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.

Lactation curves of commercial ewes rearing lambs.

Three-hour milk production measurements determined by machine milking at 3-d intervals throughout a 63-d lactation period were used to describe lactation curves for crossbred ewes lambing at 1 and 2 yr of age and rearing single and twin lambs. Age of ewe, type of rearing, and day of lactation affected (P < 0.05) milk production. Over the 63-d lactation, average daily milk production was 2.56 and 2.63 kg, respectively, for 1- and 2-yr-old ewes rearing single lambs and 2.73 and 3.47 kg, respectively, for 1- and 2-yr-old ewes rearing twins. Milk production of 2-yr-old ewes rearing twin lambs peaked at 21 d of lactation, and that of 1- and 2-yr-old ewes rearing singles peaked between 27 and 30 d of lactation. The largest differences in the lactation curves among age and rearing ewe classes were found in early lactation. These differences were reduced by midlactation, and by late lactation, milk production for all ewes was similar. Diurnal variation in milk production by ewes was evaluated in an 8 x 8 Latin square design. Diurnal variation in milk yield measurements of eight mature ewes, each bearing and rearing twin lambs, was similar between d 21 and 24 of lactation. Time of milk production measurements within a day did not affect yield determinations. Extrapolation from 3-h production estimates to daily milk production is valid in determining a ewe's milk contribution in support of lamb growth.

Comparison of weigh-suckle-weigh and machine milking for measuring ewe milk production.

Thirteen crossbred ewes were used to compare weigh-suckle-weigh (WSW) and machine milking (MM) methods for determining milk production of ewes that were rearing single or twin lambs. At parturition, ewes were 13 mo of age and produced six single lambs and seven pairs of twin lambs. Milk production estimates were initiated on d 6 of lactation and a 3-d rotation of the two techniques was implemented. On d 6, milk production was measured using WSW; on d 7, MM was used. No measurement was made on d 8. The 3-d rotation was repeated 20 times throughout a 63-d lactation, resulting in 20 point estimates of milk production for each method of measurement for each ewe. The WSW procedure consisted of a 3-h period in which lambs were withheld from suckling their dams. This was followed by a suckling period, a second 3-h withholding period, and a second suckling period. Differences in pre- and postsuckling lamb weights of the second suckling period were defined as milk consumption and, indirectly, 3-h milk production. The MM procedure included an administration of 10 IU of oxytocin (i.v.), followed by evacuation of the udder with a machine using commercially available sheep milking equipment, and the milk was discarded. Lambs were withheld from suckling the ewes for a 3-h period, followed by a repetition of the oxytocin and machine milking procedures. Milk from the second milking was weighed. Milk production estimates determined using the WSW and MM techniques were similar (P = .42). Average 3-h milk production was 340 and 351 g for WSW and MM, respectively. Machine milking provides a reliable tool in evaluating the milk-producing ability of ewes that are rearing single or twin lambs.

Indices de seleçäo para tamanho e peso de leitegada / Selection indexes for litter size and weight in pigs

Ajustaram-se 42 índices de seleçäo para tamanho e peso de leitegada, para suínos das raças Large White, Landrace e Duroc. Os resultados indicam a possibilidade de obter ganhos genéticos para tamanho e peso de leitegada. O uso de índices com restriçäo ao progresso genético no tamanho da leitegada foi considerado viável, e superior aos índices convencionais nas raças Large White e Duroc

Estimation of Fitness Components in DROSOPHILA MELANOGASTER . I. Heterozygote Viability Indices.

We examine the assumption of "dominance" with regard to viability of the Cy and Pm marker chromosomes in D. melanogaster . This assumption is often invoked for the extraction of wild-type second chromosomes from natural populations and for the calculation of relative viability indices. Significant genotypic variances for viability are found among both Cy/+(j) and Pm/+(i) heterozygotes in California and Japanese populations. The magnitude of the Pm/+( i) genotypic variance is substantially less than that of the Cy/+(j) heterozygotes (less than one half). Significant reciprocal effects are also found to influence Cy/+(j), Pm/+(i) and +(i)/+(j) viabilities. We conclude that viability indices of heterozygotes based on the Curly method are biased. We suggest that viability indices in the future be expressed relative to the viability of the Cy/Pm genotype (Curly-Plum method) or possibly that of the Pm/+(i) genotype (Plum method).

