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Several lines of evidence support the notion that Bone Morphogenetic Proteins (BMPs) and gonadotropic hormones are major regulators of ovarian follicle development by inducing gonadotropin-mediated steroid hormone production and regulating ovarian follicle cell proliferation. Research from our laboratory and elsewhere have demonstrated that BMPs play important roles during the early stages of folliculogenesis. Despite the extensive research to reveal the mechanism of interaction between BMPs and gonadotropic hormones in the process of folliculogenesis, the exact mechanism of such an interaction is not adequately understood. Previously, we developed a unique mouse model characterized by a short-term attenuation of the BMP signaling system using passive immunization against bone morphogenetic protein 4 (BMP-4) and bone morphogenetic protein receptor 1B (BMPR1B). This model unequivocally demonstrated that the attenuation of BMP action was an effective method of enhancing fertility reserve and promoting follicle and ovulation rates in female mice. In addition, this study pointed to the possibility of bi-directional mutual regulation between BMPs, Follicle-Stimulating Hormone (FSH), and Luteinizing Hormone (LH). To gain further insight into this mechanism we used this mouse model to examine the protein expression and mRNA level of BMPR1B, Follicle-Stimulating Hormone Receptor (FSHR) and Luteinizing Hormone/Choriogonadotropin Receptor (LHCGR) in multiple stages of follicle development in female mice. Immunofluorescent analysis of female mice treated with anti-BMPR1B antibodies showed a significant upregulation of BMPR1B, FSHR, and LHCGR in the ovarian granulosa cells during the main stages of follicle development, whereas treatment with anti-BMP4 antibodies showed no effect. In addition, attenuation of BMPR1B resulted in upregulation of the FSHR (exclusively expressed in the granulosa cell) and LHCGR mRNA levels in the ovary. The present study implies that BMPs engage indirectly in regulating the later stages of folliculogenesis, in addition to their direct role in the regulation of the early stages of follicle development, by enhancing granulosa cell sensitivity to gonadotropins through upregulating the receptor expression. We propose that our mouse model is siutable to elucidate the mechanism of interaction between BMPs and gonadotropins in folliculogenesis.

Stochastic simulation was used to test the hypothesis that optimum-contribution selection with genomic relationships using marker loci with low minor allele frequency (MAF) below a predefined threshold (referred as TGOCS) to control inbreeding maintained more genetic variation than pedigree relationships (POCS) at the same rate of true genetic gain (∆G_true). Criteria to measure genetic variation were the number of segregating QTL loci (quantitative trait loci) and the average number of founder alleles per locus. Marker alleles having a MAF below 0.025 were used in forming the genomic relationships in TGOCS strategy. For centering in establishing genomic relationships, when the allele frequency of marker loci with low MAF set to 0.5 the TGOCS strategy maintained 66% fewer founder alleles than POCS and there were 30% fewer QTL segregating. This TGOCS strategy maintained 61% fewer founder alleles than GOCS and 28% fewer segregating QTL loci. When the allele frequency of marker loci with low MAF was set to observed allele frequency these figures were 8%, 2%, 5% and 2%, respectively. Using marker loci with low MAF in the TGOCS strategy was inferior to both GOCS and POCS. Both TGOCS and GOCS were affected by the same constraint that is LD (linkage disequilibrium) between markers and QTL. Therefore, POCS is a more efficient method to maintain genetic variation in the population until a better way to use genomic information in optimum-contribution selection is identified.

Most honey produced globally is classed as table honey, for direct consumption, as distinct from higher value medicinal grade honeys. Economic value of honey was based on domestic table honey price in AU$ derived from Australia (AU) and the United States (US), from 2010-2021 and sourced from AU honey processors and the US Department of Agriculture. For 2021, average AU and US domestic honey values were AU$5.70 and AU$6.53 per kg respectively. Domestic price slopes for 2010-2021 were similar for AU and US at an increase of AU$0.28 per year. Characteristics for honey production (HP) per hive per year were collated from four manuscripts and three AU datasets, presenting a substantial range of means (8.5 to 123.3 kg), and standard deviations (2.6 to 42.8 kg). Variability in HP between studies is attributed to differences in phenotyping, genotype, environment and production scale.

