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There are two classes of anthelmintic (levamisole and benzimidazoles) have been used to control gastrointestinal nematodes of goats and sheep on smallholder and commercial farms in Fiji for more than 40 years. Given the potential this provides for the development of anthelmintic resistance (AR). A study was conducted to determine the level of AR on eleven farms across the Western and Northern divisions of Fiji. Efficacy was determined by faecal egg count reduction tests (FECRT) following administration of levamisole (LEV), albendazole (ALB), levamisole + albendazole combination (LEV+ALB), ivermectin (IVM), moxidectin (MOX) and the Haemonchus specific closantel (CLO). At day 14 following administration, resistance (FECRT < 95%) to ALB was found 6 of 7 farms tested, while levamisole resistance was observed on 1 of 4 goat farms and 2 of 3 sheep farms. Full susceptibility (FECRT > 95%) to IVM was found in all 3 sheep farms and 3 of 4 tested goat farms while MOX was fully effective on the 7 farms tested. The combination of LEV+ALB was effected on all 4 goat farms and 2 of 3 sheep farms. There was evidence of reduced efficacy of CLO against Haemonchus contortus on goat but not sheep farms. Reduced efficacy of ALB and LEV against both Haemonchus contortus and Trichostrongylus colubriformis was observed with overall average efficacy percentages being LEV (91.6%), ALB (65.3%), LEV + ALB (94.4%), IVM (97.4%), and MOX (98.7%). Moxidectin exhibited persistent efficacy to day 28 on 50% of goat farms and up to 42 days against Haemonchus contortus on sheep farms. CLO exhibited sustained efficacy against Haemonchus contortus for 28 days in both goats and sheep.

The popularity of goat farming in Lao PDR is constrained by diseases. Information on the type and prevalence of diseases in Lao goats is scattered in both the formal and informal literature, and the actual causes of common clinical syndromes are not known definitively. The situation is exacerbated by a lack of veterinary and extension services in rural areas and clear control strategies. Therefore, the work reported in this thesis was designed with four broad objectives: 1) collate the disparate data on diseases of Lao goats within the context of goat production, marketing systems and the available veterinary services in the country; 2) determine animal-level and herd-level prevalence of common clinical syndromes in Lao goats, to determine risk factors for herd-level occurrence of the most prevalent clinical syndromes; 3) determine causation for important clinical syndromes of goats in Lao PDR (eye infection, proliferative lip and facial lesions and respiratory disease) and pathogen genetic relatedness by conducting phylogenetic analysis; and 4) introduce and establish molecular diagnostic methods relevant to most common goat diseases at the Lao National Animal Health Laboratory (NAHL). Initially a review of the existing literature on goat diseases in Lao PDR was conducted to collate scattered data in the formal and informal literature. Secondly, a monthly survey based on the observations of smallholder goat farmers was conducted over 22 months to identify the prevalence of clinical syndromes and associated risk factors. Then a case-control study was conducted using PCR-based diagnostics and sequencing to identify causative infectious agents for three of the clinical syndromes in Lao goats. Lip and mouth lesions (presented on 12.2% of monthly visits), diarrhoea (9.3%) and eye lesions (9%) were the most prevalent syndromes based on farmer observations. Occurrence of any type of clinical syndrome and eye lesions were positively associated with increasing herd size and provision of salt respectively. The case-control study was used to determine the causation of eye infection, proliferative lip and facial lesions and respiratory disease, but not diarrhoea due to the unavailability of adequate number of samples. The case-control study involved 41 – 50 samples from cases and the same number from matched controls for each syndrome. The main cause of eye infections was infectious keratoconjunctivitis (pinkeye) caused by Mycoplasma conjunctivae. The main cause of proliferative lip and facial lesions was orf (contagious ecthyma, scabby mouth) caused by the orf virus. The main cause of the chronic respiratory syndrome was atypical pneumonia caused by Mycoplasma ovipneumoniae. These provided the first definitive determination of causation of three important clinical syndromes in Lao goats. The findings of this thesis have important implications for improved disease diagnosis, control and future research to support Lao goat production.

Maintaining genetic diversity and variation in livestock populations is critical for allowing natural and artificial selection genetic improvement well as for avoiding inbreeding. The Laotian government and farmers are concerned that there has been a decrease in genetic diversity and an increase in inbreeding among native goats in their village-based smallholder system. The objective of this study was to investigate the genetic diversity of Lao native goats in a small-scale farming system in central Laos using genotype data. The results showed that there was a close genetic relationship between Lao native goats with Chinese goat breeds and a low to moderate genetic differentiation among goat populations in Central Laos ranging from 0.0112 to 0.0427. This goat population had close to zero inbreeding coefficients (-0.093 to 0.052).

