A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers

Abstract

To generate a domestic horse genome map we integrated synteny information for markers screened on a somatic cell hybrid (SCH) panel with published information for markers physically assigned to chromosomes. The mouse-horse SCH panel was established by fusing pSV2neo transformed primary horse fibroblasts to either RAG or LMTk mouse cells, followed by G418 antibiotic selection. For each of the 108 cell lines of the panel, we defined the presence or absence of 240 genetic markers by PCR, including 58 random amplified polymorphic DNA (RAPD) markers and 182 microsatellites. Thirty-three syntenic groups were defined, comprised of two to 26 markers with correlation coefficient (r) values ranging from 0.70 to 1.0. Based on significant correlation values with physically mapped microsatellite (type II) or gene (type I) markers, 22 syntenic groups were assigned to horse chromosomes (1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 15, 18, 19, 20, 21, 22, 23, 24, 26, 30, X and Y). The other 11 syntenic groups were provisionally assigned to the remaining chromosomes based on information provided by heterologous species painting probes and work in progress with type I markers.

A Primary Male Autosomal Linkage Map of the Horse Genome

“…The assignments of SGCV17 and SGCV32 to linkage groups on ECA10 and ECA6, respectively (supported by lod scores of 9.98 for SGCV17 and of 7.72 for SGCV32), contradict both their reported FISH mapping to ECA9 (Godard et al 1997). By somatic cell hybrid mapping, Shiue et al (1998) similarly placed SGCV17 on ECA10, giving support to our linkage data. New FISH experiments with the SGCV17 and SGCV32 cosmids indicate that they may indeed map to ECA10 and ECA6, respectively (G. Guérin, pers.…”

“…Chromosomal assignments of linkage groups are based on one or more of the markers being physically mapped by in situ hybridization (vertical bars close to chromosomes). The only exceptions are the LEX30-LEX39-MPZ027-LEX20 linkage group on ECA1, the HMS5-HTG15-ASB10-LEX34-LEX14-PGM linkage group on ECA5, the SGCV28-LEX15-LEX38 linkage group on ECA7, the HTG4-HMS3-HTG8 linkage group on ECA9, and HMS20-HTG13 on ECA16, which chromosomal assignments are based on synteny data (Shiue et al 1998; see also Bailey et al 1997;Godard et al 1997). The assignment of the HMB2-HMS1 group to ECA15 is based on a previously observed linkage between one of these markers and physically anchored markers on this chromosome (Godard et al 1997).…”

Genetic diversity of two Brazilian populations of the Pampas deer (Ozotoceros bezoarticus, Linnaeus 1758)

“…Among these, are the numerous loci that can be assayed at relatively low cost and without previously knowledge of its genome, the sampling of the whole genome, and their high polymorphism (Perez-Sweeney et al, 2003). In mammals, RAPD technique has been used to solve several tasks like hybridization detection (Tsvirka et al, 2006), species diagnosis (Martinez and Danielsdottir, 2000;Basckevich et al, 2004), genetic mapping (Shiue et al, 1999), evaluation of genetic diversity and population differentiation (Petrosyan et al, 2002;Spiridonova et al, 2004), and determination of systematic relationships between taxa (Bellinvia et al, 1999;Mishra et al, 2002).…”

Mapping the horse genome and its impact on equine genomics for identification of genes for monogenic and complex traits – a review

“…While there had been five synteny panels in the horse since 1992 (LEAR et al, 1992;WILLIAMS et al, 1993;BAILEY et al, 1995;RANEY et al, 1998), the most important one was the UC Davis panel generated by SHIUE et al (1999). It included 450 markers and represents the origin for the developed horse-human comparative maps (CAETANO et al, 1999). A 3000-rad panel was developed by KIGUWA et al (2000).…”

“…There are three equine genomic BAC-libraries available: the equine BAC library of the Children`s Hospital of Oakland Research Institute, CHORI-241 (GODARD et al, 1998), one generated by the Texas A&M University (TAMU) and the other by the Institut de la National Recherche Agronomique (INRA-LGBC library) . CAETANO et al (1999) published an extensive comparative map between horse and man containing 68 equine type I loci. The most topical comparative map between horse, donkey and human was generated by cross-species painting (YANG et al, 2004).…”