The saltwater crocodile industry in northern Australia produces skins for high-value leather products. Most eggs are harvested from the wild, providing multiple livelihood benefits to rural and Aboriginal communities in the area. Economic values derived from an independent model for each trait were AU$620.40 for skin grade (a binary trait), AU$-0.95/day for days to market and AU$105.30/hatchling for number of hatchlings per clutch. Economic values were converted to economic weights expressed on the basis of a clutch of the breeding female for a comparison among traits. Based on phenotypic standard deviations of traits, skin grade had the highest emphasis (50%) followed by days to market (38%). Economic values derived in this study should be used to assist management decisions. Setting up structured breeding programs for saltwater crocodiles in northern Australia is less desirable given the wider benefits of harvesting eggs from the wild for rural and Aboriginal communities.

Livestock farming provides a major source of animal protein and occupation opportunities for a large proportion of the world's population, and its profitability could be effectively increased by improvement of either feed efficiency (Zamani, 2017) or reproductive performance (Abdoli et al., 2016). Therefore, genetic improvement of reproductive efficiency is an important objective for animal production industries. Reproduction is a complex biological process with low to medium heritability, which indicates significant influences of environmental and non-additive genetic effects on reproductive performance (Zamani and Abdoli, 2019). Because of the low heritability of reproduction traits, classic selection methods are generally inefficient to achieve rapid genetic progression of reproduction performance in livestock species (Abdoli et al., 2019). However, the use of genetic markers may efficiently enhance the selection response of reproduction traits (Abdoli et al., 2016). Regarding the polygenic nature of reproduction traits, the determination of genetic markers and genetic pathways involved in reproduction efficiency needs intensive molecular genetic studies and use of high-throughput technologies, including genome-wide association studies, whole-genome sequencing, and whole transcriptome analysis.

Simulation was used to illustrate the effects of genomic selection on estimates of genetic parameters, comparing values when genomic relationships were ignored with those obtained accounting for the joint relationship matrix of genotyped and non-genotyped individuals. Analyses were carried out with increasing truncation of earlier records, pedigrees and genotype information. Results showed that estimates from pedigree only analyses could be markedly biased downwards as more historical data is ignored, especially with strong genomic selection, causing predicted breeding values for selection candidates in the last generation to be under-dispersed.

Information on body weight and average daily gain (ADG) of growing animals is key not only to monitoring performance, but also for use in genetic evaluations in the pursuit of achieving sustainable genetic gain. Accurate calculation of ADG, however, requires serial measures of body weight over at least 70 days. This can be resource intensive and thus alternative approaches to predicting individual animal ADG warrant investigation. One such approach is the use of continuously collected individual animal partial body weights. The objective of the present study was to determine the utility of partial body weights in predicting both body weight and ADG; a secondary objective was to deduce the appropriate length of test to determine ADG from partial body weight records. The dataset used consisted of partial body weights, predicted body weights and recorded body weights recorded for 8,972 growing cattle from a range of different breed types in 35 contemporary groups. The relationships among partial body weight, predicted body weight and recorded body weight at the beginning and end of the performance test were determined and calculated ADG per animal from each body weight measure were also compared. On average, partial body weight explained 90.7 ± 2.0% of the variation in recorded body weight at the beginning of the post-weaning gain test and 87.9 ± 2.9% of the variation in recorded body weight at its end. The GrowSafe proprietary algorithm to predict body weight from the partial body weight strengthened these coefficients of determination to 95.1 ± 0.9% and 94.9 ± 0.8%, respectively. The ADG calculated from the partial body weight or from the predicted body weight were very strongly correlated (r = 0.95); correlations between these ADG values with those calculated from the recorded body weights were weaker at 0.81 and 0.78, respectively. For some applications, ADG may be measured with sufficient accuracy with a test period of 50 days using partial body weights. The intended inference space is to individual trials which have been represented in this study by contemporary groups of growing cattle from different genotypes.

