Anas Khanshour

Microsatellite Analysis of Genetic Diversity and Population Structure of Arabian Horse Populations

The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.

Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing

BackgroundMaternal inheritance is an essential point in Arabian horse population genetics and strains classification. The mitochondrial DNA (mtDNA) sequencing is a highly informative tool to investigate maternal lineages. We sequenced the whole mtDNA D-loop of 251 Arabian horses to study the genetic diversity and phylogenetic relationships of Arabian populations and to examine the traditional strain classification system that depends on maternal family lines using native Arabian horses from the Middle East.ResultsThe variability in the upstream region of the D-loop revealed additional differences among the haplotypes that had identical sequences in the hypervariable region 1 (HVR1). While the American-Arabians showed relatively low diversity, the Syrian population was the most variable and contained a very rare and old haplogroup. The Middle Eastern horses had major genetic contributions to the Western horses and there was no clear pattern of differentiation among all tested populations. Our results also showed that several individuals from different strains shared a single haplotype, and individuals from a single strain were represented in clearly separated haplogroups.ConclusionsThe whole mtDNA D-loop sequence was more powerful for analysis of the maternal genetic diversity in the Arabian horses than using just the HVR1. Native populations from the Middle East, such as Syrians, could be suggested as a hot spot of genetic diversity and may help in understanding the evolution history of the Arabian horse breed. Most importantly, there was no evidence that the Arabian horse breed has clear subdivisions depending on the traditional maternal based strain classification system.

An international meta-analysis confirms the association of BNC2 with adolescent idiopathic scoliosis

Adolescent idiopathic scoliosis (AIS) is a common spinal deformity with the prevalence of approximately 3%. We previously conducted a genome-wide association study (GWAS) using a Japanese cohort and identified a novel locus on chromosome 9p22.2. However, a replication study using multi-population cohorts has not been conducted. To confirm the association of 9p22.2 locus with AIS in multi-ethnic populations, we conducted international meta-analysis using eight cohorts. In total, we analyzed 8,756 cases and 27,822 controls. The analysis showed a convincing evidence of association between rs3904778 and AIS. Seven out of eight cohorts had significant P value, and remaining one cohort also had the same trend as the seven. The combined P was 3.28 × 10−18 (odds ratio = 1.19, 95% confidence interval = 1.14–1.24). In silico analyses suggested that BNC2 is the AIS susceptibility gene in this locus.

A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly hair coat trait (Crd) in horse

BackgroundCurly horses present a variety of curl phenotypes that are associated with various degrees of curliness of coat, mane, tail and ear hairs. Their origin is still a matter of debate and several genetic hypotheses have been formulated to explain the diversity in phenotype, including the combination of autosomal dominant and recessive alleles. Our purpose was to map the autosomal dominant curly hair locus and identify the causal variant using genome-wide association study (GWAS) and whole-genome sequencing approaches.ResultsA GWAS was performed using a Bayesian sparse linear mixed model, based on 51 curly and 19 straight-haired French and North American horses from 13 paternal families genotyped on the Illumina EquineSNP50 BeadChip. A single strong signal was observed on equine chromosome 11, in a region that encompasses the type I keratin gene cluster. This region was refined by haplotype analysis to a segment including 36 genes, among which are 10 keratin genes (KRT-10, -12, -20, -23, -24, -25, -26, -27, -28, -222). To comprehensively identify candidate causal variants within all these genes, whole-genome sequences were obtained for one heterozygous curly stallion and its straight-haired son. Among the four non-synonymous candidate variants identified and validated in the curly region, only variant g.21891160G>A in the KRT25 gene (KRT25:p.R89H) was in perfect agreement with haplotype status in the whole pedigree. Genetic association was then confirmed by genotyping a larger population consisting of 353 horses. However, five discordant curly horses were observed, which carried neither the variant nor the main haplotype associated with curliness. Sequencing of KRT25 for two discordant horses did not identify any other deleterious variant, which suggests locus rather than allelic heterogeneity for the curly phenotype.ConclusionsWe identified the KRT25:p.R89H variant as responsible for the dominant curly trait, but a second dominant locus may also be involved in the shape of hairs within North American Curly horses.

