C. Lisa

Molecular genetics in aquaculture.

Abstract Great advances in molecular genetics have deeply changed the way of doing research in aquaculture, as it has already done in other fields. The molecular revolution started in the 1980’s, thanks to the widespread use of restriction enzymes and Polymerase Chain Reaction technology, which makes it possible to easily detect the genetic variability directly at the DNA level. In aquaculture, the molecular data are used for several purposes, which can be clustered into two main groups. The first one, focused on individuals, includes the sex identification and parentage assignment, while the second one, focused on populations, includes the wide area of the genetic characterization, aimed at solving taxonomic uncertainties, preserving genetic biodiversity and detecting genetic tags. For the future, the increase in the number of molecular markers and the construction of high density genetic maps, as well as the implementation of genomic resources (including genome sequencing), are expected to provide tools for the genetic improvement of aquaculture species through Marked Assisted Selection. In this review the characteristics of different types of molecular markers, along with their applications to a variety of aquaculture issues are presented.

Genetic characterization of the Bardigiano horse using microsatellite markers

Abstract The study was aimed at investigating the genetic structure of the Bardigiano horse and its relationships with the Haflinger, Maremmano and Arabian breeds using 11 microsatellite markers. A total of 94 alleles were detected across the breeds, with a mean of 8.5 alleles per locus and a mean observed heterozygosity of 0.69. Compared to the other breeds, the Bardigiano horse showed quite a high genetic variability, as indicated by the mean number of alleles (7.0 vs 6.1÷7.6) and by the observed heterozygosity (0.72 vs 0.66÷0.71). Moreover, the genotype distributions in the Bardigiano groups of different sex and age were not significantly different. The overall Fst value showed that the genetic differences among breeds accounted for 7.8% (P=0.001) of the total variation, and the pairwise Fst values were all significant. The assignment test allocated between 96.8 and 98.9% of the individuals to the population they were collected from, with a mean probability of assignment of about 97% for all breeds, except for the Arabian, where it approached 100%. The results have highlighted that the Bardigiano breed has a high within and between breed variability, which is considerably more than could be expected by looking at its evolution history. This justifies the need for the development of additional breeding strategies to preserve the existing genetic variability.

PCR–RFLP analysis of mitochondrial DNA in tench Tinca tinca

Polymorphism was detected at ND1, ND6, D-loop and cyt b segments of mtDNA in 105 tench (Tinca tinca L.), using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique and five composite haplotypes were identified. The diversity indices and the results of the population comparisons revealed that the identified markers provide a powerful tool for further studies on this species.

Genetic variability in tench (Tinca tinca L.) as revealed by PCR-RFLP analysis of mitochondrial DNA

Four mitochondrial DNA segments, ND1, ND6, cyt b and D-loop, were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 14 tench (Tinca tinca L.) populations located in Europe and Asia; data on 5 Italian populations previously analyzed for the same mtDNA segments were also included in the study. All the considered segments were polymorphic and originated a total of 9 composite haplotypes which were clustered into 2 haplogroups, A and B, possibly corresponding to the Western and Eastern phylogroups previously described in tench. Nine out of 19 populations showed polymorphism, with haplotype diversity ranging from 0.246 to 0.643 and nucleotide diversity from 0.009 to 0.078. Seventy-five percent of the pairwise comparisons were significant, indicating a high between-population variability. The Neighbour-Joining tree revealed the presence of 3 clusters, including pure populations, with only a A or B haplogroup, and mixed populations, with both haplogroups. The possibility of identifying populations with different haplotypes has practical implications for both conservation and supportive stocking.

Variability of μ-Calpain and Calpastatin genes in cattle

Abstract A preliminary analysis on the variability of μ-Calpain (CAPN1) and Calpastatin (CAST) genes in six cattle breeds was carried out, focusing the attention on CAPN1 g.5709C>G, CAPN1 g.6545C>T, and CAST g.282C>G SNPs, which have been suggested to affect beef tenderness in cattle. The results indicate that the two genes are polymorphic in all the analysed breeds, with significant between-breed differences. On the basis of their variability, only CAPN1 g.6545C>T and CAST g.282C>G SNPs seem appropriate to be considered as potential markers for beef tenderness.

Variability in candidate genes revealed associations with meat traits in the Piemontese cattle breed

In the last years an increasing number of associations between single nucleotide polymorphisms (SNPs) in candidate genes and production traits have been reported in beef cattle, but very often the results were not validated and few studies considered breeds homozygous for the allele responsible for the muscular hypertrophy. Therefore, we analysed the variability of 19 previously reported SNPs in 12 genes (GH, GHR, GDF8, GHRL, IGF2, LEP, LEPR, MYF5, NPY, POMC, UCP2, UCP3) in the hypertrophic Piemontese breed and investigated the effects of the observed polymorphisms on growth and conformation. Fourteen SNPs were polymorphic and a significant linkage disequilibrium was observed between SNPs in GHR, LEP and NPY genes, for which both single-SNP and haplotype effects were estimated. Negligible effects on the investigated traits were observed for GHRL, MYF5, NPY, POMC, UCP2 and UCP3 genes. The GHR gene significantly affected daily gain and its effect was further increased when haplotypes were considered. The C allele at LEP-1 and LEP-2 had moderate negative effects on the considered traits, whereas the C allele at LEP-3 mostly had positive effects; haplotypes in the LEP gene showed weaker but favourable associations with all the traits. The C allele at IGF2 and LEPR had favourable effects on daily gain and negative effects on meat conformation traits. The associations observed for GHR and LEP were consistent with those of previous studies, providing additional evidence of their usefulness as markers. Practical aspects of the applications to the breeding programme of the Piemontese breed need to be examined.

Variability of Leptin gene promoter in cattle

Abstract A preliminary analysis on the variability of Leptin gene promoter in seven cattle breeds was carried out, focusing the attention on the SNP at nt 1759, which has been suggested to affect some quantitative traits in cattle. In addition, the linkage disequilibrium with the C305T mutation in exon 2 of Leptin gene was tested. The results indicate that the Leptin gene promoter is polymorphic in all the analysed breeds, with significant betweenbreed differences. Pairwise comparison of genotypes at the two considered SNPs revealed a significant linkage disequilibrium, with the presence of the haplotypes 1759C - 305T and 1759G - 305C.