Feasibility of pedigree recording and genetic selection in village sheep flocks of smallholder farmers

Pedigree recording and genetic selection in village flocks of smallholder farmers have been deemed infeasible by researchers and development workers. This is mainly due to the difficulty of sire identification under uncontrolled village breeding practices. A cooperative village sheep-breeding scheme was designed to achieve controlled breeding and implemented for Menz sheep of Ethiopia in 2009. In this paper, we evaluated the reliability of pedigree recording in village flocks by comparing genetic parameters estimated from data sets collected in the cooperative village and in a nucleus flock maintained under controlled breeding. Effectiveness of selection in the cooperative village was evaluated based on trends in breeding values over generations. Heritability estimates for 6-month weight recorded in the village and the nucleus flock were very similar. There was an increasing trend over generations in average estimated breeding values for 6-month weight in the village flocks. These results have a number of implications: the pedigree recorded in the village flocks was reliable; genetic parameters, which have so far been estimated based on nucleus data sets, can be estimated based on village recording; and appreciable genetic improvement could be achieved in village sheep selection programs under low-input smallholder farming systems.     

Breeding programmes for smallholder sheep farming systems: II. Optimization of cooperative village breeding schemes

A simulation study was conducted to optimize a cooperative village‐based sheep breeding scheme for Menz sheep of Ethiopia. Genetic gains and profits were estimated under nine levels of farmers' participation and three scenarios of controlled breeding achieved in the breeding programme, as well as under three cooperative flock sizes, ewe to ram mating ratios and durations of ram use for breeding. Under fully controlled breeding, that is, when there is no gene flow between participating (P) and non‐participating (NP) flocks, profits ranged from Birr 36.9 at 90% of participation to Birr 21.3 at 10% of participation. However, genetic progress was not affected adversely. When there was gene flow from the NP to P flocks, profits declined from Birr 28.6 to Birr ?3.7 as participation declined from 90 to 10%. Under the two‐way gene flow model (i.e. when P and NP flocks are herded mixed in communal grazing areas), NP flocks benefited from the genetic gain achieved in the P flocks, but the benefits declined sharply when participation declined beyond 60%. Our results indicate that a cooperative breeding group can be established with as low as 600 breeding ewes mated at a ratio of 45 ewes to one ram, and the rams being used for breeding for a period of two years. This study showed that farmer cooperation is crucial to effect genetic improvement under smallholder low‐input sheep farming systems.     

Breeding practices,growth, and carcass potential of fat-tailed Washera sheep breed in Ethiopia

On-farm survey of farmers' breeding practices, breeding objectives, and selection criteria and on-station feedlot performance evaluation of Washera sheep were undertaken in Ethiopia. The survey revealed that most (79.8%) of the farmers had no breeding ram. The mating system was predominantly uncontrolled. A majority (75.5%) of the sheep owners reported that they herded their sheep flock by mixing with other livestock species mainly with cattle. During grazing, 44.6% of the farmers mix their sheep flock with neighboring sheep flocks. The major sheep production objective was to generate income from the sale of live sheep. Fast growth, appearance, coat color, and pedigree performance were important ram selection criteria, respectively. Ability to breed at early age, pedigree information, mothering ability, and lambing interval were important selection criteria for ewe, respectively. The on-station performance study involved evaluation of feedlot gains and carcass production under five levels of feeding regimes (300, 400, 500, 600, and 700 g day⁻¹ of concentrate feed) for a period of 93 days. The results indicated that the feedlot growth and carcass performance of Washera sheep were very high, with average daily weight gains of up to 126 g and carcass weight of 16 kg, with the optimal level of supplementation for Washera sheep being at 500 g of concentrate per day for a period of 93 days.     

