GWAS Identifies a Region Containing the SALL1 Gene in Variation of Pigmentation Intensity Within the Chestnut Coat Color of Horses.

Chestnut coat color in horses is determined by a missense mutation within the MC1R gene. However, the intensity of the chestnut color can vary widely within individuals possessing this genotype. Here, we investigated this variation using standardized photographs of 96 horses. Each horse was ranked lightest to darkest within the cohort for phenotype by 3 blinded observers. A genome-wide association study utilizing the relative shade ranking as the phenotype and using 268 487 single-nucleotide polymorphisms (SNPs) genotyped using the Affymetrix Equine 670k array identified a single significantly associated region on chromosome 3 (P = 2.934 × 10-8). Analysis of whole-genome sequences for horses spanning the diverse range of chestnut color identified candidate SNPs within the coding sequence of the only gene in the region: SALL1. The function of SALL1 is largely unknown, though it is predicted to interact with the Hermansky-Pudlak Syndrome type 1 (HPS1) protein, which causes partial albinism in humans. However, with only one study suggesting a circumstantial influence of the SALL1 protein on pigmentation, additional work is needed to confirm this new coat color locus in larger populations and investigate the function of this protein for impacts on equine health.

Suicide-related interpersonal needs of young Iranian people: A preliminary validation of thwarted belongingness and perceived burdensomeness constructs.

The aim of the current study was to validate the Interpersonal Needs Questionnaire (INQ-15) and to test its reliability in Persian-speaking Iranian undergraduate students. In this cross-sectional study, 485 undergraduate students (age: 20.66 ± 1.42, 60% female) were assessed on the two subscales of perceived burdensomeness (PB) and thwarted belongingness (TB) and the Suicide Behavior Questionnaire-Revised (SBQ-R). Exploratory structural equation modelling (ESEM) confirmed the construct validity of INQ-14, excluding INQ#9. In addition, INQ#8, articulated in an equivalent Persian phrasing, loaded well on TB. The measurement model tested by confirmatory factor analysis (CFA) suggested INQ#11 to be eliminated, resulting in INQ-13-P to consist of PB and TB-7. The internal consistency and convergent/discriminant validity were established. The concurrent validity of PB was solidly established in terms of past year suicidal ideation (PY-SI) above and beyond anxiety, depression, prior suicidality, and TB-7. The effect of PB on PY-SI was stronger, where prior suicidality had already occurred or the perceived likelihood of future suicide (PLFS) was high. Moreover, TB-7 could only indicate PY-SI, where prior suicidality had already occurred or PLFS was high, albeit when PB was omitted. The interaction term was significant; however, beyond anxiety and depression, the effect of TB-7 on PY-SI was significant where PB was very high (n = 40, 8.25%). Therefore, future studies can utilize INQ-13-P as a valid and reliable instrument in Persian-speaking populations. However, further studies should examine the construct validity of TB and its relationship with suicide ideation in different populations.

Genetic Diversity of Persian Arabian Horses and Their Relationship to Other Native Iranian Horse Breeds.

The principal aims of this study were to explore genetic diversity and genome-wide selection signatures in Persian Arabian horses and to determine genetic relationship of Persian Arabians with other Iranian horse breeds. We evaluated 71 horses from 8 matrilineal strains tracing to 47 mares from the mid to late 19th century, using the equine 670k single nucleotide polymorphism (SNP) BeadChip. Mean observed and expected heterozygosity were (0.43) and (0.45), respectively, average inbreeding measures (inbreeding estimates based on runs of homozygosity and pedigree information) were low, indicating high genetic diversity in Persian Arabian horses. Analysis of population genetic structure using STRUCTURE and principal component analysis suggested that Persian Arabian horses can be divided into 3 groups, however the groups do not match traditional matrilineal strains. In total, 15 genomic regions were identified by at least 2 of the 3 implemented methods, Tajima's D, H, and H12, as potentially under selection in Persian Arabian horses. Most of these peaks were found on chromosome 9, overlapping with QTLs previously associated with horse temperament. Biological function analysis of identified candidate genes highlighted enrichment of GO term "response to lipopolysaccharide" and KEGG pathway "chemokine-mediated signaling pathway," which are associated with immune responses and may have been targets of selection in Persian Arabian horses. Independent analyses of SNP data from 30 horses of 4 other Iranian breeds suggested distinct population structure between Persian Arabian, and Turkemen and Caspian horse breeds. Overall, the results of this study suggest a rich genetic diversity in the Persian Arabian horses and a clear genetic differentiation with Turkemen and Caspian breeds.

Refining the evolutionary tree of the horse Y chromosome.

The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.

Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses.

The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds.

Validation and psychometric properties of Suicide Behaviors Questionnaire-Revised (SBQ-R) in Iran.

BACKGROUND: Suicide is increasing in young Iranian population, which necessitates the employing of valid, yet abridged instruments assessing the constellation of suicide-related behaviors. The study aimed at validating Suicide Behavior Questionnaire-Revised (SBQ-R) among Iranian undergraduates. METHODS: A total of 487 undergraduates were surveyed in 2018. Construct validity of SBQ-R was examined via confirmatory factor analysis (CFA), and Spearman's correlation with two single-item indices of suicide acceptability (SA) and lifetime suicidal ideation (LSI) was determined. Logistic regression and Kruskal-Wallis tests were used to examine the cut-off points (≥ 7 and ≥ 8) and categorizations as per item 1. RESULTS: The mean SBQ-R score was 5.79 ±â€¯3.55. Cut-off points ≥ 7 and ≥ 8 categorized 150 (30.8%) and 123 (25.2%) samples with suicide risk, respectively. Women obtained significantly higher scores on all indices, except items 1 and 4. CFA confirmed the model with sound goodness-of-fit, with factor loadings of 0.70 to 0.83. Composite reliability and average variance extracted were 0.87 and 0.63, respectively. The SBQ-R's correlation with SA and LSI confirmed its concurrent validity. Regression analysis confirmed the ability of both cut-off points to distinguish the participants with high SA and LSI; however, the cut-off point ≥ 8 produced better results regarding high LSI. Based on item 1, normal versus low- and high-risk samples were significantly different in terms of SA, LSI, and adjusted total score of SBQ-R (P < 0.0001). CONCLUSION: SBQ-R is an economic and psychometrically sound tool, which can be utilized to identify suicide-related behaviors and risks in young Iranian population.

Social-Ecological measure of resilience: an adapted measure for Persian-speaking university students.

Background: There is no validated instrument for Persian-speaking students to apply the social-ecological resilience theory (SERT), which emphasizes the ecological resources for developing resilience. The study aimed at developing the student social-ecological resilience measure(Student-SERM) in Iran's context. Methods: Three separate samples of undergraduates participated in this mixed-methods research from the University of Tehran, Iran. Phase-1 qualitatively explored the resilience features in the university setting, to devise the university-specific subscale (USS). