Genetic diversity analysis using lowly polymorphic dominant markers: the example of AFLP in pigs.

DNA markers are commonly used for large-scale evaluation of genetic diversity in farm animals, as a component of the management of animal genetic resources. AFLP markers are useful for such studies as they can be generated relatively simply; however, challenges in analysis arise from their dominant scoring and the low level of polymorphism of some markers. This paper describes the results obtained with a set of AFLP markers in a study of 59 pig breeds. AFLP fingerprints were generated using four primer combinations (PC), yielding a total of 148 marker loci, and average harmonic mean of breed sample size was 37.3. The average proportion of monomorphic populations was 63% (range across loci: 3%-98%). The moment-based method of Hill and Weir (2004, Mol Ecol 13:895-908) was applied to estimate gene frequencies, gene diversity (F(ST)), and Reynolds genetic distances. A highly significant average F(ST) of 0.11 was estimated, together with highly significant PC effects on gene diversity. The variance of F(ST) across loci also significantly exceeded the variance expected under the hypothesis of AFLP neutrality, strongly suggesting the sensitivity of AFLP to selection or other forces. Moment estimates were compared to estimates derived from the square root estimation of gene frequency, as currently applied for dominant markers, and the biases incurred in the latter method were evaluated. The paper discusses the hypotheses underlying the moment estimations and various issues relating to the biallelic, dominant, and lowly polymorphic nature of this set of AFLP markers and to their use as compared to microsatellites for measuring genetic diversity.

Genetic diversity within and between European pig breeds using microsatellite markers.

An important prerequisite for a conservation programme is a comprehensive description of genetic diversity. The aim of this study was to use anonymous genetic markers to assess the between- and the within-population components of genetic diversity for European pig breeds at the scale of the whole continent using microsatellites. Fifty-eight European pig breeds and lines were analysed including local breeds, national varieties of international breeds and commercial lines. A sample of the Chinese Meishan breed was also included. Eleven additional breeds from a previous project were added for some analyses. Approximately 50 individuals per breed were genotyped for a maximum of 50 microsatellite loci. Substantial within-breed variability was observed, with the average expected heterozygosity and observed number of alleles per locus being 0.56 [range 0.43-0.68] and 4.5 respectively. Genotypic frequencies departed from Hardy-Weinberg expectations (P < 0.01) in 15 European populations, with an excess of homozygotes in 12 of them. The European breeds were on average genetically very distinct, with a Wright F(ST) index value of 0.21. The Neighbour-Joining tree drawn from the Reynolds distances among the breeds showed that the national varieties of major breeds and the commercial lines were mostly clustered around their breeds of reference (Duroc, Hampshire, Landrace, Large White and Piétrain). In contrast, local breeds, with the exception of the Iberian breeds, exhibited a star-like topology. The results are discussed in the light of various forces, which may have driven the recent evolution of European pig breeds. This study has consequences for the interpretation of biodiversity results and will be of importance for future conservation programmes.

Genetic contribution of the Arabian to the Italian Haflinger horse.