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (F_ST: 0.011–0.043) and negligible inbreeding coefficients (F_IS: −0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92–6.85Mb, with short ROH segments (1–5Mb length) being the most prevalent (66.34%). Longer ROH segments (20–40 and >40Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.

Polymorphisms at PRNP gene locus have been associated with resistance against classical scrapie in goats. Genetic selection on this gene within appropriate breeding programs may contribute to the control of the disease. The present study characterized the genetic profile of codons 146, 211 and 222 in three dairy goat breeds in Greece. A total of 766 dairy goats from seven farms were used. Animals belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287) and a foreign breed, Damascus (n = 215). Genomic DNA was extracted from blood samples from individual animals. Polymorphisms were detected in these codons using Real-Time PCR analysis and four different Custom TaqMan^® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated based on individual animal genotypes. Chi-square tests were used to examine Hardy-Weinberg equilibrium state and compare genotypic distribution across breeds. Genetic distances among the three breeds, and between these and 30 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index F_ST with Arlequin v3.1 software; a Neighbor-Joining tree was created using PHYLIP package v3.695. Level of statistical significance was set at P = 0.01. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied population. Significant frequency differences were observed between the indigenous Greek and Damascus breeds. Alleles 222K and 146S had the highest frequency in the two indigenous and the Damascus breed, respectively (ca. 6.0%). The studied breeds shared similar haplotypic frequencies with most South Italian and Turkish breeds but differed significantly from North-Western European, Far East and some USA goat breeds. Results suggest there is adequate variation in the PRNP gene locus to support breeding programs for enhanced scrapie resistance in goats reared in Greece. Genetic comparisons among goat breeds indicate that separate breeding programs should apply to the two indigenous and the imported Damascus breeds.

Lao People's Democratic Republic (Lao PDR) is a small and developing nation in South-east Asia. Agriculture is its lifeblood, employing 61% of the labour force in 2019, compared to 2.6% in Australia (The World Bank 2021). Small family farms are predominant, relying on rice and crop cultivation to feed the household and generate surplus for income. Livestock are essential for providing manure, consuming non-edible plants and household waste, and serving as a bank account, to be sold when cash is needed. While these systems are vital for human survival, as a tool for household economic growth, there is room for improvement. Goats are gaining popularity among Lao farmers due to their strong export potential. Neighbouring Vietnam is a major importer of Lao goats which receive a price premium of 30% over Vietnamese crossbred goats and Lao farmers keep approximately 70% of the slaughter value (Gray et al. 2019). The objective of this study was to assess the current level of inputs to understand the scope to improve goat production.

A structured survey was conducted of 70 smallholder farmers raising goats in the main goat raising province of Savannakhet in central Lao PDR and was approved by University of New England Human Ethics Committee (HE19-218). The survey was conducted in the local language, responses were recorded using mobile acquired data software CommCare® (Dimagi Ltd. Cambridge, MA, USA), and descriptive statistics were generated.

Farm capital was limited, with a low annual income (AU$1558/year, range = AU$249–6981), a dependence on family labour, and participation in a diverse range of enterprises to ensure household resilience to shocks. This meant there would be trade-offs to high-input investments in goat raising. Farmers reported limited access to animal health services and most relied on neighbours (67%) and family (57%) for information. Farmers had reasonable access to water and land (3.6 ha, range = 0–20 ha). Most farmers (64%) depended completely on free grazing of communal land for goat nutrition and grazed goats for 6 h/day in the wet season and 8 h/day in the dry season. This was predominantly unsupervised. This illuminated increasing grazing duration as a possible low risk intervention to boost nutrition. Uncontrolled breeding resulted in year-round kidding which coincided with low nutrition availability for goats in the late dry and early and late wet seasons (Fig. 1). Increased cropping activity likely reduced grazing duration and nutrition available for goats in the late wet season. Growing forages utilising available land with strategic feeding and/or fodder conservation were recommended.

Most farmers viewed disease as the main constraint to production, particularly facial lesions (most likely Orf" 87%) and diarrhoea (57%). Disease management was reactive and unregulated, with 61% of farmers responding by opting for drugs to treat illness, and when asked how they obtained them, 74% purchased them themselves from stores. Increasing farmer disease knowledge through participatory training sessions and explanation of low-cost, accessible and practical treatments are being implemented to directly empower farmers as animal health services are limited. Improving goat house hygiene is one of the low-input preventive strategies that are also being pursued.

These data reflect a low-input system with limited capital. A project has commenced optimising current inputs to maximise productivity outputs while maintaining a low-input system. Social and lifestyle benefits are also being monitored as they are required to motivate households to adopt new management strategies when resources are limited.

