Melanophilin Polymorphism of Exons 8 and 13 in Rabbits: Parent Breeds and Interbreed Cross Rodnik

New breeds of fur-bearing animals are multi-breed crosses. Selection requires new methods for genetic control. This article describes a new early-maturing and highly-productive crossbreed of rabbits called Rodnik obtained at the Afanasyev Research Institute for Fur Farming and Rabbit Breeding, Russia. It was a result of multi-stage generations of crossings between such breeds as White Giant, Soviet Chinchilla, and Californian. However, in terms of polylocus genotypes of highly polymorphic elements, the Rodnik rabbits are closer to the White Giant breed. The article describes the changes in the genetic pool of this three-breed cross through a comparative analysis of the nucleotide sequences of exons 8 and 13 of the melanophilin (mlph) color gene. The research featured the rabbit breeds of White Giant, Soviet Chinchilla, and Californian, as well as their Rodnik cross. The analysis of the mlph gene in Oryctolagus cuniculus involved bioinformatics methods based on the nucleotide sequence of the reference genome UM_NZW_1.0 (GCF_009806435.1) from the GenBank database. The exon-intron structure was determined using the Splign software; the conditions and stages of PCR, including the design of primers for exonic regions, were developed using the online version of BLAST3. Exons 8 and 13 made it possible to identify the differences between chinchilla-colored rabbits and other breeds. In some color properties, the Rodnik cross was closer to the Californian parent breed. A single nucleotide polymorphism (SNP) was detected in two nucleotides in exon 8 and in one nucleotide in exon 13. The haplotypes of two SNPs in exon 8 and one SNP in exon 13 of the mlph gene were homozygous and coincided with the White Giant breed. The Soviet Chinchilla and Californian breeds carried a heterozygous haplotype for two SNPs in exon 8, as well as in the homozygote of another nucleotide (C–T) in exon 13 in the same positions. The identified SNPs did not correlate with color. However, the Rodnik cross was closer to the White Giant in terms of genotypes and polymorphisms of some highly polymorphic genomic elements. The mlph gene might become part of selection as it belongs to the Ras oncogene superfamily and the largest exophilin subfamily of Rab effector proteins that coordinate vesicular transport and some adipogenesis stages.