Genetic diversity and population structure in remnant subpopulations of Nordestino horse breed

This study analyzed four remnant subpopu- lations of Nordestino horse breed to detect genetic structure and diversity through 14 microsatellite markers. Hair root follicles from a total of 393 horses were collected. There were 61 animals from Salitre Valley (JUAZ-BA) located at Bahia state, 89 from North and Central North ecoregions located at Piaui state (NCEN-PI), 185 animals from Sertao and Sertao do Sao Francisco ecoregions (SERT-PE) and 58 animals from Agrestina city (AGRE-PE) located at Pernambuco state. Genetic diversity, genetic differentiation and bottleneck effects were examined in the 4 remnant subpo- pulations of Nordestino horse breed. There was high allelic diversity and the F is value did not show evidence of a significant predominance of mating among relatives, probably because of crossbree- ding among populations. Recent bottleneck effects were not detected in the 4 subpopulations, but the IAM and TPM model did suggest a bottleneck effect. This may be a reflection of the decreased number of breeding animals caused by castration of males, mechanization processes and changes in life style in the rural areas. The bottleneck event was not enough to lead a genetic differentiation among the 4 remnant subpopulations of Nordestino horse. There was no evidence of genetic diffe- rentiation, so the 4 subpopulations formed one genetic group.

Microsatellite analysis of genetic variability in Waler horses from Australia

Abstract. The Waler horse breed is an integral part of Australian history. The purposes of this study were to analyse the genetic variability in Waler horses from Australia and to investigate genetic relationships with other horse breeds. We examined the genetic diversity of 70 Waler horses sampled from seven breeding stations in Australia. Also we analysed the relationships of these horses with 11 other horse breeds. Analysis of the genetic structure was carried out using 15 microsatellite loci, genetic distances, AMOVA, factorial correspondence analysis and a Bayesian method. We found that the genetic diversity in the Waler was greater than the domestic horse mean and exceeded that of all endangered horse breeds. Our findings also revealed moderate population subdivision rather than inbreeding. All genetic similarity measures indicated that the Thoroughbred might be a key ancestor to the Waler. This study indicates that there is no immediate concern for loss of variation in Waler horses. Also, there clearly has been a strong input from the Thoroughbred into the Waler horse breed. However, the genetic evidence suggests that this input was not just direct but also came through other types of horses with a Thoroughbred cross background.

A multi-ethnic meta-analysis confirms the association of rs6570507 with adolescent idiopathic scoliosis

Adolescent idiopathic scoliosis (AIS) is the most common type of spinal deformity and has a significant genetic background. Genome-wide association studies (GWASs) identified several susceptibility loci associated with AIS. Among them is a locus on chromosome 6q24.1 that we identified by a GWAS in a Japanese cohort. The locus is represented by rs6570507 located within GPR126. To ensure the association of rs6570507 with AIS, we conducted a meta-analysis using eight cohorts from East Asia, Northern Europe and USA. The analysis included a total of 6,873 cases and 38,916 controls and yielded significant association (combined P = 2.95 × 10−20; odds ratio = 1.22), providing convincing evidence of the worldwide association between rs6570507 and AIS susceptibility. In silico analyses strongly suggested that GPR126 is a susceptibility gene at this locus.

