Rare phenotypes in domestic animals: unique resources for multiple applications.

Preservation of specific and inheritable phenotypes of current or potential future importance is one of the main purposes of conservation of animal genetic resources. In this review, we investigate the issues behind the characterisation, utilisation and conservation of rare phenotypes, considering their multiple paths of relevance, variable levels of complexity and mode of inheritance. Accurately assessing the rarity of a given phenotype, especially a complex one, is not a simple task, because it requires the phenotypic and genetic characterisation of a large number of animals and populations and remains dependent of the scale of the study. Once characterised, specific phenotypes may contribute to various purposes (adaptedness, production, biological model, aesthetics, etc.) with adequate introgression programmes, which justifies the consideration of (real or potential) existence of such characteristics in in situ or ex situ conservation strategies. Recent biotechnological developments (genomic and genetic engineering) will undoubtedly bring important changes to the way phenotypes are characterised, introgressed and managed.

GRAIN: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach.

GRain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GRain calculates, together with the 'classical' inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered., 88, 169 and Kalinowski et al., (2000) Conserv. Biol., 14, 1375 as well as an ancestral history coefficient (AHC ), defined here for the first time. AHC is defined as the number that tells how many times during pedigree segregation (gene dropping) a randomly taken allele has been in IBD status. Furthermore, GRain enables testing of heterogeneity and/or purging of inbreeding depression with respect to different founders/ancestors by calculating partial coefficients for all previously obtained coefficients.

Multifunctionality and provision of ecosystem services by livestock species and breeds at global level.

Beyond providing food, livestock species are linked to a wide range of uses and ecosystem services (ESs). Based on information reported by 41 countries on 3 361 national breed populations to the Domestic Animal Diversity Information System of the Food and Agriculture Organization of the United Nations, we investigated how factors such as species, region, breed adaptedness, or management system associate with the recognition of provision of a set of 52 ESs. Among species, a greater number of cultural ESs were reported for horses (2.47 for horses vs 0.75 on average across all species), while the major ruminant species (cattle, goats and sheep) were on average associated with more provisioning ESs (2.99 vs 2.39), and more regulating and maintenance ESs (1.86 vs 1.32). Compared to European breeds, African livestock contribute more provisioning ES (3.95 vs 1.88). Native breeds and, to a lesser extent, locally adapted breeds, were linked to more ESs than were exotic breeds (5.97 and 4.10 vs 2.90, respectively), regardless of the ES category considered. The total number of ES reported was greater for breeds primarily kept under Back Yard/Farm Yard and extensive management systems than in other production environments. Different "bundles" of ES were identified in relation to the interdependence among themselves, or according to species or regional specificities. Overall, our results highlight that native and locally adapted breeds, which tend to be raised in less specialized production systems than exotic breeds, are reported to play multiple roles contributing to rural community livelihoods and environmental sustainability of food systems.

On the origin of the Slovenian Cika cattle.

In 2002, it was discovered that several Cika cattle in the mountain areas of Slovenia had escaped the official policy of cross-breeding. Here, we report a genetic characterization to assess their status as autochthonous breed. We compared genotypes for 14 microsatellite markers in 150 Cika cattle individuals with data from 16 Central European cattle breeds. We show that Cika cattle are genetically as diverse as other Eastern Alpine breeds, are more diverse than Austrian Simmental but less than the Balkan Busha cattle. STRUCTURE analysis showed Pinzgauer admixture in several individuals but also indicated a unique genetic identity for Cika. This analysis also allowed a selection of the most genetically pure Cika individuals as assessed by the panel of microsatellites. These original Cika cattle form an Eastern Alpine breed cluster together with Pinzgauer and Pustertaler cattle. Cika cattle should be considered as an authentic and valuable genetic resource, which offers clear opportunities for sustainable agriculture and landscape conservation in marginal and mountain areas.

An ABC estimate of pedigree error rate: application in dog, sheep and cattle breeds.

On the basis of correlations between pairwise individual genealogical kinship coefficients and allele sharing distances computed from genotyping data, we propose an approximate Bayesian computation (ABC) approach to assess pedigree file reliability through gene-dropping simulations. We explore the features of the method using simulated data sets and show precision increases with the number of markers. An application is further made with five dog breeds, four sheep breeds and one cattle breed raised in France and displaying various characteristics and population sizes, using microsatellite or SNP markers. Depending on the breeds, pedigree error estimations range between 1% and 9% in dog breeds, 1% and 10% in sheep breeds and 4% in cattle breeds.

