Assessing genetic diversity in Italian goat populations using AFLP markers

Colostrum Quality in Different Goat Breeds Reared in Northern Italy

This study aimed to characterize the colostrum quality in three different local goat breeds of Northern Italy (i.e., Frisa Valtellinese, Orobica, and Lariana) and a cosmopolitan one (i.e., Camosciata delle Alpi) (n = 30 per breed), reared under traditional semi-extensive and intensive systems, respectively. Lariana showed the highest percentage of fat (10.18 ± 3.14%) and total solids (30.73 ± 4.89%) but the lowest percentage of lactose (1.87 ± 0.82%; p < 0.05); Orobica had the lowest percentage of fat (7.13 ± 2.48%), total solids (24.11 ± 5.48%), and protein (10.77 ± 4.53%) but the highest percentage of lactose (3.16 ± 0.73%; p < 0.05). This suggests that breeds which have a more pronounced meat aptitude (i.e., Frisa and Lariana) have a higher concentration of components than breeds with more dairy aptitude (i.e., Orobica and Camosciata). Uni- and multivariate analyses showed that IgG is the parameter that best differentiates local breeds from cosmopolitan ones (p < 0.01). Colostrum from Frisa goats showed the highest IgG concentration (100.90 ± 8.11 mg/mL), while the lowest concentration was in the Camosciata breed (74.75 ± 20.16 mg/mL). Finally, the highest lactoferrin concentration was in Frisa (1781.3 ± 892.6 µg/mL) and the lowest in Camosciata and Lariana (763.1 ± 357.9 and 1148.0 ± 858.6 µg/mL, respectively; p < 0.05). Differences between Camosciata and local breeds could be due to the different farming systems, in addition to the genetic characteristics. The higher quality of colostrum produced by some local goats could be an adaptive characteristic that helps the growth and survival of the kids.

Comparison of Female Verzaschese and Camosciata delle Alpi Goats' Hematological Parameters in The Context of Adaptation to Local Environmental Conditions in Semi-Extensive Systems in Italy

Local livestock breeds are pivotal to ensure sustainable agriculture and represent a real genetic resource in the context of genetic variability reduction. This study aimed at broadening the knowledge about hematological values in female Verzaschese and Camosciata delle Alpi goats (an Italian local and a cosmopolitan goat breed, respectively) and investigating factors affecting them (i.e., breed, age, season). Blood samples were collected monthly from 34 Verzaschese and 37 Camosciata delle Alpi female goats kept under the same semi-extensive farming system for a whole year. The main hematological parameters were evaluated, and descriptive as well as inferential statistical analyses were performed. Reference intervals for complete blood cell count were established and several inter-breed differences were found. In particular, most of the red blood cell parameters were higher in Verzaschese than Camosciata delle Alpi (p < 0.05) suggesting a greater gastrointestinal parasites’ resilience of the local breed. The age effect (p < 0.05) was consistent with the literature while the season effect (p < 0.05) could be explained by the melatonin immunostimulant action and gastrointestinal parasitism influence. Overall, differences in blood values could be attributed to physiological changes and adaptive strategies developed through centuries highlighting the remarkable rusticity and adaptation to the environment and farming system of the local breed.

Origin, demographics, inbreeding, phylogenetics, and phenogenetics of Karamaniko breed, a major common ancestor of the autochthonous Greek sheep