Characterization of the Polish Primitive Horse (Konik) maternal lines using mitochondrial D-loop sequence variation

The Polish Primitive Horse (PPH, Konik) is a Polish native horse breed managed through a conservation program mainly due to its characteristic phenotype of a primitive horse. One of the most important goals of PPH breeding strategy is the preservation and equal development of all existing maternal lines. However, until now there was no investigation into the real genetic diversity of 16 recognized PPH dam lines using mtDNA sequence variation. Herein, we describe the phylogenetic relationships between the PPH maternal lines based upon partial mtDNA D-loop sequencing of 173 individuals. Altogether, 19 mtDNA haplotypes were detected in the PPH population. Five haplotypes were putatively novel while the remaining 14 showed the 100% homology with sequences deposited in the GenBank database, represented by both modern and primitive horse breeds. Generally, comparisons found the haplotypes conformed to 10 different recognized mtDNA haplogroups (A, B, E, G, J, M, N, P, Q and R). A multi-breed analysis has indicated the phylogenetic similarity of PPH and other indigenous horse breeds derived from various geographical regions (e.g., Iberian Peninsula, Eastern Europe and Siberia) which may support the hypothesis that within the PPH breed numerous ancestral haplotypes (found all over the world) are still present. Only in the case of five maternal lines (Bona, Dzina I, Geneza, Popielica and Zaza) was the segregation of one specific mtDNA haplotype observed. The 11 remaining lines showed a higher degree of mtDNA haplotype variability (2–5 haplotypes segregating in each line). This study has revealed relatively high maternal genetic diversity in the small, indigenous PPH breed (19 haplotypes, overall HapD = 0.92). However, only some traditionally distinguished maternal lines can be treated as genetically pure. The rest show evidence of numerous mistakes recorded in the official PPH pedigrees. This study has proved the importance of maternal genetic diversity monitoring based upon the application of molecular mtDNA markers and can be useful for proper management of the PPH conservation program in the future.

The Genetic Architecture of Adolescent Idiopathic Scoliosis

Adolescent idiopathic scoliosis (AIS) is the most common pediatric spinal deformity, affecting 2–3% of school-age children worldwide. This disease is typically classified by age at onset, with the great majority occurring around the time of the adolescent growth spurt, the so-called AIS. AIS can progress rapidly, threatening pain, deformity, and pulmonary dysfunction. Heritability of AIS is high, and population studies have consistently found that AIS is best explained by a polygenic inheritance model, in which many genetic risk factors combine to cause the disease. Population studies have associated AIS with genetic markers near interesting candidate genes, including the homeobox transcription factor LBX1, the G protein-coupled receptor GPR126, the paired box transcription factors PAX1 and PAX3, as well as the SRY-box SOX9. Moreover, gene targeting in zebrafish and mouse model systems have identified candidate genes, which offer an exciting new area of investigation into molecular mechanisms of AIS. AIS candidate genes thus far identified function in muscle, nerve, and cartilage specification in early development, suggesting neuromuscular and/or cartilage disease origins, but their role in later human development and growth of the axial spine is an unexplored area of developmental biology. Continued gene discovery efforts, aided by next-generation genomic platforms, are a priority for the field and will provide the tools for biological investigations of AIS pathogenesis.

Genome-wide meta-analysis and replication studies in multiple ethnicities identify novel adolescent idiopathic scoliosis susceptibility loci

&NA; Adolescent idiopathic scoliosis (AIS) is the most common musculoskeletal disorder of childhood development. The genetic architecture of AIS is complex, and the great majority of risk factors are undiscovered. To identify new AIS susceptibility loci, we conducted the first genome‐wide meta‐analysis of AIS genome‐wide association studies, including 7956 cases and 88 459 controls from 3 ancestral groups. Three novel loci that surpassed genome‐wide significance were uncovered in intragenic regions of the CDH13 (P‐value_rs4513093 = 1.7E‐15), ABO (P‐value_ rs687621 = 7.3E‐10) and SOX6 (P‐value_rs1455114 = 2.98E‐08) genes. Restricting the analysis to females improved the associations at multiple loci, most notably with variants within CDH13 despite the reduction in sample size. Genome‐wide gene‐functional enrichment analysis identified significant perturbation of pathways involving cartilage and connective tissue development. Expression of both SOX6 and CDH13 was detected in cartilage chondrocytes and chromatin immunoprecipitation sequencing experiments in that tissue revealed multiple HeK27ac‐positive peaks overlapping associated loci. Our results further define the genetic architecture of AIS and highlight the importance of vertebral cartilage development in its pathogenesis.