Assessing genetic gain, inbreeding, and bias attributable to different flock genetic means in alternative sheep sire referencing schemes

Flocks participating in sire referencing schemes can achieve greater genetic gains than those achievable by within-flock selection. However, requirements for joining these schemes can be prohibitive to some producers. The objectives of this study were to determine whether less restrictive schemes or schemes of shorter duration could achieve rates of gain and reduce inbreeding as efficiently as continuous sire referencing schemes (SRS) and to investigate whether bias from different genetic means could be reduced by these alternative schemes. Pedigree and performance data for a single trait with a within-flock heritability of 0.25 were simulated (50 replications) for 15 flocks with 40 to 140 ewes per flock. Founder genetic means for each flock were sampled from a normal distribution with mean 0 and SD equal to the trait's genetic SD. After 10 yr of random mating, flocks had the opportunity to join an SRS and begin selection for the simulated trait. Yearling rams were chosen as reference sires randomly from the top one-sixth of the population ranked on BLUP EBV. Every year, in each flock, 3 reference sires were mated to 10 ewes. Six sire referencing scenarios were considered, in which all flocks participated in a SRS for 1) 15 yr; 2) 5 yr before discontinuing the scheme; 3) 10 yr before discontinuing the scheme; 4) 2 out of every 3 yr; 5) 15 yr with reference sire mating by natural service; and 6) no years (no use of SRS). Ewes not mated to reference sires were mated either to their own home-bred sires exclusively or to a mixture of homebred and unrelated purchased rams of unknown merit. Genetic gain was equivalent whether the SRS used AI or natural service matings, although inbreeding was lower with natural service. Across all scenarios, genetic gain and inbreeding were greater when excess ewes were mated exclusively to homebred sires. Genetic gains without SRS were 80 to 82% lower than when the scheme operated for 15 yr, whereas inbreeding was considerably greater. Other scenarios were intermediate in both gain and inbreeding levels. In all SRS scenarios, bias in EBV attributable to differing flock genetic means rapidly decreased in the first 5 yr of sire referencing. Levels of bias did not substantially increase when flocks discontinued SRS after 5 or 10 yr, suggesting that further participation in an SRS may not be necessary to manage risk. Natural service and noncontinuous SRS are viable options to continuous AI SRS in terms of genetic gain, inbreeding, and bias reduction.     

Predicting rates of inbreeding for livestock improvement schemes

This article presents a deterministic method to predict rates of inbreeding (deltaF) for typical livestock improvement schemes. The method is based on a recently developed general theory to predict rates of inbreeding, which uses the concept of long-term genetic contributions. A typical livestock breeding population was modeled, with overlapping generations, BLUP selection, and progeny testing of male selection candidates. Two types of selection were practiced: animals were either selected by truncation on estimated breeding values (EBV) across age classes, or the number of parents selected from each age class was set to a fixed value and truncation selection was practiced within age classes. Bulmer's equilibrium genetic parameters were obtained by iterating on a pseudo-BLUP selection index and deltaF was predicted for the equilibrium situation. Predictions were substantially more accurate than predictions from other available methods, which ignore the effect of selection on deltaF. Predictions were accurate for schemes with up to 20 sires. Predicted deltaF was somewhat too low for schemes with more than 20 sires, which was due to the use of simple linear models to predict genetic contributions. The present method provides a computationally feasible (i.e., deterministic) tool to consider both the rate of inbreeding and the rate of genetic gain when optimizing livestock improvement schemes.     

Analysis of production objectives and breeding practices of dairy goats in Kenya

Production objectives and breeding practices of smallholder households participating in dairy goat breeding projects were analysed in relation to their ability to bring about sustainable genetic improvement in the dairy goat flocks in Kenya. A stratified survey involving 311 goat keepers in 4 project sites was used. This employed both qualitative and quantitative research methods to get a holistic view of dairy goats, and take into account the full array of contributions of dairy goats to the smallholder households. Milk production and sales of breeding stock were high priority functions for the objective to create a financial buffer. The breeding objective traits that farmers perceived as being of primary importance were milk yield, growth rate, body size, fertility and disease tolerance. There were logical trade-offs in the choice of these traits by farmers. Female dairy goats were mainly culled due to old age, poor fertility, small body size and poor health. Farmers did not place a large significance on unsatisfactory milk performance when culling female goats, mainly due to the very small production size and the high demand existing for breeding animals. Factors affecting milk yield and flock size presented satisfied a P < 0.1 significance level. The performance levels of dairy goats were mainly influenced by breeding strategies and the resource availability at the farm level. The optimisation of genotype x environment interactions remains the biggest challenge given the objectives set by the farmer.     

