The study investigated the genetic make-up of different ecotypes of indigenous chickens (ICs) in Kenya based on major histocompatibility complex (MHC)-linked and non-MHC microsatellite markers. Blood samples were collected from eight regions (48 birds per region) of Kenya: Kakamega (KK), Siaya (BN), West Pokot (WP), Turkana (TK), Bomet (BM), Narok (NR), Lamu (LM) and Taita-Taveta (TT) and genotyped using two MHC-linked and ten non-MHC markers. All MHC-linked and non-MHC markers were polymorphic with a total of 140 alleles, of which 56 were identified in MHC-linked markers. Mean number of alleles (Na and Ne), private alleles, heterozygosity and genetic distances were higher for MHC-linked markers compared with non-MHC markers. The ad hoc statistic ΔK detected the true numbers of clusters to be three for MHC-linked markers and two in non-MHC markers. In conclusion, Kenyan ICs belong into two to three genetically distinct groups. Different markers systems have different clustering system. MHC-linked markers divided ICs into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. These IC ecotypes host many and highly diverse MHC-linked alleles. Higher allelic diversity indicated a huge amount of genetic variation in the MHC region of ICs and supported their reputation of being hardy and resistant to diseases.

Characterization and genetic diversities among members of a species are fundamental to their improvement and conservation. This study was conducted to characterize and estimate genetic diversity in the ecotypes of the locally adapted Muscovy duck in Nigeria using blood proteins (haemoglobin, transferrin and albumin) and enzyme (carbonic anhydrase) markers. Blood samples collected from 20, 40 and 20 adult Muscovy ducks sampled randomly from the Rain Forest, Derived Savanna and Guinea Savanna ecotypes, respectively, were typed for blood proteins and enzyme polymorphism with cellulose acetate paper. Genetic variability in the studied population was accessed using heterozygosity (H), effective number of allele (ne) and polymorphism (percent P). All the 13 allelic variants expressed at the four loci were expressed in the Derived Savanna ecotype but 12 each in the Rain Forest and Guinea Savanna ecotypes. Results showed that all the four loci were polymorphic (100 percent) and the estimated heterozygosity among them was similar (0.424–0.481). Similarity in the estimated genetic variability parameters among ecotypes indicate that the sub-populations understudy was under similar evolutionary forces and there were no appreciable differences among them.

Poultry biodiversity conservation is a great challenge for many countries. Within the last several years, the number of endangered local breeds has increased, leading to a considerable loss of genetic resources. A similar trend was observed among the poultry breeds, including chicken, local turkey and goose breeds/lines established in Bulgaria, part of which is definitely lost. Currently these breeds/lines are at risk and/or threatened with extinction. The information obtained by phenotypic characterization of these breeds is the first step for planning the management of poultry genetic resources through setting up improved selection schemes and conservation strategies. In this paper, we reviewed the current state of knowledge regarding the morphological and phenotypic diversity of local poultry breeds and some old productive poultry lines in Bulgaria.

Egg production performance of 571 local Ghanaian chickens and 107 SASSO T44 chickens kept under improved management conditions were analysed. Average egg weight, hen-day egg production and feed conversion ratio (FCR) were determined for the three experimental chicken ecotypes. Hen-day production was significantly (P < 0.05) higher in the savannah local chicken ecotype than the forest ecotype and SASSO T44 chickens. Egg weights of local Ghanaian chickens compared favourably with values reported for local chickens in Africa. On the average, SASSO T44 had significantly (P < 0.05) higher egg weights and feed intake compared with the local chicken ecotypes. The local chicken ecotypes on the other hand, had significantly (P < 0.05) better feed conversion ratios than SASSO T44 chicken. Local Ghanaian chicken ecotypes have a more efficient FCR per every unit of egg produced compared with the control population. Low feed intake, good feed conversion ratios and adaptation to the environment are traits local chicken harbour which can be exploited in future breeding programmes to improve on chicken meat and egg production in Ghana. Ghanaian local chickens could thus be a valuable genetic resource for the development of an efficient egg production chicken breed adaptable to the humid tropical climates.

