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.     

Evaluation of the efficiency of alternative two-tier nucleus breeding systems designed to improve meat sheep in Kenya

A deterministic approach was used to genetically and economically evaluate the efficiency of five two‐tier nucleus breeding systems for meat sheep in Kenya. The nucleus breeding systems differed in terms of whether the system was closed or open, in the type of animals that were involved in the movement of genetic superiority and in the number of selection pathways in each system. These systems were compared under four alternative breeding objectives based on monetary genetic gain and profit per ewe. The first objective simulated a situation where the flock size cannot be increased due to non‐feed related constraints (FLOCK). The second specifically assumed that the flock size is restricted due to limited amount of feed resources (FEED). The third and fourth objectives assumed that sheep performed only tangible roles (TR) and both tangible and intangible roles (IR) in the production system respectively. Monetary genetic gains were highest for all objectives in an open nucleus system with a certain proportion of commercial‐born ewes being introduced in the nucleus while at the same time utilizing young rams from the nucleus to breed sires and dams for the nucleus and commercial sector (ONyre). Utilizing young rams in a closed nucleus system for the dissemination of superior genes resulted in higher annual monetary genetic gain than utilization of old rams. Profit per ewe was significantly higher for FLOCK and IR in ONyre. In a closed system that allowed for downward movement of dams from the nucleus to the commercial sector to breed sires and dams, profit per ewe was highest for FEED and TR. The success of a nucleus breeding system should also focus on the profitability and logistics of establishing it. The implication of these results on the choice of two‐tier nucleus breeding systems for the improvement of meat sheep is discussed.     

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.     

Optimal village breeding schemes under smallholder sheep farming systems

Despite challenges in the implementation of livestock genetic improvement programs in developing regions, including centralized nucleus breeding schemes, these programs can contribute to the improvement of the livelihood of smallholder farmers. In this paper, we present a community- or village-based breeding scheme in which breeding activities are carried out by communities of smallholder farmers. We evaluated genetic responses and the rate of inbreeding from alternative village sheep breeding schemes that were based on a survey of existing flock structure and breeding management in a sheep-barley system in Ethiopia. This survey showed that individual flock sizes were small, and that the majority of farmers practiced mixed grazing and uncontrolled mating of their flocks in communal grazing lands within villages. Here we evaluated within-village schemes (selection across flocks within a village) and across-village schemes (selection across villages) at different intensities of ram selection (i.e. proportions of rams selected, P). Our results showed that under within-village schemes, intensity of selection could not be increased (i.e. P could not be decreased below 0.149) when the rate of inbreeding was constrained to an acceptable level of 0.01, resulting in low genetic gain. The most optimal scheme was found to be across-village selection with at least three villages cooperating and P = 0.05. Our results also indicated that genetic gain from village breeding schemes with mass selection and BLUP selection is comparable. Village breeding schemes can make a significant contribution to the genetic improvement of livestock in Ethiopia and other developing countries.     

Assessment of the genetic and economic impact of performance recording and genotyping in Australian commercial sheep operations

With the new opportunities from DNA technology, multitier breeding schemes have the potential to become more effective and more integrated. Integrated breeding schemes can also be better adapted to account for potential genotype by environment interactions (G × E) between tiers. In this case, phenotypic and genotype information from lower tiers becomes more valuable as it involves measurement of traits that directly represent the breeding objective. The objective of this study was to compare scenarios that represented different selection strategies and their economic effectiveness in fine‐wool commercial sheep operations that exploit multitier breeding structures. Genomic selection (GS) applied in the multiplier and the commercial tier presented the largest additional revenue among all scenarios, as it resulted in the largest amount of genetic progress. The largest benefits from GS were outweighed by the genotyping costs, which made DNA parentage the most feasible strategy for the multiplier tier, resulting in the highest cumulative net present value (CNPV). The benefits of phenotypes and genotype information from the commercial environment were larger in the presence of G × E between the nucleus and the commercial tier. The CNPV was larger with a 50% reduction in genotyping costs, which increased the returns of GS scenarios by 2.7‐fold on average. Higher selection intensity when selecting multiplier rams also resulted in larger benefits. In this case, returns for the breeding scheme were 3.5‐fold higher when 33% of multiplier males were selected based on commercial information, compared to scenarios selecting 50% of the available multiplier rams. The benefits of collecting commercial phenotypes and genotypes were long term, which means that return on investment often took more than 10 years to be achieved, and were largely dependent on two‐stage selection to reduce cost while maintaining selection efficiency and on the cost of a genotype test.     