In the past two decades, goat numbers have increased rapidly throughout Lao Peoples Democratic Republic (Lao PDR) due to rising demand for Lao goat meat from Vietnam. This provides an economic opportunity for Lao smallholders who are already benefiting from the growing goat trade. Despite increased market opportunity, goat production has remained traditional throughout Laos. The predominant management system is characterised by lowinputs, free-grazing, uncontrolled mating and opportunistic sale. Scientific literature suggests that the productivity of these systems is limited by technical constraints, including poor management, poor nutrition and prevalent disease. Previous development projects have begun to address these technical constraints through improved goat husbandry practices. However, there is little evidence of these practices being implemented by farmers in the long term or being adopted at a widespread scale. A contributing factor is lack of understanding of the social and cultural contexts surrounding goat production in Laos. In other developing countries, socio-cultural factors have had a profound influence on smallholders’ decision making. Their integration into the design of development projects has been linked to greater long-term livelihood impacts. To enhance the impacts of the research for development project titled “Goat production systems and marketing in Lao PDR and Vietnam” (LS/2017-34) funded by the Australian Centre for International Agricultural Research (ACIAR), this Masters Thesis investigated the sociological aspects of goat raising. Semi-structured interviews were conducted with 30 smallholder goat farmers across five villages in South-Central Laos. The semi-structured interviews revolved around three research questions:

1. What are the goat raising experiences of rural households in Laos?

2. What are the perceived benefits and burdens that small landholders have around goat raising?

3. What role do goats play in cultural and social networks/practices, and social learning amongst households?

Grounded theory methodology was used to analyse interview transcripts. The interviews revealed that goats occupy an agricultural niche in Lao smallholder farming systems that yield unique livelihood benefits. Goats were a profitable and liquid asset, providing income for small expenses that occurred frequently, such as paying utility bills and medical expenses, buying food and clothing and emergency expenses. Goats have been integrated into socio-cultural ceremonies, often replacing cattle and buffalo. This has enabled farmers to practice sociocultural traditions at a lower cost, more proportionate to their socio-economic status. Managing goats in free-grazing systems was considered easy and benefited the wider farming system by enabling household labour and land to be allocated to cropping, and for goat manure to fertilise crop plantations. The small herd size of goats (10-15 head) is unlikely to be increased dramatically without cancelling the time-saving benefits of current free grazing systems. This is because the trade-offs associated with free-grazing management such as occasional goat theft, goat injury through dog attacks and car accidents, and goat damage to crops, are likely to become unsustainable with larger, unsupervised goat herds. Low-input project interventions that enhance or at least do not interfere with goats’ specific roles, are likely to benefit the widest cohorts of farmers. Interventions that meet this criterion include improving goat kid management, goat house design and cleaning, and disease management.

Farmers relied on their experiences and observations of goat raising in their communities to inform their management decisions. Farmers valued trial and error as a learning strategy to judge the efficacy of project interventions and modify them to suit their own contexts and constraints more appropriately. Farmers also took guidance from exchanging experiences with other goat farmers. This thesis questions the assumption that technical interventions are inherently optimal and beneficial for smallholder farming systems. Development projects should not advocate increased inputs into the goat enterprise without considering trade-offs to the whole farming system. An understanding of the unique roles and purposes of goats, farmer objectives, learning styles, and trade-offs to goat raising should inform the assumptions that underpin the strategies adopted by development projects and ideally lead to sustained impacts in rural communities.

New South Wales Department of Primary Industries' second-most western station, Condobolin Agricultural Research and Advisory Station will be host to the "Measured Goats in the Rangelands project". This five-year co-investment between New South Wales Department of Primary Industries and the Meat and Livestock Donor Company project will also work collaboratively with the Animal Genetics and Breeding Unit. The project will utilise three goat breeds – Boer, Kalahari Red and wild "Rangeland", both in purebred and crossbred forms to become a multi-breed genomic reference population. All project animals born will have a goat specific 70k SNP genomic test to identify parentage, breed composition and heterozygosity. Furthermore, performance, health, reproduction and structural traits will be recorded in large contemporary groups. The aim is to breed and measure over 8,000 animals in a self-replacing style breeding nucleus over 4 years. This project aims to provide trait and breed means, update genetic parameter estimates for meat goats, obtain heterosis estimates, and provide new links into the KIDPLAN database. The project will also generate new traits and knowledge to update the assumptions used for the KIDPLAN analysis. Finally, the project has a major adoption and extension focus to increase the uptake and adoption of KIDPLAN breeding values at a seedstock and commercial level.