The role of reproductive technologies in breeding schemes for livestock populations in developing countries

The world is faced with the challenge to meet the increasing demand for livestock products while conserving animal genetic resource diversity and maintaining environmental integrity. Genetic improvement of local breeds can help to improve the livelihood of the livestock keepers, to increase the production of animal products and to conserve genetic diversity. Implementing breeding schemes in developing countries has proven to be very difficult. The objective of this paper is to discuss the role of reproductive technologies for the creation and dissemination of genetic improvement in livestock populations in developing countries. In the paper opportunities are discussed for implementing breeding schemes which minimize the need for extensive pedigree and performance recording. It is shown that genetic progress can be generated in a small population. Community-based breeding schemes offer a good starting point for involving farmers in improving local breeds. Artificial insemination to exchange genetic material between communities offers an opportunity to increase the rate of genetic improvement while restricting the rate of inbreeding. Furthermore, artificial insemination is a promising technique for dissemination of genetic gain to producers at a relatively low cost. Opportunities to use semen sexing in a crossbreeding scheme are presented. It is concluded that tailor-made solutions and long-term commitment are needed in order to meet the needs of farmers to increase their livelihoods and to meet the needs of the growing population of consumers.     

Reducing inbreeding rates with a breeding circle: Theory and practice in Veluws Heideschaap

Breeding circles allow genetic management in closed populations without pedigrees. In a breeding circle, breeding is split over sub‐populations. Each sub‐population receives breeding males from a single sub‐population and supplies breeding males to one other sub‐population. Donor‐recipient combinations of sub‐populations remain the same over time. Here, we derive inbreeding levels both mathematically and by computer simulation and compare them to actual inbreeding rates derived from DNA information in a real sheep population. In Veluws Heideschaap, a breeding circle has been in operation for over 30 years. Mathematically, starting with inbreeding levels and kinships set to zero, inbreeding rates per generation (ΔF) initially were 0.29%–0.47% within flocks but later converged to 0.18% in all flocks. When, more realistically, inbreeding levels at the start were high and kinship between flocks low, inbreeding levels immediately dropped to the kinship levels between flocks and rates more gradually converged to 0.18%. In computer simulations with overlapping generations, inbreeding levels and rates followed the same pattern, but converged to a lower ΔF of 0.12%. ΔF was determined in the real population with a 12 K SNP chip in recent generations. ΔF in the real population was 0.29%, based on markers to 0.41% per generation based on heterozygosity levels. This is two to three times the theoretically derived values. These increased rates in the real population are probably due to selection and/or the presence of dominant rams siring a disproportionate number of offspring. When these were simulated, ΔF agreed better: 0.35% for selection, 0.38% for dominant rams and 0.67% for both together. The realized inbreeding rates are a warning that in a real population inbreeding rates in a breeding circle can be higher than theoretically expected due to selection and dominant rams. Without a breeding circle, however, inbreeding rates would have been even higher.     

Smallholder goat breeding and flock management practices in the central rift valley of Ethiopia

The study was conducted in the central rift valley of Ethiopia to define Arsi-Bale goat keepers’ breeding objectives and breeding practices and to describe flock management practices and rate of inbreeding in Arsi-Bale goat population. Two-stage sampling techniques were employed to select study sites and 202 respondents. Semistructured questionnaire and group discussion were used to collect the required information. Data were analyzed using statistical package for social science. Rate of inbreeding in the population and indices were also calculated. On average, each respondent holds around 12 goats in which 30.7, 66.6 and 2.7% were males, females and castrates, respectively. The most important purpose of goat production in the study area was for milk utilization. Farmers have multiple breeding objectives and they considered both subjective and objective selection criteria with slightly more emphasis on morphological characteristics for buck selection than replacement doe selection. Only 39.1% (n = 79) of respondents have their own breeding bucks. None of the respondents practiced controlled mating. Average rate of inbreeding in the population was around 0.20. Arsi-Bale goats are found to be adaptive to the prevailing condition. Therefore, any breed improvement strategy to be designed or implemented in the study area and other similar areas should consider important traditional breeding practices.     

Characterization of the production system and breeding practices of indigenous goat keepers in Hai district,Northern Tanzania: implications for community-based breeding program

Indigenous breeding practices of the farmers and the livestock production system form the bases for designing community-based breeding programs. The aim of this study was to characterize production system and examine breeding practices of the indigenous goat farmers in Hai district in Northern Tanzania to determine their relevance in establishing a community-based breeding program in the area. A cross-sectional survey was conducted in which information was collected from 160 households randomly selected from 6 villages. Average household herd was 29.2 goats with majority keeping less than 20 goats. Major reasons for keeping goats were income generation, meat and milk production. Controlled mating was practiced mainly using apron and castration. Castration was practiced using traditional methods to control breeding and improve meat quality. Farmers in the study area had large goat flocks and a small buck to doe ratio. Farmers do not have a good understanding of inbreeding and its negative effects but practise other good breeding methods which could impact the productivity of their animals. Diseases and feed shortages were the main constraints to production. Opportunities exist for a community-based breeding program to genetically improve goat productivity.

     

Design of a village breeding programme for a llama population in the High Andes of Bolivia

No national breeding programme for llamas is in place in Bolivia. Initiatives for genetic improvement are rarely found and are usually carried out by NGOs working in rural development or improvement of livestock production or research stations. Farmers in the Province of Ayopaya in the District of Cochabamba have formed a breeders’ organization with the aim of improving fibre production. In this study, a detailed outline of a breeding programme with a focus on organizational and technical details is described. Facing constraints like illiteracy of farmers, bad infrastructure and lack of finances, a simple breeding programme is set up. The breeding goal is a higher fleece weight while keeping the fleece quality at the current high level. Greasy fleece weight and fibre diameter are identified as main selection criteria. Mass selection of males is carried out. Selected males are either exchanged between farmers and used in the herds or are kept during the mating season in a central mating station owned by the breeders’ organization. Model calculations were carried out with the program zplan , which is based on a deterministic approach. zplan evaluates the genetic and economic efficiency of breeding strategies considering one cycle of selection. Scenarios with only intra-herd use, using only the central mating station or combinations of those were compared in terms of expected genetic gain and expected increase of inbreeding. Fastest genetic progress is achieved when the males are kept in a central mating station as the selection intensity is on a high level. Rates of inbreeding vary between 0.08 and 0.32% per generation.     

Pro-poor animal improvement and breeding — What can science do?

Livestock provide a wide variety of goods and services that generate income and support the livelihoods of millions of poor people in the developing world. Natural and human selections have shaped existing livestock genotypes throughout the estimated 12,000 year history since the first animal domestication. The result, in many production systems in the developing world, is a livestock genotype adapted to its environment and capable of meeting the needs of smallholder farmers. However, this adaptation is unlikely to be optimal and the rapid changes currently affecting the livestock sector, including policy and market changes, movements of germplasm frequently involving the importation of exotic breeds, and the increasing impacts of climate change are affecting the livestock genotype-environment optimum. This is challenging livestock production systems of smallholder farmers. Current challenges include: high rates of loss of the diversity in livestock populations, rapid transformation in smallholder production systems requiring significant changes in genotypes and their management; increased demand for quality and safe foods; increased market competition in a globalizing economy; increased need for complex partnership arrangements in the ever-changing livestock commodity chain; and lack of adaptive capacity to respond to the rapid system changes. Underlying all these is the general lack of strategies for genetic improvement of livestock in smallholder systems and poor livestock infrastructure in developing countries. Opportunities include increased demand for livestock products — and hence potential market opportunities, and new technologies with potential to leap-frog breeding progress in developing countries. This paper analyses options for pro-poor livestock improvement in developing countries, with particular emphasis on the potential role that science – both old and new – will have, from understanding the social underpinnings to innovative technical solutions. It concludes that one of the highest priority interventions for the smallholder systems is the development of innovative approaches for the strategic use of appropriate genotypes from the available range of global breed resources. The analysis strongly suggests that the highest priority ‘breeding intervention’ should be the provision of appropriate genotypes in a sustainable manner, underpinned by a good understanding of what breed resources exist that have demonstrated potential, where else they could be used, and how they would be delivered to smallholders. Efforts to improve/refine breeding skills of smallholders should proceed in parallel. Institutional arrangements and enabling policies are critical for the success in identifying and applying appropriate genetic technologies, improving access to input services and facilitating access to markets in order to translate productivity gains into incomes.     

Anthelmintic resistance of nematode parasites of small ruminants in eastern Ethiopia: exploitation of refugia to restore anthelmintic efficacy

Faecal egg count reduction tests (FECRT) were conducted in May 2003 to determine the efficacy of anthelmintics used for treatment against nematode parasites in separately managed sheep and goat flocks at Alemaya University in eastern Ethiopia. These tests revealed high levels of anthelmintic resistance to albendazole, tetramisole, the combination of these two drugs, and to ivermectin in the goat flock (predominantly infected by Haemonchus contortus and Trichostrongylus spp.), whereas all drugs were highly efficacious in the sheep flock. A second FECRT confirmed these observations. Following this, a new management system was implemented on the goat flock for a period of 9 months (January-September 2004) in an attempt to restore the anthelmintic efficacy. This involved a combination of measures: eliminating the existing parasite infections in the goats, exclusion from the traditional goat pastures, and introducing communal grazing of the goats with the university sheep flock and livestock owned by neighbouring small-holder farmers. A second series of FECRTs (Tests 3 and 4) conducted 7 months after this change in management, showed high levels of efficacy to all three drugs (albendazole, tetramisole and ivermectin) in the goat flock. This is the first field study to demonstrate that anthelmintic efficacy in the control of nematode parasites of small ruminants can be restored by exploiting refugia.     

Local chicken production system in Malawi: Household flock structure,dynamics, management and health

Household flocks of scavenging chickens were monitored from August 2002 to August 2003 in 27 villages in Lilongwe, Malawi. The objective was to evaluate the local chicken production system by investigating flock structure, utilization, management and constraints. Farmers and researchers jointly obtained data on household flocks. Mean flock size was 12.9, with a range of 1–61 chickens. The flock dynamics of chickens over 8 weeks old constituted 91% migrating out of flocks and 9% into the flocks. Primary functions based on flock dynamics were, in order of importance, household consumption, participation in socio-cultural ceremonies, selling, exchanging breeding stock and gifts. Of the flock exits, 43.9% were due to losses from diseases, predation and theft. Most flocks (85%) were housed in human dwelling units. Scavenging was the main source of feed. The majority (77.6%) of farmers supplemented their chickens erratically with energy-rich feeds, mostly maize bran. Most supplementation took place during the cold-dry season. Village chicken production offers diverse functional outputs but faces animal health (diseases, parasites, predation) and management (feeding) constraints, which require an integrated intervention approach at community and household level.     

Characterization of local chicken production systems and their potential under different levels of management practice in Jordan

This study aimed to characterize the local chickens and their production systems and to investigate the opportunities for improvement. The study was carried out in 18 villages in northern Jordan with the participation of 120 households. Data were collected by individual interviews and surveys supported with structured questionnaires. A scoring system was developed to study the effect of different levels of management on chicken performance. The main reasons for keep local chickens were egg production and generation of income. The main features of the production systems were improper housing and inadequate hygiene. Newcastle disease, predators, and parasites were the main causes of flock losses. Purchasing rate was controlled by the chickens’ phenotype, sex and age, and by season of year. The average flock size was 41.6 (±32.9) chickens per household, with a hen:cock ratio of 6.4:1. The average effective population size was 15.35, which indicated a high rate of inbreeding (5.52%). The main selection criterion adopted by farmers was egg production. There were positive significant correlations (p < 0.001) between management level and chickens’ performance. Hatchability, survivability, flock size, number of clutches, egg weight and egg mass were the major parameters that improved significantly with improvement in management level. Local chickens fulfil significant functions in the livelihood of rural smallholders; however, many constraints affected the efficiency of the production systems. Solutions should start with improving the management practices and establishing an effective breeding system.     

Choice of breeding stock,preference of production traits and culling criteria of village chickens among Zimbabwe agro-ecological zones

Free ranging chickens reared by smallholder farmers represent genetic diversity suited for particular environments and shaped by the socio-economic and cultural values of the farming systems. This study sought to investigate the existence of chicken strains and evaluate the breeding goals and strategies used by village chicken farmers in Zimbabwe. A semi-structured questionnaire was administered to 97, 56, 70, 104 and 37 households randomly selected from five agro-ecological-zones I-V, respectively. Fifteen chicken strains mostly defined by morphological traits were reported in the five eco-zones. Production criteria such as body size, and fertility were highly ranked (ranging from 1.3 – 2.6) by farmers across all the eco-zones, while cultural traits were the least preferred production traits. As a common breeding practice, farmers chose the type of hens and cocks to retain for breeding purposes and these randomly mixed and mated with others from community flocks. Chicken body size was ranked the major determinant in choosing breeding animals followed by mothering ability, and fertility. More households culled chickens associated with poor reproductive performance, poor growth rates and those intolerant to disease pathogens. The focus on many negatively correlated production traits and the absence of farmer records compromises breeding strategies in these production systems.     

