Interallelic recombination is probably responsible for the occurrence of a new αs1-casein variant found in the goat species

The as1-casein (as1-Cas) locus in the goat is characterized by a polymorphism, the main feature of which is to be qualitativeaswellasquantitative.Asystematicanalysisperformed in an autochthon southern Italy breed identified a new rare allele (M), which was characterized at both the protein and genomic level. The M protein displays the slowest electrophoretic mobility of the as1-Cas variants described so far. MS and automated Edman degradation experiments showed that this behavior was due to the loss of two phosphate residues in the multiple phosphorylation site (64S P -S P S P -S P -S P -E-70E) consecutively to a Ser fi Leu substitution at position 66 of the peptide chain (64S-S P -L-S P -S P -E-70E). This was confirmed by sequencing a genomic DNA fragment encompassing exon 9 where the 8th codon (TCG) was shown to be mutated to TTG. Sequencing of amplified genomic DNA segments spanning the 5¢ and 3¢ flanking regions of each exon allowed us to identify 23 single nucleotide polymorphisms and two insertion/deletion events in thecodingaswellasthenoncodingregions.Acomparisonof specific haplotypes defined for each of the as1-CasF, A and M alleles indicates that the M allele probably arises from interallelic recombinationbetweenalleles AandB2,followed by a C fi T transition at nucleotide 23 of the ninth exon. The region encompassing the recombination break point was putatively located between nucleotide 86 upstream and nucleotide 40 downstream of exon 8. Interallelic recombination therefore appears to be a possible means of generating allelic diversity at the as1-Cas locus, at least in the goat. The previously proposed molecular phylogeny must now be revised, possibly starting from two ancestral allelic lineages.