Short communication A reliable method for characterization of the goat CSN1S1 E allele M.L. Dettori, G.M. Vacca ⁎, V. Carcangiu, M. Pazzola, M.C. Mura, A.M. Rocchigiani Dipartimento di Biologia Animale, Università degli Studi di Sassari, via Vienna 2, 07100, Sassari, Italy article info abstract Article history: Received 16 September 2008 Received in revised form 11 March 2009 Accepted 18 March 2009 Goat αs 1 -casein, coded by the CSN1S1 gene, is a highly polymorphic protein. The E allele is characterized by the insertion of a long interspersed nuclear element (LINE) in the 19th exon of the gene. This insertion is probably responsible for the reduced levels of αs 1 -casein found in milk from animals expressing the E allele. The present study aimed to develop a robust method for the detection of the CSN1S1 E allele in goat genomic DNA, using a one-step allele-specific polymerase chain reaction (AS-PCR). Three primers were designed, based on published DNA sequences (GenBank: AJ504710 and X72221). The primers were used simultaneously in the amplification reaction. Genomic DNA samples from animals with known CSN1S1 AA, EE and AE genotypes were used as positive controls. The DNA fragments were analysed by agarose gel electrophoresis, and were found to be of the expected sizes. The fragment characterizing the A⁎ allele (A⁎ refers to the αs 1 -casein alleles bearing an intact 19th exon) was 583 bp long, and the fragment characterizing the E allele was 437 bp long, spanning part of the 18th intron, part of the 19th exon and 146 bp of the LINE inserted sequence. This method allows clear identification of the three genotypes of CSN1S1 (A⁎A⁎,A⁎E and EE) using a one-step PCR. Using this method, the frequency of the CSN1S1 E allele in a population of 300 Sarda goats was estimated to be 0.037. © 2009 Elsevier B.V. All rights reserved. Keywords: Goat CSN1S1 E AS-PCR Polymorphism 1. Introduction The goat caseins (αs 1 -, β-, αs 2 -, κ-casein) are coded by the single autosomal genes, CSN1S1 , CSN2, CSN1S2, CSN3, which cluster in a DNA segment of about 250 kbp, mapped to chromosome 6 (Rijnkels, 2002). All casein fractions are characterized by high variability (Sacchi et al., 2005). At least 16 alleles are known to occur at the CSN1S1 locus, and these are associated with different levels of αs 1 -casein in goat milk. The CSN1S1 alleles A, B1, B2, B3, B4, C, H, L and M (‘strong’ alleles) are associated with a normal content of αs 1 - casein in milk (about 3.5 g/l), the I and E alleles are associated with an intermediate content (about 1.1 g/l), and the Fand G alleles with a low level of αs 1 -casein (about 0.45 g/l). The CSN1S1 N, 01 and 02 alleles are “null” alleles, and are associated with the apparent absence of αs 1 -casein in milk (Bevilacqua et al., 2002; Ramunno et al., 2005). The extensive polymorphism at the αs 1 -casein locus has been shown to affect not only the quantity of casein in goat milk, but also the structural and nutritional characteristics and technological properties of the milk (Ramunno et al., 2007). The compar- ison between milks from homozygous CSN1S1 AA, EE, and FF (A, E and F milks) goats showed that the A milk had a higher protein, casein and fat content, and a higher casein/protein ratio than the E milk, while the F milk had the lowest values (Vassal et al., 1994; Remeuf, 1993). The CSN1S1 genotype strongly affects casein micelle size (A b E b F) and, to a lesser extent, their degree of mineralization (Remeuf, 1993). Important differences have been evidenced in the technolo- gical behaviour of milk, for rennet gel strength and gel strengthening rate, being the A milk higher than E, and E higher than F (Remeuf, 1993). Cheeses made from the A milk type had higher yields than the F ones, while the E milk showed intermediate values. Cheeses made with A milk had a lower fat content, firmer curds and a typical flavour of goat cheese less intense than the others (Vassal et al., 1994). Therefore, goats having a different αs 1 -casein genotype may produce milk with different chemical composition and processing properties, this implies the possibility to control Livestock Science 125 (2009) 105–108 ⁎ Corresponding author. Tel.: +39 079229442; fax: +39 079229592. E-mail address: gmvacca@uniss.it (G.M. Vacca). 1871-1413/$ – see front matter © 2009 Elsevier B.V. All rights reserved. doi:10.1016/j.livsci.2009.03.007 Contents lists available at ScienceDirect Livestock Science journal homepage: www.elsevier.com/locate/livsci