SUMMARY: The genetic contributions of the Arabian horse and the Austrian and German Haflingers to the registered Italian Haflinger are analysed by studying proportionate founder genetic contribution and by simulating Mendelian segregation of the founder alleles at an hypothetical locus. The Arabian proportionate contribution from the early 1960s is stabilized around 0.044, the Austrian Haflinger from the 1970s is around 0.03 and German Haflinger is always less than 0.001. The extinction probability of the Arabian gene pool reaches 0.37 in the 1950s then decreases to 0.15 in the 1990s due to the registration of the progeny of Arabian stallions. The extinction probabilities of some founder alleles are very high because of early pedigree bottlenecks. Contribution génétique du cheval Arabe à l'Haflinger italien Les contributions génétique du cheval Arabe et des Haflinger autrichien et allemand aux chevaux Haflinger italiens inscrits est analysée. On a etudié la contribution respective des differents fondateurs et on a simulé les ségrégations mendéliennes à un hypothétique locus neutre. La contribution relative de l'Arabe est stable, aux environs de 0,044; la contribution relative de l'Haflinger autrichien est d'environ 0,03 depuis les années 70 et celle de l'Haflinger allemand est toujours inferieure à 0,001. La prbabilité d'extinction du pool gènique Arabe atteint 0,37 dans les années 50 et décroit ensuite jusqu'à 0,15 dans les années 90, due fait de l'enregistrement de la descendance d'étalons Arabe. Les probabilitiés d'extinction de certains alléles fondateurs est très élevée à cause de "goulots de bouteille" intervenant précocément dans les pedigrees. RESUMEN: Contribution genética del caballo arabe al caballo italiano Haflinger Las contribuciones genéticas del caballo arabe y de los Haflinger austriacos y alemanes al Haflinger italiano registrado son analizados estudiando la contribucion genética de los animales fundatores (en porcentage) y pur medio de simulacion de la segregacion menedeliana de los alelos fundatores en un locus hipotético. La contribution proporcional arabe del inicio de los anos sesanta se estabiliza alrededor de 0,044. La contribucion genética del Haflinger austriaco de los anos setanta es alrededor de 0.03 y la contribucion del Haflinger aleman es siempre menos de 0.001. Las probabilidades de extinction del pool genético arabe alcanza el 0.37 en los anos cincuenta, disminuyendo a 0.15 en los anos noventa debido a la inclusion de la progenie de los caballos arabes. Las probabilidades de extincion de algunos alelos fundadores son muy altas debido a cuellos de botella en el arbol genealogico iniciales. ZUSSAMENFASSUNG: Einfluss von Arabers auf Italienische Haflinger Der genetische Beitrag des Arabers, des oestereichischen und deutschen Haflingers am italienischen Haflinger ist anhand von Analysen des genetischen Beitrages, der auf die Stammvaeter zurueckzufuehren ist, untersucht worden. Zudem wurde eine Simulation der mendelschen Aufspaltung von Stammvaeterallelen an einem hypothetischen Locus durchgefuehrt. Seit den fruehen 60er Jahren hat sich der arabische Anteil bei etwa 4,4 % stabilisiert, der des österreichishen Haflingers liegt seit den 70er Jahren bei 3 % und der des deutschen Haflingers bei weniger als 1 %. Die Verdraengungswahrscheinlichkeit des arabischen Genpools reichte von 37 % in den 50ern bis zu 15 % in den 90ern durch Registration der Nachkommenshaft von arabischen Hengsten. Aufgrund durch vergangener einseitiger Selektion (Stammbaumflaschenhaelse) ist die Verdraengungswahrscheinlichkeit der Stammvaeterallele sehr hoch.

Genetic variation and distances of five Italian native sheep breeds.

Genetic distances among five of the most important Italian native sheep breeds were estimated by using gene frequencies of four blood group and seven blood protein loci and by three different computing methods. The values of the three distance matrices were highly correlated. Genetic distances were found within the range values reported in the literature for local breeds. Shorter distances fitted the historical evidence of migrations.

The use of long-acting neuroleptics in impala (Aepyceros melampus).

The long-acting neuroleptics perphenazine enanthate and pipothiazine palmitate were found to be effective for the long-term tranquilization of newly-captured and captive impala (Aepyceros melampus). Perphenazine enanthate (1.5 to 5.7 mg kg-1) produced a favourable state of tranquilization with a maximum effect lasting up to 7 d. Pipothiazine palmitate (4.5 mg kg-1) produced tranquilization lasting 16 d. The animals accepted humans inside their pens, at a distance of 0.5 to 4 m, without showing any excitement. No untoward side-effects were observed.

Preliminary investigation into the nutrition of ostrich chicks (Struthio camelus) under intensive conditions.

Twenty ostrich chicks (Struthio camelus) up to 8 weeks of age were fed isocaloric diets containing protein levels of 14%, 16%, 18% and 20%. The highest mean body weight gain was obtained from feeding the 20% protein diet; however, this result was not significantly different at the 0.05 level of probability. Feed conversion favoured the 18% protein group. During the seventh and eighth week of the experimental period some chicks developed leg deformities. Clinical signs, radiological findings and response to calcium supplementation suggested an insufficient amount of calcium in the experimental diets.