Greece has a long history in autochthonous sheep, the genetic ancestry of which has been associated with four subtypes known to inhabit Greece at the end of the nineteenth century. Among them, the Karamaniko breed is still surviving, however endangered. This study was designed in order to (a) determine the phylogenetic status, (b) to evaluate the levels of inbreeding, and (c) to assess the genetic basis of coat color of Karamaniko breed. For these purposes, the mitochondrial cyt b gene was sequenced, the AFLP methodology was applied, and the MC1R was genotyped, respectively, in 72 female sheep from the Karamaniko breed. Four different novel cyt b haplotypes were defined and three MC1R genotypes were scored, whereas inbreeding levels estimated using AFLPs by the means of relatedness coefficient (r) were 0.287, with gene diversity at the levels of 0.105. Phylogenetic analysis indicated an eastern Asian tropical and subtropical origin of the Karamaniko breed, close with breeds originating from central Turkey, or a clustering within western European or Mediterranean sheep, mirroring a recent genetic divergence, with a non-random spread towards the formation of lowland breeds. The MC1R genotypes were all associated with the white coat color, in which selective breeding has probably been based on traditional morphological characters. Finally, levels of inbreeding do not constitute an indication for a particular mating plan to prevent unpleasant phenomena such as inbreeding depression, probably because of the special attention paid by the farmers towards the avoidance of relative recurrent mating.

Genetic diversity in a unique population of dugong (Dugong dugon) along the sea coasts of Thailand

Dugong (Dugong dugon) populations have been shrinking globally, due in large part to habitat fragmentation, degradation and ocean pollution, and today are listed as Vulnerable by the IUCN. Thus, determining genetic diversity in the remaining populations is essential for conservation planning and protection. In this study, measures of inter-simple sequence repeat (ISSR) markers and mtDNA D-loop typing were used to evaluate the genetic diversity of 118 dugongs from skin samples of deceased dugongs collected in Thai waters over a 29-year period. Thirteen ISSR primers revealed that dugongs from the Andaman Sea and Gulf of Thailand exhibited more genetic variation in the first 12 years of the study (1990-2002) compared to the last decade (2009-2019). Dugongs from the Andaman Sea, Trang, Satun and some areas of Krabi province exhibited greater diversity compared to other coastal regions of Thailand. Eleven haplotypes were identified, and when compared to other parts of the world (235 sequences obtained from NCBI), five clades were apparent from a total 353 sequences. Moreover, dugongs from the Andaman Sea were genetically distinct, with a separate haplotype belonging to two clades found only in Thai waters that separated from other groups around 1.2 million years ago. Genetic diversity of dugongs in present times was less than that of past decades, likely due to increased population fragmentation. Because dugongs are difficult to keep and breed in captivity, improved in situ conservation actions are needed to sustain genetically healthy wild populations, and in particular, the specific genetic group found only in the Andaman Sea.

AFLP markers based genetic diversity and population structure analysis of Kadaknath: an indigenous black meat poultry breed of India

The current study is the first worldwide to assess the genetic diversity of Kadaknath poultry using amplified fragment length polymorphism (AFLP) markers. Out of total 96 accessions, four were outliers and 92 were Kadaknath accessions of which 30 were males, 62 were females. Of these, 74 were jet black, 7 penciled and 11 were golden feather color type of Kadaknath. High level of polymorphism (23.94%) was observed in 387 loci amplified using six AFLP primer combinations. The Jaccard's similarity coefficient ranged from 0.211 to 0.754 with an average dissimilarity of 0.517. Based on the neighbor-joining method of clustering, all accessions were clustered into seven major clusters which were not consistent with their respective geographical locations. The mean values of effective multiplex ratio, polymorphic information content, resolving power and marker index were 15.16, 0.38, 9.87 and 5.85 respectively. Further, the high log-likelihood score was produced when the number of populations (K) was set at 7 while carrying out the population STRUCTURE analysis, which was also congruent with clustering analysis based on genetic diversity. The extent of genetic diversity detected in this study could be used for germplasm selection and developing conservation strategies of pure breed of Kadaknath.