Phenotypic description helps in assessing the physical attributes of species and is also an indicator of the relevance and importance attached to such attributes in their natural environments. This study was conducted to describe patterns and distribution of phenotypic diversity in Nigerian Muscovy ducks. One thousand and twenty (1 020) adult male and female Muscovy ducks reared extensively were randomly drawn from the Rain Forest, Derived Savanna and Guinea Savanna agro-ecological zones/ecotypes and were visually appraised and scored for plumage, skin, shank, feet/web, bill, bean and caruncle colours. Data on qualitative traits were analysed with descriptive statistics (percentages) while fixed effect model was used to investigate relationship between plumage and skin colours and body weight. Results revealed variations in qualitative traits; however, across ecotypes, the predominant plumage, skin, shank, feet, bill, bean and caruncle colours were mottled (45 percent), white (88 percent), yellow (50 percent), yellow (60 percent), black (58 percent), black (69 percent) and red (84 percent), respectively. Besides, significant (P < 0.05) association was observed between plumage and skin colours and body weight. The reported variations in phenotypic traits of Nigerian Muscovy ducks indicate diversity in their genome, absence of selection and the need for their selection and improvement.

The chicken major histocompatibility complex B (MHC-B) – a cluster of genes associated with natural disease resistance or susceptibility – has been investigated in experimental and inbred lines by serological typing. However, that method showed some weaknesses for its use on out breeds. This study aims to explore the genetic diversity of the MHC-B of Cameroon indigenous chicken through molecular typing with LEI0258 and MCW0371 microsatellite markers. MHC-B haplotypes of 290 chickens from four agro-ecological zones were identified and compared with published haplotypes. Alleles were analysed for genetic diversity and relationship among Cameroon chicken populations. Hypothetically new LEI0258 alleles and haplotypes were detected. Overall, polymorphism parameters were relatively high in the Cameroon western highlands. The analysis of molecular variance revealed great variability (80.00 percent) between individuals than among and within ecotypes. The inbreeding coefficients of overall populations (FIT), among population (FST) and within population (FIS) were 0.26, 0.04 and 0.22, respectively, and all were highly significant (P < 0.001). A UPGMA tree based on Nei's DA genetic distances showed a clear distinction between Cameroon and out-groups and a structuring of within-country populations into three clusters. There is a great genetic diversity of the MHC-B in Cameroon native chicken and also a need of sequencing of the identified alleles for an accurate identification prior to their assessment for natural disease resistance and responsiveness to vaccination.

Sheep breeding is a traditional activity in Peru for small farmers, who generally possess Creole animals, which are frequently ignored in public policies as well as by the scientific community, not being recognized as a breed, showing poor productivity and having crosses with exotic breeds. This study aimed to characterize Creole and Hampshire Down crossbred ewes phenotypically, for using in the conservation and improvement of the Peruvian creole sheep. The year 2012, in the rural municipality of Ite, southern coast of Peru, 200 adult ewes were evaluated, classified by possible genotype (Creole or crossbred) and farm type (wetlands or ranches). Morphological and morphometric measurements were analysed; indices were drawn up and canonical and discriminant analysis were conducted, using the statistical program R. The results showed crossbred ewes with greater meat-producing capacity than the Creole, both influenced by the environment, management, and racial miscegenation that threatens the native sheep conservation. The adaptation of flocks was seen in different conditions, but some traits must be improved, requiring adequate technical orientation and rural extension services.

The Vogan sheep (VS), a crossbreed between Djallonke sheep (DS) and sahelian sheep (SS), is a unique sheep breed in Togo. It is highly valued for its performances but its breeding is very localized in southeastern of Togo. The objective of this study was to update the breed's phenotypic characterization and to compare VS phenotypic features with those of parental populations (DS and SS). For this purpose, morphological data were collected in January 2013 from 206 animals in Vô, Kloto and Agou prefectures (Togo) and in May 2013 from 30 SS in Bobo-Dioulasso (Burkina Faso). Results showed that the coat colour was very variable. Horn shape was also variable but was generally prismatic and outward-oriented, present in all rams and fine or remains of them in ewes. Quantitative traits such as height at withers, body length, chest circumference, tail length, ear length, space between the horns and chest depth showed that VS traits are smaller than SS traits but are significantly superior when compared to DS traits. Most VS characters were influenced by geographic location (p < 0,05). This study confirmed the “intermediate” status of VS. The sustainable use of VS needs molecular characterization and a dissemination programme.

