F. Chegdani

Assessing SNP markers for assigning individuals to cattle populations

The effectiveness of single nucleotide polymorphisms (SNPs) for the assignment of cattle to their source breeds was investigated by analysing a panel of 90 SNPs assayed on 24 European breeds. Breed assignment was performed by comparing the Bayesian and frequentist methods implemented in the STRUCTURE 2.2 and GENECLASS 2 software programs. The use of SNPs for the reallocation of known individuals to their breeds of origin and the assignment of unknown individuals was tested. In the reallocation tests, the methods implemented in STRUCTURE 2.2 performed better than those in GENECLASS 2, with 96% vs. 85% correct assignments respectively. In contrast, the methods implemented in GENECLASS 2 showed a greater correct assignment rate in allocating animals treated as unknowns to a reference dataset (62% vs. 51% and 80% vs. 65% in field tests 1 and 2 respectively). These results demonstrate that SNPs are suitable for the assignment of individuals to reference breeds. The results also indicate that STRUCTURE 2.2 and GENECLASS 2 can be complementary tools to assess breed integrity and assignment. Our findings also stress the importance of a high-quality reference dataset in allocation studies.

MOLECULAR DETECTION OF CELL LINE CROSS-CONTAMINATIONS USING AMPLIFIED FRAGMENT LENGTH POLYMORPHISM DNA FINGERPRINTING TECHNOLOGY

SummaryWe have tested amplified fragment length polymorphism (AFLP) technology, in comparison with isoenzyme analysis, for the simultaneous detection of inter-and intraspecific cell line cross-contaminations (CCCs) in the cell line collection held at the Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna. Isoenzyme analysis identified four cases of interspecific CCCs. In a single expreiment, AFLP was able to identify the species of origin of all cell lines for which a reference genomic deoxyribonucleic acid was available and to detect five interspecific contaminations. Four CCCs confirmed data on isoenzymes, whereas the fifth CCC was detected in a species for which isoenzyme analysis was noninformative. In addition, AFLP was able to identify the putative source of the contaminations detected. The utility of the technology in the detection of intraspecific cell line contaminations, depends on the number of cell lines that have to be distinguished in a specific species and on the availability of highly informative fingerprinting systems. In mice, a single AFLP primer pair produced 16 polymorphisms and distinguished all the 15 strains of mouse cell lines analyzed. In humans, 18 AFLPs identified 83 different profiles in the 159 cell lines analyzed. Amplified fragment length polymorphism can conveniently be applied for cell line fingerprinting in species for which hypervariable markers are not available. In species for which a highly informative multiplex of microsatellite markers is available, AFLP can still provide a useful and cheap tool for simultaneously testing inter-and intraspecific contaminations.

Single nucleotide polymorphisms in collagen genes and association with skin quality trait

Abstract Livestock skin is largely employed in the manufacturing of clothing and shoes, sector in which Italy is a world leader. To sustain Italian products against foreign competition in the globalization era particular attention is to be focus on product quality. Here we investigate the association of SNP mutations in genes coding for collagen proteins present in animal skin with a number of phisico-chemical parameters influencing skin quality for the tanning industry. Skin and blood were sampled from 73 Italian Friesian and Italian Brown bovines and from 43 Bergamasca and Sarda ovines, classified by sex and age. Skins were characterised for a set of chemico-physical parameters (thickness, density, humidity, protein content, ashes, lipid content, hydrossi-proline and DNA content). Regions of the collagen type I, III and IV were screened for SNP discovery in the two species by sequencing a set of reference animals. In bovine 15 polymorphisms were identified: (2 in collagen type I, 9 in collagen type III alpha 2; 4 in collagen type IV alpha 3). In ovine 21 SNPs were detected (7 for collagen type I, 7 in collagen type III alpha 2, 8 in collagen type IV alpha 3). Association analysis between SNP variants and traits was carried out by single marker ANCOVA within species, considering the breed as categorical predictor and the age in months as continuous predictor. One SNP in ovine and two in bovines resulted significantly associated (P <0,05) with one or more skin traits.