Since its initial description in 2001, and with falling costs of genotyping, genomic selection has been implemented in a wide range of species. Theory predicts that the genomic selection approach to genetic improvement offers scope both for faster progress and the opportunity to make change in traits formerly less tractable to selection (hard-to-measure traits). This paper reports a survey of organisations involved in genetic improvement, across species, countries, and roles both public and private. While there are differences across organisations in what have been the most significant outcomes to date, both the increased accuracy of breeding values that underpins potentially faster progress, and the re-balancing of genetic change to include real progress in the hard-to-measure traits, have been widely observed. Across organisations, learnings have included the increasing importance of investment in phenotyping, and opportunities to evolve business models to engage more directly with a wider range of stakeholders. Genomic selection can be considered a more modular approach to genetic improvement, and its simplicity and effectiveness can transform both genetic improvement and the effectiveness of multi-disciplinary approaches to improving livestock and plant production, enabling potentially very significant increases in agricultural productivity, profitability and sustainability.

Variation in the genetic environmental sensitivity (GES) of livestock can cause genotype by environment interactions (G×E). The impacts of G×E differs depending on whether genotypes express different sensitivities across or within environments. Across environments G×E is caused by macro-GES, while within environments G×E is caused by micro-GES.

Estimation of GES is challenging especially in unbalanced datasets. The number of animals in each macro-environment and the degree of genetic connection across macro-environments both influence the estimation accuracy of genetic variance due to macro-GES. Meanwhile, it has been suggested that balanced datasets with relatively large sire family sizes are required to accurately estimate micro-GES of single recorded traits.

The aim of this thesis was to assess the data structure requirements for estimation of macro and micro-GES in unbalanced data, evaluate the accuracy of modelling micro-GES on one trait in multi-trait models, estimate the relationship between health-related traits and micro-GES of production traits, examine the interaction between macro- and micro-GES, and estimate the magnitude of macro- and micro-GES in livestock.

The data structure requirements for estimation of macro- and micro-GES in unbalanced data, was evaluated using a simulation study in Chapter 3. It was shown that the accuracies and bias of estimated variance components for simultaneous estimation of macro- and micro-GES using double hierarchical generalised linear models (DHGLMs) including a linear reaction norm depended primarily on average sire family size. Accurate and unbiased estimates variance components and EBVs of macro- and micro-GES could be obtained with a dataset with 500 sires with 20 offspring per sire on average.

The impact of differences in the number of records on the accuracy of variance component estimation when analysing multiple traits of which one exhibit micro-GES was assessed in Chapter 5. The genetic correlations were found to be slightly overestimated when the true genetic correlations were 0.5. However, the models were accurately able to identify the presence of non-zero genetic correlations, showing that these models could provide useful information.

The relationship between health-related traits and production traits were examined in Chapter 6 by estimating the genetic correlation between immune competence traits and mean performance and micro-GES of weaning weight, eye muscle area and rib and rump fat depth. It was shown that animals with high immune competence tended to also have high mean performance and micro-GES of rib and rump fat and low mean performance and micro-GES of weaning weight and eye muscle area.

The interaction between macro- and micro-GES of body weight in two subpopulations of the same cross reared in Burkina Faso and France was assessed in Chapter 7. Micro-GES of body weight showed considerable macro-GES with both heterogeneity of heritabilities and reranking between the two subpopulations.

The existence of macro-GES and micro-GES were found for yearling weight of Australian Angus beef cattle and body weight of purebred and crossbred broiler chicken. Furthermore, micro-GES was found in weaning weight, eye muscle area and rib and rump fat in Australian Angus beef cattle.

Whole-genome sequence (WGS) data was used to estimate genomic breeding values for growth and carcass traits in Australian Angus cattle. The study aimed to compare the accuracy and bias of genomic predictions with three marker densities, including 50K, high-density (HD) and WGS. The dataset used in this study consisted of animals born between 2013 and 2022. Body weight traits included birthweight, weight at 400 days and weight at 600 days of age. The carcass traits were carcass weight, carcass intramuscular fat and carcass marbling score. The accuracy and bias of prediction were assessed using the cross-validation. Further, for the growth traits, animals in the validation group were subdivided into two subgroups, which were moderately or highly related to the reference. Genomic best linear unbiased prediction (GBLUP) was used to compare genomic predictions with the three marker densities. The prediction accuracies were generally similar across the marker densities, ranging between 0.61 and 0.68 for the body weight traits and between 0.40 and 0.52 for the carcass traits. However, the accuracies marginally decreased as the marker density increased for all the traits studied. A similar lack of difference was found when considering the accuracy by the relatedness subgroups. The results indicated that no meaningful difference in prediction accuracy was estimated when comparing the three marker densities due to the population structure. In conclusion, there was no substantial improvement in genomic prediction when using the WGS in this study.