Globally, rural cattle keeping communities actively select and breed indigenous cattle to satisfy their interests and enhance adaptation to local landscapes. This study investigated how traditional systems in Uganda have shaped the morphometric population structure of indigenous cattle breeds. Ten linear morphometric traits were interrogated amongst 801 female cattle, comprising 46 Nganda (Bos indicus), 368 Ankole (B. taurus indicus) and 387 East African shorthorn zebu (EASZ, B. indicus). The study cattle were obtained evenly at random from 209 herds in their agro-ecological zones (AEZs) where they have been nurtured by traditional cattle keeping communities throughout Uganda. Age, AEZs and breed significantly influenced the variation of linear morphometric traits exhibiting a gradient of low, intermediate and high dimensions among the EASZ, Nganda and Ankole cattle, respectively. Likewise, the linear morphometric trait (Mahalanobis squared distance) diversity was significantly different exhibiting a gradient of low, intermediate and high variation between Nganda and EASZ, Ankole and Nganda, and Ankole and EASZ cattle, respectively. These findings demonstrate the role of agro-ecological fitness in the evolution of indigenous cattle morphometric population structure in Uganda. The study outcomes further provide a motivation to search for genes associated with the diverse morphometric features.

The existence of sexual dimorphism in the Minorcan horse, an autochthonous breed from Minorca Island in the Balearic archipelago (NW Mediterranean Sea), is established in the official standard, with females being shorter and longer than males as well as having slenderer necks and a squarer croup. However, no study so far has explored the size and shape components of this dimorphism separately. The aim of this study was to analyse the morphology of this breed using geometric morphometric methods in order to find size and shape differences between sire lines. The analysis was based on landmarks digitized in lateral view from 38 registered adult Minorcan horses (20 males and 18 females) within an age range of 3–14 years (average 7 years) with different performance goals. The analyses did not reveal any significant differences between the “shape” and “size” of male and female animals, for the landmarks studied, so the sexes are functionally similar.

Argentina's annual camelid fibre production is estimated at 60 000 kg for llama (Lama glama), somewhat more than 2 000 kg for guanaco (Lama guanicoe) and about 845 kg for vicuña (Vicugna vicugna). The potential for increasing these amounts is huge considering that barely 30 percent of llamas are shorn and considering the size of the wild camelid population in the country. A compilation of published and unpublished work confirms that almost 50 percent of the llamas are single-coated, about 40 percent have white fleeces and that average fibre diameter is about 22 µm in the main llama production area. In general, there is a wide variation in fleece weights and fibre quality between and within herds. However, a llama fleece classing and pricing system is not yet in place to motivate implementation of breeding programmes. Guanaco and vicuña fleeces are double-coated but the fine undercoat represents more than 80 percent of the fleece weight. The proportion of down fibre remaining after mechanical dehairing is only 50 percent in guanacos and 70 percent in vicuñas. The guanaco undercoat fibre diameter is about 16 µm and vicuña fibre diameter is typically between 13 and 14 µm. Both fibres are relatively short. Research is needed to establish optimum shearing season and shearing frequency that results in fibre quality demanded for handcraft and industry in each of the three species.

Data on breeding management, breed and trait preference for pigs were collected from smallholder farmers in Kiambu and Kakamega Counties of Kenya. The production systems evaluated were semi-intensive and extensive and depicted varying pig production intensities, production objectives, pig performances as well as farmers’ breed and trait preferences. The perception of the importance of traits was evaluated to obtain a more balanced objective view on production and/or breeding objectives. The data collected were analysed through computation of indices, which represented a weighted average of all rankings of a particular trait. In the semi-intensive system, preference for performance traits such as size, growth rate and body weight, scored the same index (0.181), followed by the reproduction trait – prolificacy (0.161). In the extensive system, the indices for these traits were 0.187, 0.183, 0.163 and 0.106, respectively. Spearman's non-parametric rank correlations were calculated for ranking of traits of economic importance to indicate the directional effects and plausible trade-offs between traits. In the semi-intensive system, correlations were moderate between growth rate and both size and weight. In the extensive system, correlations were moderate for growth rate with both size and body weight. Appropriate breeds that suit the divergent production systems need to be identified and utilized based on performance and adaptability to ensure efficient resource use.

