Horse owners choose whether or not to train American Saddlebred horses (ASHs) to perform the 4-beat gaits called rack and slow gait. The rack and slow gait are similar to ambling gaits shown to be associated with variation in the DMRT3 gene in other breeds but are trained rather than naturally occurring gaits. A premature stop codon in the DMRT3 gene (DMRT3_Ser301STOP) caused by the Ch23:g.22999655C>A SNP has an effect on the pattern of locomotion in horses and allows for the pacing gait and strong association with performance of ambling gaits in diverse breeds. We used horse show records to identify ASHs trained to perform as 5-gaited horses and compared them to other Saddlebreds for the prevalence of the A allele of the Ch23:g.22999655C>A SNP of DMRT3. Genomic DNA was typed using a PCR-RFLP technique for 5-gaited ASHs (n = 55), 3-gaited or harness ASHs (n = 64) and ASHs not shown (n = 128). We did not observe differences in the frequencies of the Ch23:g.22999655C>A SNP of DMRT3 when comparing 5-gaited ASHs to other ASHs (P > 0.22). These results suggest that DMRT3 alleles do not affect the choice of breeders to train and show ASHs as 5-gaited horses.

Abnormalities of sexual development causing infertility in horses have been investigated since the early 1970's. Conventional cytogenetic analysis by karyotyping has been the primary tool used to investigate these horses. Abnormalities have a broad range, from a phenotypically normal mare with gonadal dysgenesis to a horse with ambiguous external genitalia and internal male and female organs. Cytogenetic analysis can determine genetic sex but cannot identify mutations or deletions of genes involved in the sex determination pathway. Molecular technologies have been developed to confirm cytogenetic results and to aid in identifying the genetic causes of abnormal sex determination in horses. In this paper, we review the historical development of methods used to understand abnormal sexual development in the horse as well as summarize cases reported over the last 40-50 years.

Changes in the inbreeding coefficient, F, in the Thoroughbred horse over the past 45 years have been investigated by genotyping 467 Thoroughbred horses (born between 1961 and 2006) using the Illumina Equine SNP50 bead chip, which comprises 54,602 SNPs uniformly distributed across the equine genome. The Spearman rank correlation coefficient, r, between the year of birth and F was estimated. The results indicate that inbreeding in Thoroughbreds has increased over the past 40 years, with r = 0.24, P < 0.001 demonstrating that there is a highly significant, though relatively weak correlation between the year of birth and inbreeding coefficients. Interestingly, the majority of the increase in inbreeding is post-1996 and coincides with the introduction of stallions covering larger numbers of mares.

Male-to-female 64,XY sex reversal is a frequently reported chromosome abnormality in horses. Despite this, the molecular causes of the condition are as yet poorly understood. This is partially because only limited molecular information is available for the horse Y chromosome (ECAY). Here, we used the recently developed ECAY map and carried out the first comprehensive study of the Y chromosome in XY mares (n=18). The integrity of the ECAY in XY females was studied by FISH and PCR using markers evenly distributed along the euchromatic region. The results showed that the XY sex reversal condition in horses has two molecularly distinct forms: (i) a Y-linked form that is characterized by Y chromosome deletions and (ii) a non-Y-linked form where the Y chromosome of affected females is molecularly the same as in normal males. Further analysis of the Y-linked form (13 cases) showed that the condition is molecularly heterogeneous: the smallest deletions spanned about 21 kb, while the largest involved the entire euchromatic region. Regardless of the size, all deletions included the SRY gene. We show that the deletions were likely caused by inter-chromatid recombination events between repeated sequences in ECAY. Further, we hypothesize that the occurrence of SRY-negative XY females in some species (horse, human) but not in others (pig, dog) is because of differences in the organization of the Y chromosome. Finally, in contrast to the Y-linked SRY-negative form of equine XY sex reversal, the molecular causes of SRY-positive XY mares (5 cases) remain as yet undefined.

