Evaluation of a new variant in the aggrecan gene potentially associated with chondrodysplastic dwarfism in Miniature horses

Chondrodysplastic dwarfism in Miniature horses is an autosomal recessive disorder previously associated with four mutations (D1, D2, D3*, and D4) in the aggrecan (ACAN) gene. The aim of this study was to identify additional variants in the candidate ACAN gene associated with chondrodysplastic dwarfism in Miniature horses. Fifteen dwarf Miniature horses were found to possess only one of the dwarfism-causing variants, and two possessed none of the variants. The ACAN exons (EquCab3.0) of seven dwarf Miniature horses were sequenced. A missense SNP in coding exon 11 (g.95271115A > T, c.6465A > T—RefSeq XM_005602799.2), which resulted in the amino acid substitution p.Leu2155Phe (RefSeq XP_005602856.2), was initially associated with the dwarf phenotype. The variant was tested and found present in 14 dwarf foals as well as one parent of each, and both parents of a dwarf possessing two copies. Genetic testing of 347 phenotypically normal Miniature horses demonstrated that none had more than one of the dwarf alleles or c.6465A > T. However, a study of large breeds revealed the presence of c.6465A > T, which was present in homozygosis in two Mangalarga Marchador horses. We suggest that c.6465A > T as a marker of disequilibrium or complex interactions in the Miniature horse genome could contribute to the associated dwarfism.

Runs of Homozygosity as Footprints of Selection in the Norik of Muran Horse Genome

The aim of this study was to analyse the genome-wide distribution of runs of homozygosity (ROH) segments in the genome of Norik of Muran horse and to identify the regions under strong selection pressure. Overall, 25 animals genotyped by the GGP Equine70k chip were included in the study. After SNP pruning, 54479 SNPs (75.72%) covering 2.25 Gb of the autosomal genome were retained for scan of ROH segments distribution. The ROHs were present in the genome of all animals and covered in average 13.17% (295.29 Mb) of autosomal genome expressed by the SNP loci. The highest number of ROHs was identified on autosome 1 (404), while the lowest proportion of autosome residing in ROH showed ECA31 (38). The footprints of selection, characterized by SNPs with extreme frequency in ROHs across specific genomic regions, were defined by the top 0.01 percentile of signals. Overall, nine genomic regions located on seven autosomes (3, 6, 9, 11, 15, 23) were identified. The strongest signal of selection showed three autosomes ECA3, ECA9 and ECA11. The protein-coding genes located within these regions suggested that the identified footprints of selection are most likely consequences of intensive breeding for traits of interest during the grading-up process of the Norik of Muran horse.

The identification and classification of endogenous retroviruses in the horse genome

Endogenous retroviruses (ervs) are sequences that derived from ancient retroviral infections of germ cells and integrated in humans, mammals and other vertebrates millions years ago. These ervs are inherited according to Mendelian expectations as all other genes in the genome. Coding sequences are flanked by two ltrs (long terminal repeat sequences). Most ervs are defective however some ervs still have open reading frames in their genome. These ervs settle close to functional genes or within the genes and can influence or control functions of the host genes using their ltrs. Most integration has deleterious effects. However some integration could be example of positive co-adaptation as syncitin. The first equine endogenous beta retrovirus which is ecerv-beta1 has been found in 2011 by Antoinette C.van der Kuyl1. The first known beta retrovirus and few pol gene similar to foamy retrovirus were only known endogenous retroviruses fixed in the domestic horse (equuscaballus) genome. Our aim of the study was to identify other endogenous retrovirus sequences in an equine genome and classify them into groups. Based on the high number of sines (equine repetitive element) in the horse genome we hypothesized that certain ervs will be located sufficiently close to sines that they will be amplified using an unbiased sine-pcr approach with degenerate primers. The nearest sine element was located 5.5 kbp upstream at the 5’of the ecerv-beta1. Pan-pol pcr was also used to find novel ervs based on 640 bp long region of pol gene which is the most conserved region of ervs. 27 complete and novel ervs that are 13 beta, 13 gamma, 1 spuma and 249 candidate endogenous retroviruses have been revealed using ltr_struc tool and double checked by retrotector online tool and ncbi-blast tool. It was proven that ecerv-beta1, which has 2 ltrs with 1% divergence between ltrs has a polymorphism among 13 different breeds.