鲁西黄牛开放和闭锁核心群育种方案的对比分析

鲁西黄牛是中国优良的地方品种,为了更有效的制定适宜的育种方案,加快鲁西黄牛肉用品系的选育,本研究在鲁西黄牛青年公牛体系和核心群育种方案的基础上,分别设定开放和闭锁核心群育种方案,采用确定性模型评估了开放和闭锁核心群育种体系的育种效果。结果表明,开放与闭锁核心群育种方案相比,综合遗传进展提高了0.80％;育种产出量提高了9.39％;育种效益提高了10.64％;世代间隔延长了0.90％,开放核心群体系优于闭锁核心群体系。这充分说明,在鲁西牛核心群育种方案中,开放核心群育种体系优于闭锁核心群育种体系。     

Purebreeding of Red Maasai and crossbreeding with Dorper sheep in different environments in Kenya

The aim of this article was to study opportunities for improvement of the indigenous and threatened Red Maasai sheep (RM) in Kenya, by comparing purebreeding with crossbreeding with Dorper sheep (D) as a terminal breed, in two different environments (Env. A and a harsher Env. B), assuming different levels of genotype‐by‐environment interaction (G × E). Breeding goals differed between environments and breeds. Four scenarios of nucleus breeding schemes were stochastically simulated, with the nucleus in Env. A. Overall, results showed an increase in carcass weight produced per ewe by more than 10% over 15 years. Genetic gain in carcass weight was 0.17 genetic SD/year (0.2 kg/year) across scenarios for RM in the less harsh Env. A. For survival and milk yield, the gain was lower (0.04–0.05 genetic SD/year). With stronger G × E, the gain in the commercial tier for RM in the harsher Env. B became increasingly lower. Selection of females also within the commercial tier gave slightly higher genetic gain. The scenario with purebreeding of RM and a subnucleus in Env. B gave the highest total income and quantity of meat. However, quantity of meat in Env. A increased slightly from having crossbreeding with D, whereas that in Env. B decreased. A simple and well‐designed nucleus breeding programme would increase the genetic potential of RM. Crossbreeding of RM with D is not recommended for harsh environmental conditions due to the large breed differences expected in that environment.     

Genetic and economic evaluation of Japanese Black (Wagyu) cattle breeding schemes

Deterministic simulation was used to evaluate 10 breeding schemes for genetic gain and profitability and in the context of maximizing returns from investment in Japanese Black cattle breeding. A breeding objective that integrated the cow-calf and feedlot segments was considered. Ten breeding schemes that differed in the records available for use as selection criteria were defined. The schemes ranged from one that used carcass traits currently available to Japanese Black cattle breeders (Scheme 1) to one that also included linear measurements and male and female reproduction traits (Scheme 10). The latter scheme represented the highest level of performance recording. In all breeding schemes, sires were chosen from the proportion selected during the first selection stage (performance testing), modeling a two-stage selection process. The effect on genetic gain and profitability of varying test capacity and number of progeny per sire and of ultrasound scanning of live animals was examined for all breeding schemes. Breeding schemes that selected young bulls during performance testing based on additional individual traits and information on carcass traits from their relatives generated additional genetic gain and profitability. Increasing test capacity resulted in an increase in genetic gain in all schemes. Profitability was optimal in Scheme 2 (a scheme similar to Scheme 1, but selection of young bulls also was based on information on carcass traits from their relatives) to 10 when 900 to 1,000 places were available for performance testing. Similarly, as the number of progeny used in the selection of sires increased, genetic gain first increased sharply and then gradually in all schemes. Profit was optimal across all breeding schemes when sires were selected based on information from 150 to 200 progeny. Additional genetic gain and profitability were generated in each breeding scheme with ultrasound scanning of live animals for carcass traits. Ultrasound scanning of live animals was more important than the addition of any other traits in the selection criteria. These results may be used to provide guidance to Japanese Black cattle breeders.     

Improving production efficiency in the presence of genotype by environment interactions in pig genomic selection breeding programmes

We simulated a genomic selection pig breeding schemes containing nucleus and production herds to improve feed efficiency of production pigs that were cross‐breed. Elite nucleus herds had access to high‐quality feed, and production herds were fed low‐quality feed. Feed efficiency in the nucleus herds had a heritability of 0.3 and 0.25 in the production herds. It was assumed the genetic relationships between feed efficiency in the nucleus and production were low (r_g = 0.2), medium (r_g = 0.5) and high (r_g = 0.8). In our alternative breeding schemes, different proportion of production animals were recorded for feed efficiency and genotyped with high‐density panel of genetic markers. Genomic breeding value of the selection candidates for feed efficiency was estimated based on three different approaches. In one approach, genomic breeding value was estimated including nucleus animals in the reference population. In the second approach, the reference population was containing a mixture of nucleus and production animals. In the third approach, the reference population was only consisting of production herds. Using a mixture reference population, we generated 40–115% more genetic gain in the production environment as compared to only using nucleus reference population that were fed high‐quality feed sources when the production animals were offspring of the nucleus animals. When the production animals were grand offspring of the nucleus animals, 43–104% more genetic gain was generated. Similarly, a higher genetic gain generated in the production environment when mixed reference population was used as compared to only using production animals. This was up to 19 and 14% when the production animals were offspring and grand offspring of nucleus animals, respectively. Therefore, in genomic selection pig breeding programmes, feed efficiency traits could be improved by properly designing the reference population.     

A Method of Modelling Pig Breeding Schemes

Optimal use of limited resources as nucleus and testing capacity is important when organizing crossbreeding schemes in pigs. This paper introduces a method of modelling pig crossbreeding schemes consisting of nucleus, multiplier and commercial tiers. As an efficient alternative to the gene flow method (Hill, W.G. 1974. Anim. Prod. 18, 117-139), lag, original genetic level and annual genetic improvement for each line and cross are combined into one single evaluation criterion, the average discounted revenues of the breeding scheme. An optimum allocation of nucleus and testing capacity within breeding schemes, as well as an optimum solution between schemes can be found. As an example, the optimization of a four-way crossbreeding scheme is shown. the optimum allocation of nucleus capacity was 35% and 15% in each dam line and sire line, respectively. The corresponding figures for testing capacity were 23% and 27%.     

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.     

Community-based alternative breeding plans for indigenous sheep breeds in four agro-ecological zones of Ethiopia

Based on the results of participatory approaches to define traits in the breeding objectives, four scenarios of ram selection and ram use were compared via deterministic modelling of breeding plans for community-based sheep breeding programmes in four diverse agro-ecological regions of Ethiopia. The regions (and production systems) were Afar (pastoral/agro-pastoral), Bonga and Horro (both mixed crop-livestock) and Menz (sheep-barley). The schemes or scenarios differed in terms of selection intensity and duration of ram use. The predicted genetic gains per year in yearling weight (kilograms) were comparable across the schemes but differed among the breeds and ranged from 0.399 to 0.440 in Afar, 0.813 to 0.894 in Bonga, 0.850 to 0.940 in Horro, and 0.616 to 0.699 in Menz. The genetic gains per year in number of lambs born per ewe bred ranged from 0.009 to 0.010 in both Bonga and Horro. The predicted genetic gain in the proportion of lambs weaned per ewe joined was nearly comparable in all breeds ranging from 0.008 to 0.011. The genetic gain per year in milk yield of Afar breed was in the order of 0.018 to 0.020 kg, while the genetic gain per generation for greasy fleece weight (kg) ranged from 0.016 to 0.024 in Menz. Generally, strong selection and shorter duration of ram use for breeding were the preferred options. The expected genetic gains are satisfactory but largely rely on accurate and continuous pedigree and performance recording.     

Genomic selection strategies in dairy cattle: Strong positive interaction between use of genotypic information and intensive use of young bulls on genetic gain

We tested the following hypotheses: (i) breeding schemes with genomic selection are superior to breeding schemes without genomic selection regarding annual genetic gain of the aggregate genotype (ΔG(AG) ), annual genetic gain of the functional traits and rate of inbreeding per generation (ΔF), (ii) a positive interaction exists between the use of genotypic information and a short generation interval on ΔG(AG) and (iii) the inclusion of an indicator trait in the selection index will only result in a negligible increase in ΔG(AG) if genotypic information about the breeding goal trait is known. We examined four breeding schemes with or without genomic selection and with or without intensive use of young bulls using pseudo-genomic stochastic simulations. The breeding goal consisted of a milk production trait and a functional trait. The two breeding schemes with genomic selection resulted in higher ΔG(AG) , greater contributions of the functional trait to ΔG(AG) and lower ΔF than the two breeding schemes without genomic selection. Thus, the use of genotypic information may lead to more sustainable breeding schemes. In addition, a short generation interval increases the effect of using genotypic information on ΔG(AG) . Hence, a breeding scheme with genomic selection and with intensive use of young bulls (a turbo scheme) seems to offer the greatest potential. The third hypothesis was disproved as inclusion of genomically enhanced breeding values (GEBV) for an indicator trait in the selection index increased ΔG(AG) in the turbo scheme. Moreover, it increased the contribution of the functional trait to ΔG(AG) , and it decreased ΔF. Thus, indicator traits may still be profitable to use even when GEBV for the breeding goal traits are available.     