Innate immune stimulants, particularly those that can trigger trained immunity and influence the adaptive immune response, have potential as antibiotic alternatives, especially for use in livestock industries. Trained immunity is the ability of the innate immune response to develop epigenetic and metabolic shifts, which allow rapid responses to subsequent challenges, and influence the direction of the adaptive immune response. This ability has potential for use by livestock managers, to induce specific rapid immunity in livestock.

Bovine respiratory disease has negative health and economic consequences for the cattle feedlot industry in Australia. Vaccines are used to prevent infection by some pathogens associated with the disease, and antibiotics are used to treat the disease once identified, but absolute protection is not afforded to every animal. Innate immune stimulants may have an important role to play in enhancing immunity against a range of pathogens associated with the disease and if trained immunity is triggered, may be able to shape the adaptive immune response, enhancing overall immune strength.

Amplimune is an innate immune stimulant containing fractions of cell walls of the non-pathogenic Mycobacterium phlei. Research has been conducted in Canada and America, administering Amplimune to calves and dairy cows but similar studies have not been executed in Australia. Hence the aim of this thesis was to test the safety of Amplimune when administered to Australian cattle and to investigate the mechanism of action on bovine immune responses. Further aims were to explore whether concurrent administration of Amplimune, with commercial vaccines against bovine respiratory disease, would enhance adaptive immune responses to those vaccines and to define the transcriptional response of bovine immune cells to in vitro stimulation with Amplimune.

The summation of this thesis was that Amplimune was proven safe when administered to cattle, the pro-inflammatory effect of Amplimune on ex vivo and in vitro bovine immune cells was illuminated, and we identified that Amplimune was associated with a Th1/Th17 type response which was potentially indicative of trained immunity. The mechanistic and transcriptomic studies on Amplimune are the first of their kind, adding significantly to the body of knowledge on the effect of Amplimune on bovine immune cells in vitro. Moreover, this thesis has clarified the potency of Amplimune in modulating the cytokine profile, hence shaping the adaptive immune response. The results of experiments in this thesis are important for the progression of approval for the use of Amplimune in the Australian cattle industry.

It is almost fifty years since the first World Congress on Genetics Applied to Livestock Production (WCGALP) was convened in Spain in 1974. This paper, targeted for the early-career scientist session, details the history and evolution of WCGALP, and outlines gender composition of the Permanent International Committee, session chairs, plenary and invited speakers, and authors. Data containing 24,351 author records from all WCGALP proceedings, and old programs were used for the analyses. In the early years, there were few women involved in any aspect of WCGALP, however, more recent congresses have featured an increasing proportion of women on WCGALP committees and serving as session chairs. Based on recent data, gender is not playing a determining role in selection of submitted papers for oral presentations. We recommend greater gender diversity on WCGALP committees and encourage early-career scientists to actively participate in WCGALP conferences to further increase the diversity of future congresses.

Genetic improvement has been limited in the Australian honey bee population, despite the direct and indirect economic significance of the industry. Recently, significant industry and community investment has established the foundation for a national R&D and improvement program centred on objective evaluation and genomic selection, underpinning strong industry and community engagement. This paper outlines the key elements of that program, its goals, and early steps in implementation, and highlights the transformative potential of the program.

Common bean (Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding values (GEBV) for grain yield (GY), CKT, Fe, and Zn in an African bean panel of 358 genotypes in a two-stage analysis. In Stage 1, best linear unbiased estimates (BLUE) for each trait were obtained from 898 genotypes across 33 field trials in East Africa. In Stage 2, BLUE in a training population of 141 genotypes were used in a multivariate genomic analysis with genome-wide single nucleotide polymorphism data from the African bean panel. Moderate to high genomic heritability was found for GY (0.45 ± 0.10), CKT (0.50 ± 0.15), Fe (0.57 ± 0.12), and Zn (0.61 ± 0.13). There were significant favorable genetic correlations between Fe and Zn (0.91 ± 0.06), GY and Fe (0.66 ± 0.17), GY and Zn (0.44 ± 0.19), CKT and Fe (-0.57 ± 0.21), and CKT and Zn (-0.67 ± 0.20). Optimal contributions selection (OCS), based on economic index of weighted GEBV for each trait, was used to design crossing within four market groups relevant to East Africa. Progeny were predicted by OCS to increase in mean GY by 12.4%, decrease in mean CKT by 9.3%, and increase in mean Fe and Zn content by 6.9 and 4.6%, respectively, with low achieved coancestry of 0.032. Genomic selection with OCS will accelerate breeding of high-yielding, biofortified, and rapid cooking African common bean cultivars.