Genetic diversity and distance of Iranian goat breeds (Markhoz, Mahabadi and Lori) compared to the Beetal breed using inter-simple sequence repeat (ISSR) markers

Abstract. The aim of this study was to investigate the genetic diversity and structure in three Iranian native goat breeds (Markhoz, Mahabadi and Lori) and the Beetal imported breed using inter-simple sequence repeat (ISSR) markers and also to investigate ISSR markers' potential in order to genetically separate single (S) and twin-birth (T) subpopulations. Blood samples were collected from 210 animals for this purpose. In total, 16 primers were used, and finally 5 primers were selected based on the number of clear bands and the level of polymorphisms. The result of this study showed that 76 of 86 observed fragments were polymorphic. Genetic diversity for each breed ranged from 0.23 in the Beetal breed to 0.26 in the Markhoz breed; this represents a relatively similar genetic diversity in these breeds. An unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on the Nei's standard genetic distance between the breeds studied showed that three Iranian goat breeds (Mahabadi, Lori and Markhoz) were clustered closer together, while the Beetal breed formed a separate cluster. In the constructed dendrogram of the subpopulations, the S and T subpopulations of each breed were clustered together. The constructed dendrogram of the Beetal breed and the S and T subpopulations of all breeds studied showed a separate cluster for the Beetal breed as an imported breed and another cluster for the S and T subpopulations as Iranian native breeds. The current study showed that the ISSR markers studied had no potential to genetically separate S and T subpopulations. On the other hand, these ISSR markers can be used for the clustering of distinct populations.

Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip

BACKGROUND

Among the European countries, Italy counts the largest number of local goat breeds. Thanks to the recent availability of a medium-density SNP (single nucleotide polymorphism) chip for goat, the genetic diversity of Italian goat populations was characterized by genotyping samples from 14 Italian goat breeds that originate from different geographical areas with more than 50 000 SNPs evenly distributed on the genome.

RESULTS

Analysis of the genotyping data revealed high levels of genetic polymorphism and an underlying North-south geographic pattern of genetic diversity that was highlighted by both the first dimension of the multi-dimensional scaling plot and the Neighbour network reconstruction. We observed a moderate and weak population structure in Northern and Central-Southern breeds, respectively, with pairwise FST values between breeds ranging from 0.013 to 0.164 and 7.49 % of the total variance assigned to the between-breed level. Only 2.11 % of the variance explained the clustering of breeds into geographical groups (Northern, Central and Southern Italy and Islands).

CONCLUSIONS

Our results indicate that the present-day genetic diversity of Italian goat populations was shaped by the combined effects of drift, presence or lack of gene flow and, to some extent, by the consequences of traditional management systems and recent demographic history. Our findings may constitute the starting point for the development of marker-assisted approaches, to better address future breeding and management policies in a species that is particularly relevant for the medium- and long-term sustainability of marginal regions.

On the way to functional agro biodiversity: coat colour gene variability in goats

Functional agro biodiversity defines the exploitation of biodiversity to provide ecosystem services, support sustainable agricultural production and benefit the regional and global environment and the public at large (ELN-FAB, 2009; www.eln_fab.eu). Tracking of animal products back to the breed of origin based on their genetic make-up undoubtedly falls in this category. The aim of this paper was to identify and validate a set of single nucleotide polymorphisms (SNPs) in goat coat colour genes, most of which have not been investigated before, to trace five goat populations of the Italian Alps and their product. Several regions of 28 genes influencing coat colour pathways were amplified in eight animals (two per breed). Sequence comparison revealed 48 SNPs and three INDEL (INsertion DELetion). No breed-specific alleles were detected; however, several SNPs showed an uneven frequency distribution between breeds. In BIO, the genotype frequency distribution of a non-synonymous SNP suggested a possible role of TYRP1 in brown eumelanic goat coat colour. A total of 29 independent SNPs in 20 genes were selected and used to allocate 159 minimally related goat samples using STRUCTURE 2.2 and GeneClass 2 software. STRUCTURE 2.2 assigns 99% of individuals to the correct breed considering the prior information on putative breed of origin for each sample and 81% using only the genotypic data. The three algorithms available in GeneClass 2 performed with nearly equal efficiency, with 86% and 87% correct allocations. All the methods yielded an average probability of assignment >0.92 and a specificity index >0.86. Despite their coat colour variability, individuals belonging to ORO were fully assigned, showing that, in the absence of a breed-specific allele tied to coat colour, the best assignment resulted for the most genetically distinct breed. The lowest rate of correct assignment was observed in Verzaschese (73%), not ascertained in the breed panel used in the SNP discovery phase.