Distribution and prevalence of footrot in Bhutan

The first cases of footrot in Bhutan were reported in sheep in 1990 at the National Sheep Breeding Centre (NSBC), which supplies breeding animals to village sheep flocks throughout Bhutan. Despite the presence of footrot at the Centre the distribution of apparently disease-free sheep continued. Cases of footrot were reported in village flocks soon after the disease was diagnosed at NSBC. A national survey was designed to establish the distribution and prevalence of footrot in Bhutan. This detected footrot in 19/94 village sheep flocks surveyed. The 19 affected flocks were distributed among nine different administrative districts whereas the villages selected were in 13 of a total of 16 sheep growing districts. The highest within-flock prevalences were among the seven flocks sampled in Bumthang district (mean 20.4%). The prevalence of the disease within flocks was generally much lower in other affected districts and in three districts a single affected animal was identified in the sample of 14 sheep examined in each village. Nationally, footrot prevalence was estimated to be 3.1% (95% CI 2.16-4.04%). There was a positive association between the receipt of animals from NSBC and the presence of footrot. The prevalence of the disease was higher in flocks with a migratory system of management than in those using a sedentary system. The relative risk of there being footrot in a migratory flock was nine-times higher than in a non-migratory flock. Only one strain of Dichelobacter nodosus (serogroup B) was identified among the 234 isolates obtained from the 19 affected flocks. Sheep with footrot healed quickly when treated with a vaccine made from this strain.     

Characteristics of two duck farming systems in the Mekong Delta of Viet Nam: stationary flocks and moving flocks, and their potential relevance to the spread of highly pathogenic avian influenza

Ducks are considered to play a major role in the spread of highly pathogenic avian influenza (HPAI) H5N1 in Viet Nam, but detailed information on their management is limited. We distinguished two different systems (1) stationary duck flocks that are not commonly driven to rice fields beyond village boundaries and that are confined overnight on farms and (2) moving duck flocks that are intentionally driven to rice fields beyond village boundaries, that are not returning to home farms for extended periods and that are housed overnight in temporary enclosures in rice paddies. A total of 115 stationary and 22 moving flock farmers were interviewed in 2007 in the Mekong Delta of Viet Nam. Moving duck flocks are larger than stationary flocks, which is indicative of their more commercial production. Moving flock farmers apparently are more aware of HPAI risks than stationary flock farmers, as their flocks are more likely fully vaccinated and have less contact with chickens during scavenging. On the other hand, the spread of HPAI virus between birds might be promoted by moving duck flocks as they repeatedly use transport vehicles and numerous rice paddies for scavenging and are often visited by hatchery owners in the field for purchasing duck eggs. In addition, long distances travelled by moving duck flocks might also result in widespread dissemination of HPAI virus. Further studies are necessary to describe HPAI prevalence and travel patterns of moving duck flocks and to explore the moving duck flock network in detail.     

On farm observations to increase genetic gain in breeding schemes for village poultry production – A simulation study

To improve genetic gain of breeding programs for village poultry production, breeding schemes with observations obtained in village production systems using individual (VIO) and group recording (VGO) were examined under different levels of genotype-by-environment-interactions (GxE). GxE was modeled by varying the correlation between traits measured in the breeding station and village environments for bodyweight (r_{g_BW}) and egg production (r_{g_EP}). Relative and absolute genetic gains obtained from VIO and VGO were used for comparison between the schemes. Results showed that village observations significantly improved genetic gains compared to the scheme without birds tested in the village. The improvement was only slightly larger with individual observations than with group observations. Higher r_{g_BW} and r_{g_EP} led to lower relative genetic gain, but a higher absolute gain of VIO and VGO. It is recommended to apply a breeding scheme using group recording of village performance when strong GxE in breeding for village poultry is expected.