Optimisation of pig breeding programs aims to increase the genetic gain in pig populations and to decrease the rate of inbreeding in the pig nucleus population. Genomic selection is a potential breeding strategy that can increase genetic gain and is also expected to decrease the rate of inbreeding in livestock breeding programs. Pigs are selected based on multiple correlated traits in the nucleus population. It might be difficult to improve response to selection in favourable direction for individual breeding objective traits because of an interplay between complex correlation structure and the economic value of each trait. On top of that, genomic selection might also shift genetic gain towards hard-to-measure traits. More work is needed on how genomic selection benefits the overall merit of breeding objectives and individual breeding objective traits.

Post-weaning survival (PWS) is an important breeding objective trait in the sire line of pigs. The benefits of genomic selection for PWS depend on the structure of the reference population, which should have both genotypes and phenotypes. Animal breeders might not be interested in genotyping dead pigs because dead pigs cannot be selection candidates. However, genotyping dead and live pigs might increase the genetic gain for PWS in comparison to genotyping live animals alone. While improving genetic gain, it is also important to reduce the rate of inbreeding because pigs are selected in a closed elite herd. Genomic markers might also increase genetic diversity because genomic relationships are more accurate than pedigree relationships. With the availability of genomic marker information, it is also easier to account for the dominance effect than pedigree information in the genetic evaluation model in the presence of dominance. Therefore, the broad objective of this thesis was to investigate the benefits of using genomic selection in pig breeding programs. This thesis explored multiple new avenues of using genomic information to increase the rate of genetic gain and decrease the rate of inbreeding in pig breeding programs.

In chapter 3, a premise was tested that the overall pig breeding objective achieves additional genetic gain in genomic selection compared to pedigree selection, but some traits achieve larger additional genetic gain than other traits. Results in a deterministic simulation study showed that genomic selection scenarios based on different sizes of reference populations increased overall response in the breeding objectives by 9% to 56% and 3.5% to 27% in the dam and sire lines, respectively, compared to pedigree selection. In the dam line of pigs, reproductive traits such as sow mature weight, number born alive, and sow longevity achieved 123% to 403%, 73 % to 351%, and 58% to 278% larger genetic gain in genomic selection compared to the pedigree selection respectively. In comparison, backfat thickness, average daily gain, and feed conversion ratio achieved 6% to 14%, 4% to 11%, and 7% to 9% smaller genetic gain in genomic selection than pedigree selection, respectively. In the sire line of pigs, post-weaning survival, drip loss, and middle portion percentage achieved larger genetic gain in genomic selection than the pedigree selection. Achieving larger genetic gain for reproduction traits in the dam line and post-weaning survival and meat and carcass quality traits in the sire line increased the overall merit of pig breeding objectives in genomic selection compared to the pedigree selection.

In chapter 4, a premise was tested that genotyping both live and dead animals realises more genetic gain for PWS (assuming a PWS of 90%) in pigs compared to the scenario where only live animals are genotyped. Stochastic simulation was conducted to compare genetic gain in the scenarios of either genotyping live and dead animals or genotyping live animals only. Genetic gain for PWS in these genotyping strategies was compared at 1% pedigree inbreeding in optimum contribution selection. Results showed that genetic gain with genotyping all live animals was 52% higher than pedigree selection. On top of that, genetic gain with genotyping live and 20 to 100% of dead animals was 14 to 33% higher than genotyping only live animals. Genotyping live and dead animals increased the accuracy of the genomic breeding values of live animals compared to genotyping only live animals, which resulted in a larger genetic gain for PWS.