Mating practices and the dissemination of genetic disorders in domestic animals, based on the example of dog breeding.

On the basis of simulations and genealogical data of ten dog breeds, three popular mating practices (popular sire effect, line breeding, close breeding) were investigated along with their effects on the dissemination of genetic disorders. Our results showed that the use of sires in these ten breeds is clearly unbalanced. Depending on the breed, the effective number of sires represented between 33% and 70% of the total number of sires. Mating between close relatives was also found to be quite common, and the percentage of dogs inbred after two generations ranged from 1% to about 8%. A more or less long-term genetic differentiation, linked to line breeding practices, was also emphasized in most breeds. F(IT) index based on gene dropping proved to be efficient in differentiating the effects of the different mating practices, and it ranged from -1.3% to 3.2% when real founders were used to begin a gene dropping process. Simulation results confirmed that the popular sire practice leads to a dissemination of genetic disorders. Under a realistic scenario, regarding the imbalance in the use of sires, the dissemination risk was indeed 4.4 times higher than under random mating conditions. In contrast, line breeding and close breeding practices tend to decrease the risk of the dissemination of genetic disorders.

Inbreeding depression on semen quality in Austrian dual-purpose simmental bulls.

Using pedigree data, the inbreeding coefficients of 715 Austrian dual-purpose Simmental (Fleckvieh) bulls stationed in two artificial insemination (AI) centres in Upper and Lower Austria were calculated and incorporated in statistical models for the analysis of semen quality. Five semen quality parameters (volume, concentration, motility, number of spermatozoa per ejaculate and percentage of viable spermatozoa) of approximately 30,000 ejaculates, used in two separate data sets, were investigated. The mixed model included the fixed effects age class of the bull, bull handler, semen collector, month and year of collection, number of collection per bull and day, time interval since last collection, the linear continuous effect of the inbreeding coefficient of the bull, interactions between age class and month, and age class and interval since last collection, respectively, as well as the random effect of the bull and the random residual effect. Non-linear effects of inbreeding were significant for motility only. Despite the quite low inbreeding coefficients (mean 1.3%), all semen quality traits showed inbreeding depression, in four of the five traits significantly in at least one of the data sets. The magnitude of inbreeding depression was small, which might partly be caused by the low inbreeding levels and a potential pre-selection of the bulls in the AI centres. However, monitoring of inbreeding depression on fertility traits is recommended to avoid unrecognized deterioration of such traits.

Impact of conservation measures on demography and genetic variability of livestock breeds.

Conservation of animal genetic resources requires regular monitoring and interventions to maintain population size and manage genetic variability. This study uses genealogical information to evaluate the impact of conservation measures in Europe, using (i) data from the Domestic Animal Diversity Information System (DAD-IS) and (ii) a posteriori assessment of the impact of various conservation measures on the genetic variability of 17 at-risk breeds with a wide range of interventions. Analysis of data from DAD-IS showed that 68% of national breed populations reported to receive financial support showed increasing demographic trends, v. 51% for those that did not. The majority of the 17 at-risk breeds have increased their numbers of registered animals over the last 20 years, but the changes in genetic variability per breed have not always matched the trend in population size. These differences in trends observed in the different metrics might be explained by the tensions between interventions to maintain genetic variability, and development initiatives which lead to intensification of selection.

Pedigree analysis in the Austrian Noriker draught horse: genetic diversity and the impact of breeding for coat colour on population structure.