Evaluation of confidence limit estimates of cluster analysis on molecular marker data

BACKGROUND

Diversity studies employ cluster analysis as a statistical tool, whereby relationships between individuals are shown in a dendrogram, mostly accompanied by bootstrap support for merging branches to indicate confidence limits. The objective of this study was to evaluate the reliability of the currently applied method of obtaining confidence limit estimates in cluster analysis and to propose an improved alternative bootstrap method.

RESULTS

It was illustrated via a simulation study that conventional bootstrap support for cluster analysis was affected by the sample size. The reliability of merging branches decreased with increasing number of individuals in the sample. Unlike the current bootstrap support for cluster analysis, the proposed method provides confidence intervals for the similarity coefficients between individuals. To facilitate the interpretation of similarity coefficients and confidence intervals, alternative graphical presentations are proposed for both 'similarity coefficients' and 'confidence interval range'.

CONCLUSION

The proposed bootstrap method is not affected by the number of individuals in the sample.

Genetic variability of six indigenous goat breeds using major histocompatibility complex-associated microsatellite markers

The present study aimed at analyzing the genetic variability of indigenous goat breeds (Capra hircus) using the MHC-associated microsatellite markers BF1, BM1818, BM1258, DYMS1, and SMHCC1. The following breeds were included: Chinese Xuhuai, Indian Changthangi and Pashmina, Kenyan Small East African (SEA) and Galla, and Albanian Vendi. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from nine in the Galla to 14.5 in the Vendi breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.483 in the Vendi to 0.577 in the Galla breed, and from 0.767 in the SEA to 0.879 in the Vendi breed, respectively. Significant loss of heterozygosity (p < 0.01) indicated that these loci were not in Hardy-Weinberg equilibrium. The mean F(IS) values ranged from 0.3299 in the SEA to 0.4605 in the Vendi breed with a mean value of 0.3623 in all breeds (p < 0.001). Analysis of molecular variance indicated that 7.14% and 4.74% genetic variation existed among the different breeds and geographic groups, whereas 92.86% and 95.26% existed in the breeds and the geographic groups, respectively (p < 0.001). The microsatellite marker analysis disclosed a high degree of genetic polymorphism. Loss of heterozygosity could be due to genetic drift and endogamy. The genetic variation among populations and geographic groups does not indicate a correlation of genetic differences with geographic distance.

Small ruminant lentivirus genotype E is widespread in Sarda goat

The highly divergent SRLV genotype E has recently been characterized in Italy as a low pathogenic caprine lentivirus in the Roccaverano breed. The availability of a genotype specific diagnostic test based on a comparative assay, using a combination of genotype specific recombinant antigens allows a wide serosurvey in other goat populations. The island of Sardinia still has the highest small ruminant population of any Italian region and crossbreeding has been limited to goats, mainly with the Maltese breed. A serological survey was carried out on sheep flocks and goat herds, using individual sera as well as a bulk milk-adapted procedure. Genotype E was identified in more than 50% of goat herds and none of the sheep flocks thus supporting the idea that this genotype is specifically associated with the goat species. The full-length proviral sequence of a Sardinian isolate revealed and confirmed the deletion of dUTPase subunit and the absence of both vpr gene and the 71bp repeat of the LTR. Genetic similarity of this isolate with the prototype strain Roccaverano was not more than 84%, supporting the designation of two subtypes within genotype E. Nevertheless, in vitro properties of the Sardinian strain were different from those of the Roccaverano strain in terms of ability to infect synovial membrane and produce syncitia. Remarkable differences in the HV1 and HV2 of the env gene were recorded, with the Sardinian isolate displaying sequence motif more similar to arthritic strains. Data presented suggest diffusion of genotype E is wider than previously thought.