In chapter 5, a premise was tested that optimum-contribution selection with genomic relationships using only low MAF (minor allele frequency) markers below a predefined threshold to control inbreeding realises less rate of true inbreeding than optimum-contribution selection (OCS) with pedigree relationships. Genetic gain in genomic and pedigree-based OCS was fixed at a predefined value while comparing the rate of inbreeding. Results showed that pedigree-based OCS realised a lower rate of inbreeding than genomic-based OCS at the same rate of genetic gain. Genomic-based OCS fixed more favourable quantitative trait loci than pedigree-based OCS. In addition, genomic-based OCS selected more closely related animals than pedigree-based OCS. Therefore, pedigree-based OCS realised a lower rate of inbreeding than genomic-based OCS at the same rate of genetic gain.

Finally, in chapter 6, a premise was tested that genetic gain in pig breeding programs using dominance models that accounted for both random additive genetic and dominance effects was higher than additive models that included only random additive genetic effects under the presence of dominance. The stochastic simulation was conducted to compare models in thedam and sire line of pigs. In the sire line, similar additive genetic variances were estimated by the two models but with the additive model, the litter and residual variances were biased upward by 42% and 23%, respectively. When the model did not include a common litter effect in the dam line, the additive genetic variance was 10% smaller in comparison to the additive genetic variance estimated using the dominance model. Despite overestimating variance components using additive models, both models realised a similar rate of total true genetic gain. Since animals were selected based on additive genetic merit, the dominance model did not impact the rate of total true genetic gain. Therefore, the additive genetic model can be used for estimating breeding values if animals are selected based on additive genetic merit, even under the presence of dominance.

The results mentioned above showed the potential of genomic selection to increase genetic gain in pig breeding programs. This study investigated multiple new avenues of using genomic information for the genetic improvement in pigs. However, there are still many unanswered question. Use of genomics is beneficial for improving the accuracy of selection and genetic gain, it is not clear how to use genomics to control inbreeding. To take the advantage of genomics, more work is needed to investigate how to use genomics to control inbreeding. In addition, genomics can be useful for accounting non-additive genetic effects such as dominance and epistasis in the model. As more research emerges, use of genomics will be more useful for optimising the pig breeding programs because genomics opens up further opportunities to reveal the biology of traits.

Context. Coping with high levels of cold stress should be beneficial to survival of lambs, given the high mortality rate associated with severe winter storms. The Elsenburg Merino selection experiment involved divergent selection for reproduction. Phenotypic results comparing the positively selected H-Lines and negatively selected L-Lines suggested that cold-stress adaption could have contributed to the favourable genetic trends for survival of H-Line lambs. However, observing the genetic merit of better adapted animals depends on the presence of cold stress at the time of recording. A genotype by environment component (G × E) could, thus, be important when assessing survival/mortality phenotypes. Aim. This study proposed the genetic analysis of this possible G × E component and compared the H- and L-Lines in this regard. Methods. The sire model allowed the use of progeny phenotypes for neonatal mortality recorded during different levels of cold stress, and the possible G × E could be investigated through the reaction-norm approach. Genetic parameters were evaluated as random regression components by implementing a Gibbs sampling approach. A data set of 5723 individual lamb records was analysed as the progeny of 213 sires. Results. A modelled G × E component played an important role in mortality outcomes, with the mean estimate (and 95% confidence interval) for the slope (σ²_sb = 0.113[0.0019–0.28]) only marginally smaller than the corresponding estimate for the intercept (σ² _sa = 0.124[0.003–0.26]). The reaction-norm model showed a higher heritability (h² ± posterior standard deviation) for mortality at 3 days of age during high cold-stress (0.22 ± 0.16 at ~1100 KJm⁻²h⁻¹) than during mild (0.13 ± 0.10 at ~960 KJm⁻²h⁻¹) conditions, suggesting a greater ability to discriminate between sires at increasing stress levels. Conclusions. Failure to account for this G × E component putatively contributes to the low h² commonly reported for survival traits. The higher h² at increased levels of cold stress could have played an important part in the higher survival of the H-Line progeny, who were better at coping with cold, wet and windy conditions. Implications. Larger studies representing a wider environmental trajectory are recommended. This should be very feasible since cold stress can be derived from commonly available weather-station data.

