Microsatellite markers for evaluating the diversity of the natural killer complex and major histocompatibility complex genomic regions in domestic horses

Abstract

Genotyping microsatellite markers represents a standard, relatively easy, and inexpensive method of assessing genetic diversity of complex genomic regions in various animal species, such as the major histocompatibility complex (MHC) and/or natural killer cell receptor (NKR) genes. MHC-linked microsatellite markers have been identified and some of them were used for characterizing MHC polymorphism in various species, including horses. However, most of those were MHC class II markers, while MHC class I and III sub-regions were less well covered. No tools for studying genetic diversity of NKR complex genomic regions are available in horses. Therefore, the aims of this work were to establish a panel of markers suitable for analyzing genetic diversity of the natural killer complex (NKC), and to develop additional microsatellite markers of the MHC class I and class III genomic sub-regions in horses. Nine polymorphic microsatellite loci were newly identified in the equine NKC. Along with two previously reported microsatellites flanking this region, they constituted a panel of 11 loci allowing to characterize genetic variation in this functionally important part of the horse genome. Four newly described MHC class I/III-linked markers were added to 11 known microsatellites to establish a panel of 15 MHC markers with a better coverage of the class I and class III sub-regions. Major characteristics of the two panels produced on a group of 65 horses of 13 breeds and on five Przewalski's horses showed that they do reflect genetic variation within the horse species.

Inter- and intrabreed diversity of the major histocompatibility complex (MHC) in primitive and draft horse breeds

“…Considering the location of the microsatellites in the chromosome and their correspondence to different MHC classes, the highest polymorphism was detected in MHC III microsattelites. In horses, MHC III genes are poorly characterized, although it is believed that, similar to humans [57], these genes encode heat shock proteins, complement components and cytokines, such as those of the tumor necrosis factor family [29]. Thus, the products of this MHC region play a central role in innate immune defense [57].…”

“…Intra-MHC microsatellites are well established tools for characterizing equine MHC [29][30][31][32][33][34][35] as well as for finding associations between specific MHC alleles and disease susceptibility [24,25,28]. In addition, MHC microsatellites can detect differences within and between MHCs of different horse breeds [33].…”

Newly identified variability of the antigen binding site coding sequences of the equine major histocompatibility complex class I and class II genes

“…However, this obstacle may be overcome by using long‐read (LR) sequencing approaches 25 . Although it is possible to assess the overall variability and diversity in this region by genotyping microsatellite (MSAT) loci within the MHC, 26 expressed MHC loci will always be the prime candidates for such studies. So far, mostly MHC class II genes have been analyzed in this context.…”

Microsatellite markers of the major histocompatibility complex genomic region of domestic camels

“…Genotyping microsatellite markers is an inexpensive and relatively easy method of assessing the genetic diversity of the MHC genomic regions in various animal species. MHC-linked microsatellite markers have been identified and some of them have been used for characterizing MHC polymorphism in various species, including domestic animals such as horses ( Sommer 2005 ; Horecky et al, 2018 ; Jaworska et al, 2020 ). Microsatellite loci distributed throughout the genomes of dromedaries have been identified ( Khalkhali-Evrigh et al, 2019 ).…”