Fiji has the largest small ruminant population of the Pacific Island countries with an estimated sheep and goat population of about 14,068 and 110,196 respectively, from 764 sheep and 8,801 goat farms (Fiji National Agricultural Census, 2019). In the tropical environment of Fiji, high temperatures and rainfall strongly favour hatching and development of gastrointestinal nematodes (GIN) to the infective 3rd larval stage, although these conditions also result in short survival times of the infective larvae on pasture (Banks et al. 1990). The aim of this study was to quantify the prevalence of GIN infection in small ruminants in private farms in Fiji, and identify differences caused by small ruminant species, animal class (i.e., age and lactating status) or location (environment).

The aim of this study was to quantify the prevalence of gastrointestinal nematodes (GIN) in small ruminants raised in private farms in Fiji.

In this study, 17 farms were sampled from the Western (n = 8) and Northern (n = 9) divisions of Fiji including a total of n = 257 goats and n = 299 sheep. On each farm, approximately 10 animals were sampled from each class of small ruminant species: young animals (YA), dry females and reproductive males (DF & RM) and lactating females (LF). The larval culture was prepared using the pooled samples from all the three classes, approximately 70 g of sample from each class using vermiculite in 1:1 ratio. Cultured bottles were kept in the incubator for 7 days at 27 C. Recovery of larvae was done by adding warm water washing of the lids and the sides of the bottles in the falcon tubes.

Overall, the main differences observed in the predominance of GIN genera when comparing the two small ruminant species were for Haemonchus and Trichostrongylus. Sheep had a larger proportion of Haemonchus (43 vs 24%) and a lower presence of Trichostrongylus (25 vs 37%) when compared to goats. Oesophagostomum (14 vs 22%) and Strongyloides (16 vs 15%) had an overall lower proportion when compared to the other two genera and the prevalence across the small ruminant species was similar for sheep and goats respectively. A substantial variation in terms of GIN genera was observed across the different animal classes and no clear pattern is shown when comparing the different classes between the two small ruminant species. The only genera which was similar was Strongyloides. Haemonchus dominance followed by Trichostrongylus, Oesophagostomum and lastly Strongyloides were seen in sheep, whereas this pattern is different in goats as dominance of Trichostrongylus followed by Haemonchus, Strongyloides and lastly Oesophagostomum was noticed.

The objectives were to determine the genetic profile of scrapie codons 146, 211 and 222 in three dairy goat breeds in Greece and assess its impact on milk production and udder health. A total of 766 dairy goats from seven farms were used. Animals belonged to two native (Eghoria; n=264 and Skopelos; n=287) and one foreign breed Damascus; n=215. Genomic DNA was extracted from individual blood samples. Polymorphisms were detected using RealTime PCR analysis and four different Taqman assay mixes. Milk production and udder health traits of individual animals were recorded monthly for two consecutive milking periods. The former included daily and lactation milk yield and composition; fat, protein, lactose and solids-not-fat (SNF) content. Udder health traits included udder fibrosis, abscess and asymmetry, milk somatic cell count, and number of colony-forming units. Genotypic, allelic and haplotypic frequencies were calculated and genetic distances between breeds were estimated using fixation index FST with Arlequin v3.1 software. The effects of genotype and allele on the studied traits were assessed with mixed linear models with R package ‘lme4’. All resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied goats. Significant differences (P<0.01) in genetic profile were observed between the two native breeds and Damascus. Alleles 222K and 146S had the highest frequency (ca.6%) in the native and Damascus breeds, respectively. Resistance-associated alleles and genotypes did not affect animal traits (P>0.01) except for a mild adverse effect of codon 146 on milk SNF in native goats. Results suggest that separate breeding programs should apply to native and Damascus goats aiming at enhancing scrapie resistance. Selection for the latter is not expected to compromise animal productivity and udder health. This work was funded by the SOLID project (FP7-266367) and Onassis Foundation.

Goat numbers in Lao PDR are increasing rapidly, fuelled by exports of goats to Vietnam. Since 2017 the Australian Centre for International Agricultural Research (ACIAR) has worked with government agencies in Lao PDR and Vietnam to evaluate the sustainability and future direction of this trade and the production systems underpinning it. Research to date has identified that almost all production in Lao PDR is by smallholders and was found to contribute 35 ± 16% of household income in goat keeping households (Gray et al. 2019). Smallholder systems, particularly in the lowlands, benefit from a relatively low-cost production model in which goats are typically housed at night and released to graze unsupervised on communal land during the day. Vulnerable crops, rather than livestock, are fenced and free ranging and browsing behaviour limits the severity of helminthiasis. Goats are sold to visiting traders at high prices, commanding a premium in Vietnam of 20-40% over local Vietnamese crossbred goats with farmers capturing approximately 70% of the market value of goats they sell (Gray et al. 2019).