Evaluation of breeding objectives for purebred and crossbred selection schemes for adoption in indigenous chicken breeding programmes

1. The aim of the study was to evaluate the genetic and economic breeding objectives for an indigenous chicken (IC) breeding programme in Kenya.

2. A closed three-tier nucleus breeding programme with three breeding objectives and two selection schemes was simulated. The breeding objectives included IC dual-purpose (ICD) for both eggs and meat, IC layer (ICL) for eggs and IC broiler (ICB) for meat production.

3. Pure line selection scheme (PLS) for development of IC pure breeds and crossbreeding scheme (CBS) for the production of hybrids were considered. Two-and three-way crossbreeding strategies were evaluated under CBS and the impact of nucleus size on genetic gains and profitability of the breeding programme were investigated.

4. Males were the main contributors to genetic gains. The highest genetic gains for egg number (2·71 eggs) and growth traits (1·74?g average daily gain and 57·96?g live weight at 16 weeks) were realised under PLS in ICL and ICB, respectively.

5. The genetic response for age at first egg was desirable in all the breeding objectives, while that for fertility and hatchability were only favourable under ICL and PLS in ICD. Faecal egg count and immune antibody response had low, but positive gains except under PLS where the later was unfavourable. ICB was the most profitable breeding objective, followed by ICD and ICL under all the selection schemes.

6. Although PLS was superior in genetic gains and profitability and recommended in breeding programmes targeting ICL and ICB, a three line CBS should be considered in development of a dual-purpose breed.

7. Increasing the nucleus size beyond 5% of the IC population was not attractive as it resulted in declining profitability of the breeding programme.     

在不同杂交方案下猪的完整繁育体系的经济效益比较分析

木文用系统动力学专用仿真语言──Ｍｉｃｒｏ—ＤＹＮＡＭＯ分别模似了♂约克夏（Ｙ）×♀长白猪（Ｌ）的二元杂交、♂Ｙ×Ｆ１♀（ＹＬ）的回交、♂杜洛克（Ｄ）×Ｆ１（ＹＬ）的三元杂交完整繁育体系及无育种群的三元杂交非完整繁育体系。在ＩＢＭ－ＰＣ／ＸＴ电子计算机上实现仿真运算，得出：（１）由育种群、繁殖群和商品生产群构成的宝塔式繁育体系结构，按各群体母猪数所占比例，二元杂交分别为２．３６％、１０．７５％和８６．８９％，回交分别为２．３８％、１０．７５％和８６．８７％，三元杂交分别为２．７３％、１０．７１％和８６．５６％。为建立适合我国国情的具有合理猪群结构的完整繁育体系提供了科学依据。（２）全面分析了繁育体系的投入与产出，按投入产出比、每头种母猪的利润和单位商品肉猪（活重９０ｋｇ）利润三种指标比较了三元杂交、回交、二元杂交完整繁育体系和非完整繁育体系下三元杂交的经济效益，均得出同样结论，以单位商品肉猪１１年内获得的累积利润计算，完整繁育体系与非完整繁育体系比较，三元杂交多盈利２１．９３元，回交多盈利１７．９９元，二元杂交多盈利４．６４元，说明建立完整繁育体系具有长远的经济意义。从我国现实情况出发，以建立三元杂交的完整     

东北梅花鹿优化育种规划步骤、基本条件及对现行育种方案的分析

对东北梅花鹿优化育种规划的具体步骤和所应具备的基本条件进行了研究 ,并在分析东北梅花鹿群现状的基础上 ,得出群体的经济学和遗传参数、生物学和育种技术指数、群体结构参数、育种成本与投资参数等一系列将在育种规划计算中应用的参数 ,同时还对东北梅花鹿现行育种方案的育种效果进行了分析。     