Most behavioral traits are complex and are the product of interactions between multiple genes and/or environments. Therefore, ideal models in which to examine the relative roles of genetic effects should have, 1) variation in behavioral phenotypes, 2) the potential to identify the genetic bases of these behavioral traits, 3) an obvious association between phenotype and genotype, 4) the potential to identify relevant environmental conditions contributing to the establishment of behavioral phenotypes so that partitioning of gene-by-environment effects is possible, and 5) a strong understanding of the evolutionary forces influencing the system. Given these desires, an unexpected new animal model emerges for the study of behavioral genomics – morphs of the white-throated sparrow (Zonotrichia albicollis) exhibit alternative strategies of monogamy/high parental effort vs. promiscuity/low parental effort. These behaviors are absolutely correlated with the presence or absence of a large chromosomal rearrangement. We have amassed 22+ years of detailed behavioral, physiological, ecological, and evolutionary data on this species making it possible to identify the genetic, epigenetic, and environmental bases of behavior. Here we further outline the utility of the species, as well as present current cytogenetic and molecular data showing that rearrangements and linkage in multiple chromosomes are key to the evolution of alternative phenotypes. In addition, comparative analyses among the Zonotrichia suggest an interesting and slightly counterintuitive evolutionary pathway in this group. Genomic studies in the white-throated sparrow will identify the gene(s) associated with complex behaviors, as well as provide us with information on how environment interacts with genetic architecture to affect aggressive, social, sexual, and parental phenotypes. Morphs of the sparrow provide us with a unique opportunity to study intraspecific genomic differences, which have resulted from two separate, yet linked evolutionary trajectories. Such results can transform our understanding of the evolution of genomes.

We described the clinical, cytogenetic and molecular findings of 17 clinical equine cases presented for abnormal sexual development and infertility. Six horses with an enlarged clitoris had an XX, SRY-negative genotype, which displayed male-like behavior (adult individuals). Bilateral ovotestes were noted in 2 of those cases, while another case showed increased levels of circulating testosterone. Six horses with a female phenotype, including normal external genitalia, had an XY, SRY-negative genotype. These individuals had small gonads and an underdeveloped internal reproductive tract. Four horses with normal appearing external genitalia had an XY, SRY-positive genotype, 3 of them had hypoplastic testes and male-like behavior. In addition, one young filly with enlarged clitoris and hypoplastic testes had the same genotype but did not show male-like behavior due to her age. Three of these horses were related with 2 being siblings. These findings demonstrate the diversity of disorders of sexual development seen in the horse. Furthermore, they emphasize the need for further research to identify genes involved in abnormal sex determination and differentiation in the horse.

We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

Cytogenetic analyses of horses have benefited the horse industry by identifying chromosomal aberrations causing congenital abnormalities, embryonic loss and infertility. Technical advances in cytogenetics enabled the identification of chromosome specific aberrations. More recently, advances in genomic tools have been used to more precisely define chromosome abnormalities. In this report we review the history of equine clinical cytogenetics, identify historical landmarks for equine clinical cytogenetics, discuss how the current use of genomic tools has benefited this area, and how future genomics tools may enhance clinical cytogenetic studies in the horse. Copyright (C) 2008 S. Karger AG, Basel.

Tobiano is a white spotting pattern in horses caused by a dominant gene, Tobiano(TO). Here, we report TO associated with a large paracentric chromosome inversion on horse chromosome 3. DNA sequences flanking the inversion were identified and a PCR test was developed to detect the inversion. The inversion was only found in horses with the tobiano pattern, including horses with diverse genetic backgrounds, which indicated a common genetic origin thousands of years ago. The inversion does not interrupt any annotated genes, but begins approximately 100 kb downstream of the KIT gene. This inversion may disrupt regulatory sequences for the KIT gene and cause the white spotting pattern. This manuscript is accompanied by supplemental figures S1, S2 and S3, as well as supplemental Tables S1 and S2 (www.karger.com/doi/10.1159/000112065). The DNA sequence generated in this work has been submitted to GenBank under the following accession number: EF442014.

Tobiano is a white spotting pattern in horses caused by a dominant gene, Tobiano(TO). Here, we report TO associated with a large paracentric chromosome inversion on horse chromosome 3. DNA sequences flanking the inversion were identified and a PCR test was developed to detect the inversion. The inversion was only found in horses with the tobiano pattern, including horses with diverse genetic backgrounds, which indicated a common genetic origin thousands of years ago. The inversion does not interrupt any annotated genes, but begins approximately 100 kb downstream of the KIT gene. This inversion may disrupt regulatory sequences for the KIT gene and cause the white spotting pattern. This manuscript is accompanied by supplemental figures S1, S2 and S3, as well as supplemental Tables S1 and S2 (www.karger.com/doi/10.1159/000112065). The DNA sequence generated in this work has been submitted to GenBank under the following accession number: EF442014.

Jacqueline Smith Division of Genetics and Genomics Roslin Institute, Roslin Midlothian EH25 9PS (UK) Tel. (+44) 131 527 4200 Fax (+44) 131 440 0434 E-mail: jacqueline.smith@bbsrc.ac.uk Plant cytogenetics and genomics Bernd Friebe Department of Plant Pathology Th rockmorton Plant Sciences Center Kansas State University Manhattan, KS 66506-5502 (USA) Tel. (+1) 785 532 2364; Fax (+1) 785 532 5692 E-mail: friebe@ksu.edu