de Nava e Sapote de Pilon apresentaram menores proporções. O aumento da intensidade dos sintomas foi diferente nos órgãos da planta na seguinte ordem: caule (1,7-2,66), pecíolos (2,21-3,03) e folhagens (3,44-4,03). Nos frutos a intensidade dos sintomas observados foi inferior a 2,5, considerada leve em função da sua intensidade e distribuição. Estes são os primeiros resultados sobre a susceptibilidade a mancha anelar destes acessos, sendo muito úteis para os produtores, bem como para os programas de melhoramento do país. The papaya accessions "Tallo morado de Nava", "Amarilla de Duaba", "Amarilla de Nava" and "Sapote de Pilón" were collected from different regions of Cuba and planted under field conditions in Jagüey Grande, Matanzas - Cuba. These plants were assessed for the presence and intensity of ringspot symptoms, using a graduated scale of 1-5. Results showed an increase, with time, in the proportion of affected plants for all accessions. The accession "Amarilla de Duaba" had symptoms two months after the first assessment (MAFA), while for the remaining accessions, symptoms were noted after only five MAFA but at proportions that differed among them. At seven MAFA, the accessions "Amarilla de Duaba" and "Amarilla de Nava" had proportions equal to those of diseased plants, while "Tallo morado de Nava" and "Sapote de Pilon" showed lower proportions. The increase in symptom intensity was different for the plant organs in the following order: stem (1.7-2.66), petioles (2.21-3.03) and leaves (3.44-4.03). For fruits, the intensity of the observed symptoms was inferior to 2.5, considered light based on their intensity and distributions. These are the first results about ringspot susceptibility for these accessions, which are highly useful for farmers, as well as for breeding programs in the country.

Indirect Genetic Effects (IGEs), also known as associative effects, are the heritable effects that an individual has on the phenotype of its social partners. Selection for IGEs has been proposed as a method to reduce harmful behaviours, in particular aggression, in livestock and aquaculture. The mechanisms behind IGEs, however, have rarely been studied. The objective was therefore to assess aggression in pigs which were divergently selected for IGEs on growth (IGEg). In a one generation selection experiment, we studied 480 offspring of pigs (Sus scrofa) that were selected for relatively high or low IGEg and housed in homogeneous IGEg groups in either barren or enriched environments. Skin lesion scores, a proxy measure of aggression, and aggressive behaviours were recorded. The two distinct IGEg groups did not differ in number of skin lesions, or in amount of reciprocal fighting, both under stable social conditions and in confrontation with unfamiliar pigs in a 24 h regrouping test. Pigs selected for a positive effect on the growth of their group members, however, performed less non-reciprocal biting and showed considerably less aggression at reunion with familiar group members after they had been separated during a 24 h regrouping test. The enriched environment was associated with more skin lesions but less non-reciprocal biting under stable social conditions. Changes in aggression between pigs selected for IGEg were not influenced by G×E interactions with regard to the level of environmental enrichment. It is likely that selection on IGEg targets a behavioural strategy, rather than a single behavioural trait such as aggressiveness.