The pedigree of the current Austrian Noriker draught horse population comprising 2808 horses was traced back to the animals considered as founders of this breed. In total, the number of founders was 1991, the maximum pedigree length was 31 generations, with an average of 12.3 complete generations. Population structure in this autochthonous Austrian draught horse breed is defined by seven breeding regions (Carinthia, Lower Austria, Salzburg, Styria, Tyrol, Upper Austria and Vorarlberg) or through six coat colour groups (Bay, Black, Chestnut, Roan, Leopard, Tobiano). Average inbreeding coefficients within the breeding regions ranged from 4.5% to 5.5%; for the colour groups, the coefficients varied from 3.5% to 5.9%. Other measures of genetic variability like the effective number of founders, ancestors and founder genomes revealed a slightly different genetic background of the subpopulations. Average co-ancestries between and within breeding areas showed that the Salzburg population may be considered as the nucleus or original stock whereas all other subpopulations showed high relationship to horses from Salzburg. The target of draught horse breeding in the 21st century does not meet the breeding concept of maximizing genetic gains any more. Stabilizing selection takes place. In this study, we show that demographic factors as well as structure given by different coat colours helped to maintain genetic diversity in this endangered horse breed.

Investigation of the Booroola (FecB) and Inverdale (FecX(I)) mutations in 21 prolific breeds and strains of sheep sampled in 13 countries.

Twenty-one of the world's prolific sheep breeds and strains were tested for the presence of the FecB mutation of BMPR1B and the FecX(I) mutation of BMP15. The breeds studied were Romanov (2 strains), Finn (2 strains), East Friesian, Teeswater, Blueface Leicester, Hu, Han, D'Man, Chios, Mountain Sheep (three breeds), German Whiteheaded Mutton, Lleyn, Loa, Galician, Barbados Blackbelly (pure and crossbred) and St. Croix. The FecB mutation was found in two breeds, Hu and Han from China, but not in any of the other breeds. The 12 Hu sheep sampled were all homozygous carriers of FecB (FecB(B)/FecB(B)) whereas the sample of 12 Han sheep included all three genotypes (FecB(B)/FecB(B), FecB(B)/FecB+, FecB+/FecB+) at frequencies of 0.33, 0.58 and 0.08, respectively. There was no evidence of FecX(I) in any of the breeds sampled.

An exploratory analysis on how geographic, socioeconomic, and environmental drivers affect the diversity of livestock breeds worldwide.

This study investigates the relationships between various environmental and geographic, demographic, and socioeconomic factors with the diversity of livestock breeds reported within countries across the world. Statistical analyses were performed considering the numbers of breeds reported by 158 countries for 4 livestock mammalian species (cattle, sheep, goats, and pigs). Organization for Economic Cooperation and Development (OECD) countries reported more breeds than non-OECD countries in general. Strong and positive correlations were found between agricultural area, human population size, species population size, and number of breeds per country. When considering regression models, the species population size was found as the most important explanatory factor for the number of breeds reported by countries in the 4 species. Diversity of production systems in the country had a significant association with the number of breeds reported for sheep, goats, and pigs. The number of ruminant breeds was positively associated with the size of agricultural area and the diversity of land cover in the country. While demographic and cultural importance of a given species is a major factor associated with the number of livestock breeds within countries, this diversity is also connected to the variability in environmental and production conditions.

Review: Sustainability of crossbreeding in developing countries; definitely not like crossing a meadow .

Crossbreeding, considering either terminal or rotational crossing, synthetic breed creation or breed replacement, is often promoted as an efficient strategy to increase farmers' income through the improvement of productivity of local livestock in developing countries. Sustainability of crossbreeding is however frequently challenged by constraints such as poor adaptation to the local environment or lack of logistic support. In this review, we investigate factors that may influence the long-term success or the failure of crossbreeding programs, based on the scientific literature and country reports submitted for The Second Report on the State of the World's Animal Genetic Resources for Food and Agriculture. Crossbreeding activities vary widely across species and countries. Its sustainability is dependent on different prerequisites such as continual access to adequate breeding stock (especially after the end of externally funded crossbreeding projects), the opportunity of improved livestock to express their genetic potential (e.g. through providing proper inputs) and integration within a reliable market chain. As formal crossbreeding programs are often associated with adoption of other technologies, they can be a catalyst for innovation and development for smallholders. Given the increasing global demand for animal products, as well as the potential environmental consequences of climate change, there is a need for practical research to improve the implementation of long-term crossbreeding programs in developing countries.

Genetic diversity and population structure of the synthetic Pannon White rabbit revealed by pedigree analyses.