The use of elite nucleus units in beef cattle breeding

Simple plans for the formation and continuation of elite nucleus breeding units utilizing multiple ovulation and embryo transfer for the genetic improvement of beef cattle were investigated. Three policies of forming nucleus units were considered, each in relation to conventional breeding herds with a possible rate of annual genetic change of .17 phenotypic standard deviation (SD) units and also to breeding herds with no genetic improvement. The genetic improvement (as a genetic lift) from the formation schemes ranged from .43 to 1.38 SD units. Three policies for the continuation of the nucleus units were outlined. The best scheme resulted in almost double the total genetic change possible from conventional breeding herds over a 20-yr period. Transfer of these gains from nucleus to breeding herds and to the commercial herds also was considered. Some advantages and limitations to nucleus breeding schemes were discussed. The opportunity exists for progressive breeders, or groups, to make use of improved genetic evaluation systems (expected breeding values) and embryo transfer to greatly accelerate rates of genetic change in economic efficiency of beef cattle.     

东阿黑驴育种规划优化的研究

东阿黑驴是以德州驴为基础群向皮肉兼用型方向选育的新品种,本研究拟在其现有育种方案的基础上,探讨不同育种措施的最优化组合方案,为建立优质、高效的东阿黑驴育种体系奠定基础,为中国驴育种实践提供参考。本研究根据东阿黑驴的生产和育种现状,以选择指数法和基因流动法为基本方法,应用育种规划程序ZPLAN分析东阿黑驴现行育种方案的育种成效,对影响育种成效的各个因素进行优化分析,最终确定优化后的育种方案。结果表明,现行方案在投资规划期内可完成的遗传进展和育种效益分别为271.78和1 123.70元/（头·年）,世代间隔为5.24年,每年每个性状遗传进展分别为断奶重提高1.50 kg,18月龄体重提高0.09 kg,初产年龄缩短0.02 d,产犊间隔缩短0.17 d,皮产量增加1.04 kg。对影响育种的因素进行不同水平的组合分析,当群体规模理想状态为30 000头,主动育种群比例为0.5,育种群中种子公驴、测验公驴和种用母驴使用年限为1年,种子母驴使用年限为2年,生产群中公、母驴使用年限为1年时,可获得最大的育种遗传进展和育种效益,分别为320.40和2 945.00元/（头·年）,比现行育种方案分别高出17.9%和162.0%。东阿黑驴目前的育种方案没有达到理想育种状态,有较大的改进空间。研究通过对育种主要影响因素的不同水平优化组合,得到了最优的育种方案,使遗传进展和育种效益达到了最大化。     

北京迪卡猪核心群育种方案优化研究——群体规模及选择强度

应用确定性模型考察群体规模对北京迪卡猪核心群公猪系育种成本、育种产出、育种效益及近交系数的影响。猪规模为６０、８０、１００、１２０四个水平，公猪头猪为６、８、１０、１２四个水平。种畜的选择是基于多性状综合选择指数进行，应用基因流动法计算育种产出。结果表明，增加母猪规模，有利于提高公猪选择强度，从而加大育种产出，同时单位母猪育种成本下降，促进了育种效益的改善；公猪头数越少，公猪选择强度越大，育种进展     

Modelling of a recording scheme for market-oriented smallholder pig producers in Northwest Vietnam

Village breeding programmes are being developed by an integrated long-term project for smallholders in Northwest Vietnam to improve pig production in different production systems. In total, 120 smallholders with 169 sows in 5 of the 9 project villages were approached in single person interviews, using a structured questionnaire. Frequency analysis of data on breeding management and ranking of smallholders' trait preferences and selection criteria used for pigs were performed with SAS 9.1, using the FREQ procedure. Survey results indicate that both improved local breeds and exotic genotypes should be incorporated in future village breeding programmes for market-oriented smallholder pig production, improving the reproductive and growth performance as well as the carcass quality. In a next step, a model reflecting the status quo at farms with market-oriented pig production was developed integrating data from farmers' survey and information from the project's current recording scheme. A deterministic approach was used to assess the profitability and genetic merit of the current recording scheme. Modelling results show that the current recording scheme is unprofitable (− 33.90 € sow^− 1). As continued success of village breeding programmes depends on the profitability of breeding measures, the long-term sustainability of the current recording scheme seems unlikely. Genetic gains are achieved in production and carcass quality traits, while a small reduction in reproduction traits can be observed. In a last step, possible effects of increased pig performances on the profitability and genetic merit of the current recording scheme were evaluated. Effects of increased pig performances on the genetic and economic success of the recording scheme are generally limited. Further model calculations are necessary for finding possibilities to improve smallholder pig breeding in a profitable way.