Understanding the effects of repeated testing on behaviour is essential for behavioural tests that are re-applied to the same individuals for research and welfare assessment purposes. Assessing the repeatability of behaviour can also help us understand the influence of persistent traits vs transient states on animal responses during testing. This study examined the repeatability of behavioural responses in an attention bias test developed for sheep as a measure of affective state. Sheep were assessed in the attention bias test three times (n = 81 sheep), with testing occurring at intervals of 1 year then 2 weeks. During testing, individual sheep were exposed to a dog located behind a window for 3 s in a 4 × 4 m arena, then the dog was obscured from view, removed and sheep behaviours were recorded for 180 s. We hypothesised that behaviours in the test would have moderate-high repeatability but that the mean behavioural responses would change over consecutive trials as sheep habituated to the test environment. To estimate repeatability, data were modelled using restricted maximum likelihood linear mixed-effects models, fitting animal ID as a random effect. Vigilance behaviour, defined as having the head at or above shoulder height, was moderately repeatable (r = 0.58). Latency to eat (r = 0.20) and duration spent looking towards the previous location of the dog (attention to the dog wall) (r = 0.08) had low repeatability. Mean latency to eat did not differ significantly between trials (P = 0.2) and mean vigilance behaviour tended to decrease over the trials (P = 0.07). Mean duration of attention to the dog wall significantly decreased across the trials (P < 0.001), while mean zones crossed increased (P < 0.001), as did behaviours directed towards the exit door such as duration in proximity and pawing at the door. Overall, vigilance behaviour was moderately repeatable, suggesting it may have been driven by temperament or personality traits, while attention and feeding behaviours may have been more influenced by transient affective states or other factors, however further research is needed to better tease apart these potential effects. Sheep demonstrated some habituation to the test over consecutive trials. Care should therefore be taken during future application of the test to ensure all animals undergoing attention bias testing have equivalent experience for a valid interpretation of their relative behavioural responses.

Women’s empowerment constitutes an important aspect of the research and development agenda in the global south and has become a much-studied construct in recent years. Nevertheless, despite decades of empirical research on determinants and outcomes, there remains much that is not yet understood about the process of women’s empowerment. This includes a lack of clarity regarding the associations between empowerment resources, agency and achievements, and how agency is strengthened and constrained under different normative social contexts. This thesis contributes to closing these gaps in knowledge through the investigation of women’s empowerment within the mixed and livestock-based systems in Ethiopia. Specifically, the program of research relates to the Small Ruminant Value Chain Development (SRVCD) program that is run by the International Centre for Agricultural Research in the Dry Areas (ICARDA)-Ethiopia office.

The study of empowerment aspects of development programs is often absent within the broader empowerment literature, with this being primarily due to three reasons. First, the multi-dimensional nature of agency and empowerment poses measurement challenges in development programs. Second, indicators used for measures of agency within studies on development programs can vary significantly across contexts. Third, the quantitative measures used in such studies often fail to capture people’s values and meaning, including whether or not agents value the agency they exhibit. For this reason, concerns have been raised by many researchers regarding the tendency of empowerment studies to solely use quantitative indicators. Hence, it has been suggested that there is a need for qualitative assessments of motivations, meanings and values behind choices to enable comprehensive understanding of empowerment. Another common problem in many studies that attempt to measure women’s empowerment is that they lack clear conceptualizations of, and differentiation between, the dimensions of empowerment. This is particularly evident in relation to stating which aspects of empowerment (i.e., empowerment resources/ preconditions, agency or achievements) has been measured. Such a lack of specificity in the literature hinders the ability to understand empowerment processes as they work in practice, which further limits the ability of organisations to develop programs that successfully facilitate women’s empowerment. For example, the existing development literature demonstrates that, while women have increased their perceived levels of empowerment and freedom in many countries, the social norms that act to restrict women’s empowerment within those countries often remain unchanged. Few studies have examined the underlying reasons for this discrepancy. Moreover, most of the existing studies that investigate agency and empowerment within development program have been undertaken in relation to nonlivestock-based systems. This means that relatively little is known about women’s agency and empowerment within mixed crop and livestock systems, despite agency dynamics being known to differ from those in other types of agriculture. As such, the current program of research aimed to contribute to these knowledge gaps by addressing some of these problems ―understanding empowerment within context, clarifying empowerment pathways and the nature of agency and achievements that women and men livestock keepers’ value. It aimed at enhancing our understanding of pre-conditions for empowerment, the nature of agency and achievement, and their associations with contextual factors from gender perspectives within the mixed and livestock-based systems of Ethiopia.