Demographic history, current status, and efficiency of the mating strategy were analyzed using the pedigree of Pannon White (PW) rabbits born between 1992 and 2007. Potential accumulation of detrimental effects and loss of genetic diversity were also considered. Calculations and estimates were done most often for rabbits born in 2007, whereas other reference populations (REFPOPXXXX) were specified explicitly. The pedigree contained 4,749 individuals and 580 founders, and its completeness was 82.1% up to 10 and 94.5% up to 5 generations, respectively. Generation intervals through different pathways averaged 1.2 yr. When adjusted to the pedigree completeness, the amount of inbreeding (F(i)) of rabbits was comparable (5.54%) with that of other livestock populations, whereas the 10 (30) founders contributing the most to inbreeding explained a large part of the population inbreeding [i.e., 42.24% (73.18%)]. The ancestral inbreeding coefficient of REFPOP2004 (10.67%) was one-half that of REFPOP2007 (20.66%), showing its strong dependence on pedigree length. Family variance, inbreeding, and realized effective population size were 84.18 (REFPOP2006; this variable could not be calculated for the last year examined), 37.19, and 91.08, respectively. The effective numbers of ancestors, founders, and founder genomes were 48, 26, and 7.33, respectively. Although the circular mating scheme applied was generally effective, the large accumulated reduction in genetic variability indicates the need to revise and improve the current breeding strategy.

Individual-based assessment of population structure and admixture in Austrian, Croatian and German draught horses.

All over Europe, the number of draught horses has decreased drastically during the last 50 years. As a prerequisite for efficient management decisions, we analysed the conservation status in Austrian (Noriker Carinthia - NC, Noriker Salzburg - NS), Croatian (Croatian Coldblood - C, Posavina horse - P) and German (Altmaerkisch Coldblood - A, Black Forest horse - BF, Mecklenburg Coldblood - M, Rhenish German Draught horse - R, Saxon Thuringa Coldblood - ST, Schleswig Draught horse - Sch, South German Coldblood - SG) draught horses (434) using multilocus genotypic information from 30 (effectively 27) microsatellite loci. Populations located in areas with less intensive agricultural production (C, NC, NS, P and SG) had greater diversity within the population and estimated effective population size than A, BF, Sch, M, R and ST populations. The PCA plots revealed that populations form five separate groups. The 'Noriker' group (NC, NS and SG) and the 'Rhenish' group (A, M, R and ST) were the most distinctive (pairwise F(ST) values ranged from 0.078 to 0.094). The 'Croatian' group (C and P) was in the centre, while the BF and Sch populations formed two out-groups. A posterior Bayesian analysis detected further differentiation, mainly caused by political and geographical factors. Thus, it was possible to separate the South German Coldblood from the Austrian Noriker population where no subpopulation structure was detected. The admixture analysis revealed imprecise classification between C and P populations. A small but notable separation of R from A, M and ST populations was detected, while Sch and BF populations remained as out-groups. The information obtained should aid in making efficient conservation decisions.

Genetic characterisation and breed assignment in Austrian sheep breeds using microsatellite marker information.

Samples from 717 sheep of 11 Austrian sheep breeds were genotyped for 25 microsatellite loci. Twenty-one loci showing no deviation from Hardy-Weinberg equilibrium were used to calculate pairwise genetic distances (Nei's minimum distance and Reynolds' distance). All breeds could be clearly distinguished through these genetic distances. The shortest genetic distance was found between Alpines Steinschaf (AS) and Waldschaf (WS). Within the so-called 'Steinschaf' group [AS, Montafoner Steinschaf (MS), Krainer Steinschaf (KS) and Tiroler Steinschaf (TS)] the MS adopted an extreme status with the largest distance to the other breeds in the group. This finding resulted in the decision to consider the MS no longer as subpopulation of Alpines Steinschaf but as an independent breed. A correct breed assignment using a Bayesian approach was possible for only 66% of all individuals belonging to Alpines Steinschaf, but for at least 90% of individuals for all other breeds investigated.

Comparison of production systems and selection criteria of Ankole cattle by breeders in Burundi, Rwanda, Tanzania and Uganda.

A survey in Burundi, Rwanda, Tanzania and Uganda was conducted in order to determine the different production systems under which Ankole cattle are currently kept. Additionally, selection criteria of livestock keepers were documented. In Burundi, Rwanda and parts of Uganda, livestock keepers are sedentary and herds are small, whereas in the other areas Ankole cattle are kept in large herds, some of them still under a (semi-)nomadic system. Milk is the main product in all areas, and is partly for home consumption and partly for sale. Although the production systems vary in many aspects, the selection criteria for cows are similar. Productive traits such as milk yield, fertility and body size were ranked highly. For bulls, the trait 'growth' was ranked highly in all study areas. Phenotypic features (coat colour, horn shape and size) and ancestral information are more important in bulls than in cows. The only adaptive trait mentioned by livestock keepers was disease resistance. In areas of land scarcity (Burundi, Rwanda, western Uganda), a clear trend from pure Ankole cattle towards cross-bred animals can be observed.

Correlation between purebred and crossbred performance under a two-locus model with additive by additive interaction.

SUMMARY: The behaviour of the genetic correlation between purebred and crossbred performance (rpc) was studied under a model with two loci, in populations with varying gene frequencies, degrees of dominance, and (additive by additive) epistasis. The value of rpc depends not only on dominance and epistasis, but also on gene-frequency differences between the parental populations. The value of rpc is unity if neither epistasis nor dominance exist, or if there are the same gene frequencies in both purebred populations. Special ratios of the assumed genotypic effects and gene-frequency differences between the parental populations may also cause a rpc of unity. Therefore, a high rpc is possible with small gene-frequency differences, small non-additive gene effects, or certain ratios of the assumed genotypic effects and gene frequencies. Further, overdominance is not necessary for a negative rpc. The correlation becomes negative in the case of partial dominance in combination with epistasis and certain gene frequencies. In general, rpc decreases with increasing gene-frequency difference or increasing dominance and/or epistatic effects. ZUSAMMENFASSUNG: orrelation zwischen den Leistungen von Reinzucht- und Kreuzungstieren unter einem Zwei-Locus Modell mit Additiv mal Additiv Interaktion Das Verhalten der genetischen Korrelation zwischen den Leistungen von Reinzucht- und Kreuzungstieren (r(pc) ) wurde anhand eines Zwei-Locus Modelles in Abhängigkeit von Genfrequenzen, Dominanzgrad und Epistasie (additiv mal additiv) untersucht. Die Größe von r(pc) hängt nicht nur von Dominanzgrad und Epistasie, sondern auch von der Genfrequenzdifferenz zwischen den elterlichen Populationen ab. Der Wert von r(pc) beträgt immer eins, wenn weder Dominanz noch Epistasie wirken oder die gleichen Genfrequenzen in beiden Elternpopulationen vorliegen. Bestimmte Verhältnisse der unterstellten genotypischen Effekte und Genfrequenzdifferenzen zwischen den Elternpopulationen können ebenfalls zu einem r(pc) -Wert von eins führen. Daher ist es nicht möglich zu unterscheiden, ob ein hoher Wert für r(pc) durch geringe Genfrequenzdifferenzen, geringe nichtadditive Geneffekte oder bestimmte Verhältnisse der vorliegenden genotypischen Effekte und Genfrequenzdifferenzen zueinander verursacht wird. Weiters konnte gezeigt werden, daß keine Überdominanz für das Auftreten von nagativen Korrelationen notwendig ist. Die Korrelation wird auch dann negativ, wenn partielle Dominanz in Kombination mit Epistasie und bestimmten Genfrequenzen vorliegt. Im allegemeinen nimmt die genetische Korrlelation zwischen den Leistungen von Reinzucht- und Kreuzungstieren mit steigenden Genfrequenzdifferenzen oder steigenden Dominanz- und/oder Epistasieeffekten ab.

Effect of maternal age on milk production traits, fertility, and longevity in cattle.

Longevity is the economically most important functional trait in cattle populations. However, with an increased productive lifespan, the number of offspring born by older dams increases. A higher maternal age might have negative effects on the performance of offspring. The objective of this study was to investigate the effect of maternal age on production (energy-corrected milk yield [ECM]) and functional traits (fertility; somatic cell score, and functional longevity) in Austrian dual-purpose Simmental cows. Age of dam had a significant effect on ECM yield and longevity. The ECM yield of daughters decreased with age of dam. Although the risk of culling slightly increased with age of dam, it was lowest for daughters of oldest dams. Results for fertility were non-significant, and results for somatic cell scores were inconsistent across parities.