AFLP fingerprinting for paternity testing in ducks

1. The accuracy and reproducibility of AFLP fingerprinting was investigated in the duck (Anas Platyrhynchos), using a multicolour fluorescent labeling technique. The fluorescent labelling fragments were separated on a capillary electrophoresis-base ABI PRISM 3100 Genetic Analyzer. 2. A total of 337 AFLP peaks with 103 of them being polymorphic markers were generated by 16 sets consisting of EcoRI/TaqI primer pair combinations. The number and size range of AFLP polymorphisms detected per primer pair varied from 3 to 11 and 58 to 290 bp, respectively. About 30.6% (103/337) of AFLP peaks were detected polymorphisms, with an average of 6.4 polymorphic markers per primer pair. 3. The clear polymorphic peaks were amplified with EcoR+AC/Taq+AC primer combinations. The AFLP peaks showed high reproducibility. From the family testing, we found that the fingerprints of all the offspring were derived from one or other parent. Therefore, we conclude that AFLP fingerprinting might be a suitable method for duck paternity testing.

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.

AFLP analysis of genetic diversity of the endangered species Sinopodophyllum hexandrum in the Tibetan region of Sichuan Province, China

Amplified fragment length polymorphism (AFLP) markers were used to estimate the genetic diversity of seven wild populations of Sinopodophyllum hexandrum (Royle) Ying from the Tibetan region of Sichuan Province, China. Six primer combinations generated a total of 428 discernible DNA fragments, of which 111 were polymorphic. The percentage of polymorphic bands (PPB) was 25.93 at the species level, and PPB within population ranged from 4.91 to 12.38%. Genetic diversity (H(E)) within populations varied from 0.01 to 0.04, averaging 0.05 at the species level. As revealed by the results of AMOVA analysis, 58.8% of the genetic differentiation occurred between populations, and 41.2% within populations. The genetic differentiation was, perhaps, due to the limited gene flow (Nm = 0.43) of the species. The correlation coefficient (r) between genetic and geographical distance using Mantel's test for all populations was 0.698 (P = 0.014). The UPGMA cluster analysis revealed a similar result in that the genetic distances among the populations show, to a certain extent, a spatial pattern corresponding to their geographic locations. On the basis of the genetic and ecological information, we propose some appropriate strategies for conserving the endangered S. hexandrum in this region.

Assessing genetic diversity in indigenous Veneto chicken breeds using AFLP markers

Genetic variation in four indigenous chicken breeds from the Veneto region of Italy was assessed using amplified fragment length polymorphism (AFLP) markers. A total of 99 individuals were analysed using three AFLP primer combinations that produced 70 polymorphisms. Four indigenous Veneto chicken breeds (Ermellinata, Padovana, Pépoi and Robusta) and a reference broiler line were included in the analysis. Breed-specific markers were identified in each breed. The expected heterozygosity did not differ significantly among the indigenous Veneto chicken breeds and the broiler line. The coefficient of gene variation (Gst) value across loci indicated that almost half of the total variability was observed among breeds. Nei's standard genetic distance between pairs of breeds showed that the distance between the broiler line and the Pépoi breed was greater than the distances between the broiler line and the other three chicken breeds. Cluster analysis based on standard genetic distances between breeds indicated that the Padovana and Pépoi breeds were closely related. Factorial analysis based on a binary matrix of the AFLP data showed a clear distinction of all breeds.