The thesis has two studies each with parts. Study 1 alone has three parts that focuses on investigating the pre-conditions for empowerment (empowerment resources) and agency dimensions (decision-making areas) along with their gendered valuations. It also explored how agents exercise their agency by deviating from the normative contexts to achieve expanded agency living within a constraining social environment. A mixed-methods approach was used for Study 1, with qualitative data gathered through 30 focus group discussions (FGDs), 44 key informant interviews (KIIs), and 18 case studies of deviance in gender relations. Participants included men and women livestock keepers, community leaders and facilitators, and staff of the various SRVCD program service providers at community and district levels. Quantitative data was collected via a structured questionnaire as part of a Household Survey, which was completed by 381 livestock keepers. Key findings from Study 1 include that the social environment within which the livestock value chain development takes place is generally non-autonomy supportive for women, and that systems of access, ownership and control are biased towards men. The major empowerment resources and decision-making processes that are valued by livestock keepers are mediated by gender and location (particularly the farming systems) and play an important role in forming the contextual conditions for empowerment in mixed and livestock-based systems. Psychological well-being (autonomy, self-acceptance, and positive relations) was found to be one of the most important resources and was mediated by the interaction between gender and context. The analysis of how and under what conditions women (and men) can exercise their agency in spite of the constraining normative environment also resulted in notable findings. Agents (particularly women) own the capacity to deviate, and the intentions that lead to such new behaviors emerge not only from individuals’ attitudes, subjective norms, and perceived behavioral control (as suggested by the Theory of Planned Behavior; TPB), but also in combination with other socio-economic factors. Specifically, self-conviction (attitude and perceived behavioral control), subjective norms (within household and community), and structures (state and non-state institutions) were found to be critical factors affecting agents’ ability to deviate for positive gains. The study findings make evident that livestock keepers are aware of the negative influence of normative culture but lack the power to challenge it. It was also evident that conceptualizations of agency differ along gender lines and across locations. For example, agency indicators such as ‘joint decision-making’ need to be reconsidered within empowerment measurements because study participants reporting this do not necessarily mean that they have engaged in egalitarian decision-making processes, as is widely assumed within the field. Rather, ‘joint decision-making’ is often another indicator of men’s dominance in decision-making.

Study 2 has two parts. It incorporated relevant variables associated with the agency dimensions, as identified in Study 1. The first Part of Study 2 investigates what are the gender differences in relation to access to value chain inputs, ownership of value chain resources, decision-making, and control over value chain outputs in the context of mixed and livestockbased systems. The study involved 723 small ruminant keeping households from six districts completing a baseline questionnaire designed to analyse the small ruminant value chain in Ethiopia. Overall, the findings supported the reported gender differentials with regards to systems of access, ownership and control of major value chain inputs and outputs. Estimation results of the Binary Logistic Regression Model (BLRM) identified several variables that are significantly associated with agency dimensions, achievement, or both, with mixed results. Overall, the findings of Part 1 of Study 2 indicated that participation in small ruminant value chains may encourage more egalitarian decision-making behaviors but it does not guarantee the capacity of women for autonomous decision-making, and thus needs to be coupled with interventions targeting empowerment dimensions. The second part 2 of Study 2 explored the effect of gender transformative approaches on the normative challenge to empowerment identified in Study 1 through a qualitative literature review of ICARDA knowledge products (e.g., program reports). Drawing on the phenomenological method of qualitative literature review, community conversations (CC) were found to have positively impacted the gender aspects of social norms. Changes in knowledge, attitudes and practices related to livestock at household, community and institutional levels were identified. Nevertheless, since the knowledge products available for the review were primarily process oriented, relating to CC design and implementation, there remains a further analysis based on primary data to generate evidences that would help in scaling the experiences and outcomes locally, regionally, and nationally. It is recommended that these transformative approaches are institutionalized, such that they included within all public extension and related programs. There is also a need for the development of national gender policies, which should focus on simultaneously cultivating/strengthening intrinsic agency of women livestock keepers and transforming the socio-cultural contexts to facilitate changing gender norms, which is necessary to support women’s empowerment.