icacgm18th International Colloquim of Animal Cytogenetics and Gene Mapping 2008

Session III - New Technologies and Microarray

Microarray analysis - a new era in cytogenetics ?

Darren K Griffin and Martin E Völker

University of Kent, Canterbury, UK.

Cytogenetics continues to impact significantly upon fundamental and applied areas of research and has essentially had three "eras" that are defined by specific technological advances. The classical era (heralded by the use of colchicine and hypotonic swelling) confirmed the chromosomal basis of sex in humans, of numerous genetic disorders and of karyotypic variation between organisms, in effect giving rise to the first comparative genomics. The banding era allowed us to examine karyotypic variation more closely, both intra-specifically (e.g. for clinical application) and inter-specifically. The FISH era bridged the gap between cytogenetics and molecular biology, advancing cytogenetics into gene mapping, chromosome painting, interphase cytogenetics, CGH and zoo-FISH. The advent of the microarray has now made it possible to enter a fourth era. While much microarray work is involved in transcription profiling, genome sequencing projects have spawned tiling path microarrays (essentially whole genomes "laid bare" on a slide in chromosomal order) that can be interrogated using an approach similar to FISH to address questions fundamental to the cytogeneticist. Central to such questions is copy number variation. A copy number variant (CNV) is a polymorphism in the number of copies of a DNA fragment that is ≥1 kb - in its broadest sense, from a small deletion or duplication to a trisomy or monosomy. Many CNVs are associated with phenotypic variation and numerous genomic disorders including well-characterised microdeletions and microduplications, they can also contribute to drug response, immune defence and disease resistance. Studies in primates have revealed numerous lineage-specific CNVs, providing evidence that they contribute to evolutionary adaptations and thus play an important role in genome evolution. The stage is set for the animal cytogeneticist to investigate the role of CNVs in the evolution and phenotypic variation of the animal or group of their choice.


Application Of A Microarray Technology To SNPs Detection Within Genes Involved In Milk Production

S. Chessa (1), D. Rignanese (1), G. Conte (2), M. Severgnini (3), G. Ceriotti (1), A. Caroli (4), G. Pagnacco (1) , B. Castiglioni (5)

(1) VSA, University of Milan , Milano (Italy);
(2) DAGA, University of Pisa, Pisa (Italy);
(3) ITB-CNR, Milano (Italy);
(4) DSBB, University of Brescia, Brescia (Italy);
(5) IBBA-CNR, Milano (Italy).

Milk proteins still arise much interest because of the proved effects of the most common milk genetic polymorphisms on quantitative and qualitative milk production, as well as on milk technological properties. The role of s1-casein (CSN1S1), -casein (CSN2), k-casein (CSN3) and -lactoglobulin (LGB) polymorphisms in the genetic improvement of milk production was already demonstrated in cattle. Other polymorphisms in the non-coding regions of the genes were found in association with milk traits. Hence, polymorphisms both at the coding and non-coding regions have to be considered in order to assess which ones are responsible for the variations in milk traits and could be included in breeding programs.

The microarray technology provides for an accurate, inexpensive and high-throughput assay highly suitable for the animal genotyping. Here we describe an application of this technology to the detection of SNPs (Single Nucleotide Polymorphism) at bovine genes involved in milk production in Brown Swiss cattle. Target sequences include CSN1S1, CSN2, CSN3, LGB, DGAT1 and SCD genes. A total of 24 polymorphic sites were included in the diagnostic microarray. To reconstruct the correct genotype the combination of the results at different SNP positions must be carefully analysed.