Use of amplified fragment length polymorphism (AFLP) markers in surveys of vertebrate diversity

The amplified fragment length polymorphism (AFLP) technique is one of the most informative and cost-effective fingerprinting methods. It produces polymerase chain reaction (PCR)-based multi-locus genotypes helpful in many areas of population genetics. This chapter focuses on technical laboratory information to successfully develop the AFLP technique for vertebrates. Several AFLP protocols are described, as well as recommendations about important factors of the procedure such as the choice of enzyme and primer combinations, the choice and scoring of markers, the influence of the genome size on the AFLP procedure, and the control and estimation of genotyping errors. Finally, this chapter proposes a troubleshooting guide to help resolve the main technical difficulties encountered during the AFLP procedure.

Genetic Diversity and Genetic Structure of an Endangered Species, Trillium tschonoskii

The genetic diversity and genetic structure of Trillium tschonoskii (Maxim) were investigated using amplified fragment length polymorphism markers. Eight primer combinations were carried out on 105 different individuals sampled from seven populations. Of the 619 discernible DNA fragments generated, 169 (27.3%) were polymorphic. The percentage of polymorphic bands within populations ranged from 4.52 to 10.50. Genetic diversity (H(E)) within populations ranged from 0.0130 to 0.0379, averaging 0.0536 at the species level. Genetic differentiation among populations was detected based on Nei's genetic diversity analysis (53.03%) and analysis of molecular variance (AMOVA) (52.43%). AMOVA indicated significant genetic differentiation among populations (52.43% of the variance) and within populations (47.57% of the variance) (p < 0.0002). Gene flow was low (0.4429) among populations. Species breeding system and limited gene flow among populations are plausible reasons for the high genetic differentiation observed for this species. We propose an appropriate strategy for conserving the genetic resources of T. tschonoskii in China.

How to track and assess genotyping errors in population genetics studies

Genotyping errors occur when the genotype determined after molecular analysis does not correspond to the real genotype of the individual under consideration. Virtually every genetic data set includes some erroneous genotypes, but genotyping errors remain a taboo subject in population genetics, even though they might greatly bias the final conclusions, especially for studies based on individual identification. Here, we consider four case studies representing a large variety of population genetics investigations differing in their sampling strategies (noninvasive or traditional), in the type of organism studied (plant or animal) and the molecular markers used [microsatellites or amplified fragment length polymorphisms (AFLPs)]. In these data sets, the estimated genotyping error rate ranges from 0.8% for microsatellite loci from bear tissues to 2.6% for AFLP loci from dwarf birch leaves. Main sources of errors were allelic dropouts for microsatellites and differences in peak intensities for AFLPs, but in both cases human factors were non-negligible error generators. Therefore, tracking genotyping errors and identifying their causes are necessary to clean up the data sets and validate the final results according to the precision required. In addition, we propose the outline of a protocol designed to limit and quantify genotyping errors at each step of the genotyping process. In particular, we recommend (i) several efficient precautions to prevent contaminations and technical artefacts; (ii) systematic use of blind samples and automation; (iii) experience and rigor for laboratory work and scoring; and (iv) systematic reporting of the error rate in population genetics studies.

Genetic diversity in recent elite faba bean lines using AFLP markers

Amplified fragment length polymorphism (AFLP) markers were used to study the genetic diversity among a large set (n = 79) of inbred lines of recent elite faba bean ( Vicia faba L.) cultivars with Asian, European (Northern and Southern) and North African origin. The inbred lines were analyzed using eight selected AFLP primer combinations that produced 477 polymorphic fragments. Errors when scoring repeated lanes of one pre-amplification reaction on one gel were negligible, whereas errors when scoring lanes of two individuals of the same inbred line run on different gels were markedly higher. Scoring across gels should be backed by replicates and several appropriate check entries. Based on clustering with Jaccard's similarity coefficient and Principal Coordinate Analysis, only the Asian lines were distinct as a group, the other lines showed no marked further grouping. Nevertheless, several known pedigree relationships were verified. A priori grouping of inbred lines (geographic origin and seed size) and AFLP data corroborate available information on the history of spread and cultivation of faba bean in the studied regions. Based on the diversity observed, studies especially concerning the relationship between genetic similarity based on AFLP markers and hybrid performance within the European elite germplasm have been launched.