Management of local breeds is closely linked to the global challenges involved in genetic resources management. However, it cannot be reduced to this genetic dimension alone and is an integral part of the entire farming system of which it is a part. The aim of this paper is to show why it is essential to have an approach to local breed management that takes the dynamics of livestock farming systems (LFS) into account. After a presentation of the LFS approach, we show how genetic management is strongly linked to other dimensions of farming systems, at the farm scale as well as at more comprehensive scales. We illustrate our claim with different examples of the management of local breeds of different species.

From 1980s onwards, Indonesia's government has been implementing crossbreeding with European beef breeds through artificial insemination to improve the beef performance of local cattle, in response to the increasing demand for meat. Crossbreeding is promoted and implemented throughout the country, regardless of the various agro-ecological zones, each endowed with different feed resources in the smallholder farming systems. This study analyses the impact at farm level of crossbreeding in the different mixed farming conditions in Central Java. Quantitative and qualitative information was collected through participatory approaches involving famers (n = 252) in four study areas representing three agro-ecological zones: Wet lowlands (subdivided in two areas based on the history of breeding local cattle and crossbreeding), Wet uplands and Dry uplands. Phenotypic characteristics, reproductive performances, and carcass characteristics of Ongole and crossbred cattle were assessed, together with farmers’ reasons for keeping Ongole or crossbred breeding stock, the functions of cattle on the farms and the Gross Margins (GM) of the cattle component on Ongole and crossbred farms. Across different agro-ecological zones, crossbreeding is not changing the farming systems: herd sizes, farm types, experience in cattle keeping and functions of cattle were about the same for Ongole and crossbred farms. The agro-ecological zones differed in the cropping pattern and feed resources; however, they did not differ in amounts of dry matter and crude protein fed to individual animals. Crossbreeding is changing the individual characteristics of cattle and consequently the market prices of animals. In general, mature female crossbred cattle were approximately 25 percent heavier than mature female local cattle. Male crossbred progeny was 16 percent heavier their local counterparts, whereas female crossbred progeny was 24 percent heavier than female local cattle. In terms of reproduction performances, both local and crossbred cows performed well with calf crops ranging between 73 and 86 percent per year. Most farmers preferred crossbred over Ongole cattle. Simmental cross is the most preferred. GM for crossbred and Ongole farms were comparable within the different study areas; selling prices of crossbreds are higher, but feed costs too. Crossbreeding will continue. It is promoted by government policies and farmers are motivated to keep crossbred cattle as body weights and market prices are higher than for Ongole cattle; however, farmers said that they do not prefer upgrading to very high levels of Simmental. A viable Ongole population is needed to reduce the risk of upgrading to too high levels of Simmental.

Animal breeding for increased productivity over the past 50 to 60 years has been very successful in terms of increasing growth rate, milk yield and egg production in most livestock producing regions of the world (Rauw et al., 1998). However, this success has not registered that well in most countries in sub-Saharan Africa (SSA). Ironically, just like most developing regions, SSA is faced with the challenge to increase rapidly the agricultural productivity to help feed their growing human populations without depleting the natural resource base (Rege, 2005). Genetic improvement of livestock depends on access to genetic variation and effective methods for exploiting this variation (Rege, 2005). This is where human capacity and infrastructure for decision-support systems in animal breeding are required. This paper provides a synthesis of views from a cross-section of livestock production experts working in SSA. These views were collated through an e-conference which was held from 8th March to 20th April 2011. The e-conference discussed future research and development (R&D) needs for animal breeding and genetics in SSA and how they can be met. The e-conference attracted 43 participants from 17 countries. Results from the e-conference demonstrated that the R&D institutions and infrastructure in SSA vary widely in terms of both the physical and human capacity. Equally varied is the level of utilization of these institutions. In terms of training in Animal Breeding and Genetics, although most universities/colleges have programmes in Animal Science and teach animal breeding and genetics, there are very few practicing animal breeders. Lack of mentorship programmes and collaboration, and in some cases lack of appropriate jobs, continue to contribute to this ‘leaking pipeline’ phenomenon. The following is a summary of the consensus stemming from the conference on how the efficiency and effectiveness of livestock genetic improvement in SSA could be enhanced. First, the need to augment the approach that promotes animal breeding and genetics as part of a wider agriculture and rural development system, second, collaboration both within Africa and with those in the Diaspora should be further tapped into and utilized as a source of capacity for R&D and third, initiative of sharing resources and research platforms such as pooling data for genetic analysis from across institutions, and even across countries, should be encouraged in case where this is advantageous to do so.