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 diversity in European pigs utilizing amplified fragment length polymorphism markers.

The use of DNA markers to evaluate genetic diversity is an important component of the management of animal genetic resources. The Food and Agriculture Organisation of the United Nations (FAO) has published a list of recommended microsatellite markers for such studies; however, other markers are potential alternatives. This paper describes results obtained with a set of amplified fragment length polymorphism (AFLP) markers as part of a genetic diversity study of European pig breeds that also utilized microsatellite markers. Data from 148 AFLP markers genotyped across samples from 58 European and one Chinese breed were analysed. The results were compared with previous analyses of data from 50 microsatellite markers genotyped on the same animals. The AFLP markers had an average within-breed heterozygosity of 0.124 but there was wide variation, with individual markers being monomorphic in 3-98% of the populations. The biallelic and dominant nature of AFLP markers creates a challenge for their use in genetic diversity studies as each individual marker contains limited information and AFLPs only provide indirect estimates of the allelic frequencies that are needed to estimate genetic distances. Nonetheless, AFLP marker-based characterization of genetic distances was consistent with expectations based on breed and regional distributions and produced a similar pattern to that obtained with microsatellites. Thus, data from AFLP markers can be combined with microsatellite data for measuring genetic diversity.

Molecular characterization of the porcine MHC class I region.

A porcine cosmid library was screened with a human MHC class I cDNA. Four positive clones were isolated and mapped with different restriction endonucleases. Altogether nine SLA class I genes were identified and their positions located within restriction maps. Sizes of class I homologous DNA sequences varied between 3600 and 5800 bp. The distances between these regions ranged from 11,900 to 22,200 bp.

Inbreeding and heterosis effects on quantitative traits in a White Leghorn population under long-term reciprocal recurrent selection.

1. Inbreeding and heterosis effects for quantitative traits were estimated in two White Leghorn lines selected with reciprocal recurrent selection (RRS) since 1950. 2. Pedigreed progeny were produced from full-sib, half-sib and unrelated pure line as well as reciprocal cross line matings to estimate inbreeding and heterosis effects "within sires". 3. Inbreeding effects estimated as linear regressions agreed well with estimates considering inbreeding as fixed effect. The inbreeding depression per 10% inbreeding was highest for hatchability (6-7%), intermediate for production-related traits (3%), and about 1% for shell quality, body weight and egg weight. 4. Heterosis effects were estimated by comparing pure line and cross line progeny of the same sires. 5. Results indicate considerably less heterosis for egg production than found earlier, which is interpreted as a consequence of pure line selection.

Crossbreeding effects after long-term selection for purebred performance: a model experiment with mice : 2. Performance of three-breed crosses.

Results are presented from two replicated three-breed cross diallels that were conducted after 20 generations of selection for purebred performance in mice. The selection criteria for the different lines were: litter size at birth (LS), weaning weight at 4 weeks (WW), weight gain from week 4 to week 6 (WG), and body fat content at week 6 (FT). Additionally, a random-mating control line (C) was kept. Significant maternal heterosis was found in litter size and weaning weight. Estimates of maternal heterosis in litter size were very high, ranging from 17 to 50% of the mean of the corresponding single crosses. Maternal heterosis in weaning weight usually was negative and ranged from +9 to -11%. Significant maternal heterosis in feed efficiency and weaning weight could only be found in a few cases. Total performance of three-breed crosses was highly superior to that of single crosses and purebreds. Means of the corresponding purebreds or single crosses were of little use in predicting three-breed cross performance.

Crossbreeding effects after long-term selection for purebred performance: a model experiment with mice : 1. Performance of F1 crosses.

The influence of purebred selection on the combining abilities of five lines of mice was examined. Two replicated testcross diallels were made after 10 and 20 generations of purebred selection for litter size, weaning weight, weight gain, and feed efficiency. Average direct genetic effects were of major importance, followed by average maternal genetic effects. In all of the replications, between two and four out of ten crosses showed significant heterosis. Heterosis ranged from 0 to 38% in litter size, from 0 to 20% in weaning weight, from -11 to 11% in weight gain, and from -8 to 17% in feed efficiency. For litter size and weaning weight, heterosis estimates increased between 80 and 100% from generation 10 to 20. Weight gain and feed efficiency showed decreasing heterosis with partly negative estimates in the second diallel. Combinations exhibiting significant heterosis varied between replicates and between the two diallels.

[Breeding adaptation to avoid antagonisms between production and health in swine]. / Züchterische Bearbeitung von Antagonismen zwischen Leistung und Gesundheit beim Schwein.

Lerner (1954) with his hypothesis of genetic homeostasis has provided the explanation for most of our present antagonism-problems in high performing farm animal populations. Effective artificial selection for highly heritable traits (such as lean content and muscularity in pigs) leads to negatively correlated responses in other traits, particularly the components of reproductive fitness. There are three main antagonisms in our present breeding populations of meat type pigs, which are all caused by the dramatic genetic changes in lean content and muscularity: 1. Poor meat quality and high stress susceptibility. 2. Decreasing reproductive performance. 3. Increased leg weakness problems. The most efficient breeding strategies against these antagonisms are 1. Elimination of the recessive Halothane stress gene from at least one parental population by systematic progeny test procedures. Crossbred progeny from one homozygous stress resistant parent are at least heterozygous stress resistant and have good meat quality. 2. Use of crossbred sows from two parental breeds leads on an average of 10% to a better litter performance than purebred sows. Hybrid sows from selected dam lines can have a markedly better litter performance than 10%. 3. Avoidance of extreme muscularity or carcass length as well as tests and the selection of the breeding stock under practical (strawless) management conditions reduces the incidence. Moreover crossbred boars from unrelated parent breeds show much less leg and libido problems.

Associations between marker genotypes, halothane reaction, creatine kinase activity and meat quality characters in a sample of German Landrace pigs.

Routine blood typing of German Landrace pedigree populations and an earlier study revealed very low frequencies of the favourable alleles at the marker loci Phi, Pgd and H. The hypothesis was that in this population the whole linkage group of favourable alleles at the halothane and neighbouring marker loci may have been lost as a consequence of intense selection for leanness and type. The present study of 1050 German Landrace pigs at the Relliehausen experimental station, where some effort has been made to maintain a higher frequency of the favourable alleles PhiA (0.48), H- (0.43) and PgdA (0.70) gave quite different results. The frequency of halothane-positive pigs found by using a severe test was only 30%. Only 5.4%, 8.8%, 13.4% and 13.9% of animals with PhiA/A, H-/-, PgdA/A and PhiA/B genotypes respecitively were halothane-positive. Forty to sixty per cent of pigs with these marker genotypes could therefore be expected to be homozygous halothane-negative (N/N) animals. Creatine kinase activity and three selected meat quality characters showed highly significant differences between the A/A and the B/B genotypes for the marker loci Phi and Pgd, with the heterozygotes being intermediate. These differences are greater than those observed between halothane-negative and halothane-positive phenotypes. The only other consistently superior marker genotype in this population was the H blood group genotype H-/-. In contrast to findings from Sweden and Switzerland, the postalbumin locus Po2 and the suppressor locus S for the A-O blood groups did not exhibit useful marker qualities.(ABSTRACT TRUNCATED AT 250 WORDS)