Discrimination between selected lines of pigs using AFLP® markers

Amplified fragment length polymorphic (AFLP) markers were used to discriminate between lines of pigs, divergently selected over seven generations for components of efficient lean growth rate. A total of 270 animals with 30 animals per line were genotyped for 239 polymorphic AFLP markers. Canonical variate analysis identified linear combinations of the AFLP marker scores that grouped animals by selection line with no overlap between selection lines. Cluster analysis of AFLP marker scores identified 10 groups of animals with 226 of the 270 animals clustered into nine groups, each consisting of animals from only one selection line. AFLP marker genotyping, using the EcoRI and TaqI restriction enzymes, provided an effective means of discriminating between animals of different selection lines that have arisen from one base population.

In search of social phobia subtypes: similarity of feared social situations

The existence of subtypes of social phobia has been questioned. Although cluster analytic methods have been used to support various subtype models, a continuous model based on total number of feared social situations seems equally plausible. In a community sample, we calculated mean similarity measures for combinations of item pairs of feared social situations. Speaking fear items were significantly more similar to each other than to other items. There was also a trend for interaction fear items to be more similar to each other than to other items. These findings suggest that fear of speaking and interactional situations may represent distinct domains of socially feared situations. They should be considered separately in delineation of treatment response and may, if replicated in clinical samples, help identify meaningful subtypes of social phobia.

Identification on commercialized products of AFLP markers able to discriminate slow- from fast-growing chicken strains

The European chicken meat market is characterized by numerous quality marks: "Label de Qualité Wallon" in Belgium, "Label Rouge" in France, denominations of geographical origin, organic agriculture, etc. Most of those certified productions have specifications requiring the use of slow-growing chicken strains. The amplified fragment length polymorphism (AFLP) technique has been used to search molecular markers able to discriminate slow-growing chicken strains from fast-growing ones and to authenticate certified products. Two pairs of restriction enzymes (EcoRI/MseI and EcoRI/TaqI) and 121 selective primer combinations were tested on individual DNA samples from chicken products essentially in carcass form that were ascribed as belonging to either slow- or fast-growing strains. Within the resulting fingerprints, two fragments were identified as type-strains specific markers. One primer combination gives a band (333 bp) that is specific for slow-growing chickens, and another primer pair generates a band (372 bp) that was found to be characteristic of fast-growing chickens. The two markers were isolated, cloned, and sequenced. The effectiveness and the specificity of the two interesting determinants were assessed on individuals of two well-known strains (ISA 657 and Cobb 500) and on commercialized products coming from various origins.

Genetic distances within and across cattle breeds as indicated by biallelic AFLP markers

We tested the use of biallelic Amplified fragment length polymorphism (AFLP) polymorphisms for the estimation of relative genetic distances of cattle individuals within or across breeds. An allele permutation procedure was developed to estimate the stochastic variation of the genetic distance that is inherent to a given dataset. In a panel of 47 Holstein-Friesian cattle analysed with 248 polymorphic markers, the average genetic distance of bulls selected for breeding was slightly lower than the distance of the cows. The observed standard deviation (SD) of the distance indicated genetic subdivision, which for the bulls was explained by variation in the additive relationship derived from herdbook data. Animals from three different breeds, the highly selected Holstein-Friesian, the Italian Brown and the historic Maremmana, were compared on the basis of 106 polymorphic markers. No breed-specific fragments were observed. The mean pair-wise genetic distance within breeds was 85% of the value across breeds, but principal coordinates analysis clustered the animals according to their breed of origin. Calculation of distances between the breeds indicated a relatively divergent position of the Maremmana, relative to the two other breeds. However, biallelic markers indicate that the process of breed formation had only a limited effect on the diversity at marker loci.