High Rates of Occurrence of Spontaneous Chromosome Aberrations in DROSOPHILA MELANOGASTER.

Spontaneous mutations were accumulated for 40 generations in 140 unrelated second chromosomes with the standard gene arrangement. These were extracted from the same population by using the marked inversion technique, and the following findings were obtained: (1) In 42 out of the 140 chromosome lines, chromosome aberrations were detected by examining the salivary gland chromosomes: 40 paracentric and 15 pericentric inversions, 2 reciprocal translocations between the second and the third chromosomes, and 6 transpositions. (2) In 63 out of the 90 originally lethal-free lines, recessive lethal mutations occurred. (3) There were only 3 lines that acquired chromosome aberrations (inversions) with no lethal effects in the homozygous condition. (4) In a comparison of these results with those of the (CH), (PQ), and (RT) chromosomes in which no chromosome aberrations occurred after accumulating mutations for 22058 chromosome.generations (Yamaguchi and Mukai 1974), it was concluded that some of these 140 chromosomes carried a kind of mutator. (5) The frequency of mutator-carrying chromosome lines was estimated to be 0.66 on the basis of the distribution of the break-points on the chromosome lines and the frequency of lines that acquired neither recessive lethal mutations nor chromosome aberrations. Thus, the average number of breaks per mutator-carrying chromosome was estimated to be about 0.19/generation.On the basis of these estimates, the nature of the mutator factor was discussed.

Mutator factors and genetic variance components of viability in Drosophila melanogaster.

In the process of testing whether or not the independent-locus selection model holds true with previously estimated genetic parameters (cf. MUKAI and MARUYAMA 1971) in D. melanogaster collected near Raleigh, North Carolina, we found an abnormal phenomenon: an unusually large increase in dominance variance for viability in comparison with additive variance with the accumulation of mutations on 140 randomyl sampled, inversion-free second chromosomes. Mutations were accumulated only through males heterozygous for the Pm-carrying chromosome [In(2LR)bwV1] and the extracted second chromosomes, and the genetic variance components were estimated by using a partial diallel cross method.--Further investigations clarified that chromosome abberations occurred at a frequency of 0.0114 per second chromosome per generation (inversions: 0.0098; transpositions: 0.0011; translocation: 0.0004), and recessive lethal mutations occurred at an average rate of 0.031 per second chromosome per generation.--From these results and from the amount of change in the homozygous load, it was speculated that about 60--70% of the second chromosomes used had a kind of mutator which induced chromosome and/or chromatid breaks at a minimum rate of 0.18 per second chromosome per generation. These breaks resulted in recessive lethal mutations at a rate more than ten times higher than the normal rate. Also these breaks were most probably the cause of male recombination.--The above unusual increase in dominance variance can be explained by assuming that chromosome segments, introduced into the extracted "wild" chromosomes by male recombinations (double crossover) from the marker chromosomes [In(2LR)bwV1], showed heterosis and linkage disequilibria with deleterious mutations and possibly with other introduced segments.--Finally, the nature and possible significance of mutator factors are discussed.

The genetic variance for viability and its components in a local population of Drosophila melanogaster.

Two hundred and ninety second chromosomes extracted from a natural population of Drosophila melanogaster were analyzed to estimate the genetic variance of viability and its components by means of a partial diallel cross (Design II of Comstock and Robinson 1952). The additive and dominance variances are estimated to be 0.009 and 0.0012. Using the dominance variance and the inbreeding depression, the effective number of overdominant loci contributing to the variance in viability is estimated to be very small, a dozen or less. Either the actual number of loci is small, or the distribution of viabilities is strongly skewed with a large majority of very weakly selected loci. The additive variance in viability appears to be too large to be accounted for by recurrent harmful mutants or by overdominant loci at equilibrium with various genetic parameters estimated independently. The excess might be due to frequency-dependent selection, to negative correlations between viability and fertility, or possibly to the presence of a mutator. The selection for viability and fertility, or possibly to the presence of a mutator. The selection for viability at the average polymorphic locus must be very slight, of the order of 10(-3) or less.