Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

Abstract

Microsatellites are widely applied in population and forensic genetics, wildlife studies and parentage testing in animal breeding, among others, and recently, high-throughput sequencing technologies have greatly facilitated the identification of microsatellite markers. In this study the genomic data of Cervus elaphus (CerEla1.0) was exploited, in order to identify microsatellite loci along the red deer genome and for designing the cognate primers. The bioinformatics pipeline identified 982,433 microsatellite motifs genome-wide, assorted along the chromosomes, from which 45,711 loci mapped to the X- and 1096 to the Y-chromosome. Primers were successfully designed for 170,873 loci, and validated with an independently developed autosomal tetranucleotide STR set. Ten X- and five Y-chromosome-linked microsatellites were selected and tested by two multiplex PCR setups on genomic DNA samples of 123 red deer stags. The average number of alleles per locus was 3.3, and the average gene diversity value of the markers was 0.270. The overall observed and expected heterozygosities were 0.755 and 0.832, respectively. Polymorphic Information Content (PIC) ranged between 0.469 and 0.909 per locus with a mean value of 0.813. Using the X- and Y-chromosome linked markers 19 different Y-chromosome and 72 X-chromosome lines were identified. Both the X- and the Y-haplotypes split to two distinct clades each. The Y-chromosome clades correlated strongly with the geographic origin of the haplotypes of the samples. Segregation and admixture of subpopulations were demonstrated by the use of the combination of nine autosomal and 16 sex chromosomal STRs concerning southwestern and northeastern Hungary. In conclusion, the approach demonstrated here is a very efficient method for developing microsatellite markers for species with available genomic sequence data, as well as for their use in individual identifications and in population genetics studies.

Genetic traces of dispersal and admixture in red deer (Cervus elaphus) populations from the Carpathian Basin

“…Our previous studies with STRs have shown the existence of two distinct groups of red deer within Hungary (Szabolcsi et al 2014) and that red deer migrated into the Carpathian Basin from two directions, the west and the south (Frank et al 2017). The presence of two clades for mitochondrial lineages and Y-chromosomes was also demonstrated (Frank et al 2017(Frank et al , 2020, and concordant results were also presented by studies on mitochondrial cytochrome-b sequences (Markov et al 2015).…”

A Microsatellite Genotyping-Based Genetic Study of Interspecific Hybridization between the Red and Sika Deer in the Western Czech Republic

“…Our paper therefore most likely embodies only the second attempt at a relevant genetic analysis, performed by utilizing DNA-based methods. The research within this study exploits some of the primers developed for bovine and ovine markers, as the relevant microsatellites are often utilized in genetic analyses of the sika and other deer species, the reason being that they are conserved well in Artiodactyla [27,67]. Even though we used fewer neutral markers than the authors of the earlier genetic studies (11 compared to 13, 14, and 22), all of the H E values detected within our sika samples (0.68) exceeded those reported formerly, considering the H E = 0.48 for Poland, Russia, and Lithuania [21] besides the H E = 0.47 in the case of the Czech Republic [68].…”

“…This paper was therefore conceived to examine the presumed crossbreeding of sikas with native red deer by exploiting a genetic panel of microsatellite markers. Microsatellites are popular markers for the study of geographical structure and gene flow because they are co-dominant, multi-allelic, and abundant with a wide genome coverage [22,27]. To date, the hybridization of the deer in free-ranging areas has been explored mainly in the UK, where the morphometric and subsequent genetic analyses proved that the actual existence of the hybrids constitutes not a merely potential threat, but rather a real, unexpectedly widespread problem [15,16,20,23].…”

Molecular Sexing and Species Detection of Antlered European Hunting Game for Forensic Purposes

“…This is the case not only for humans or primates, but for other species as well. A complementary sexing protocol developed for detection of the X and Y chromosome linked Amelogenin gene or STR markers can disambiguate the confirmation of analytical results on the SRY gene [43,44].…”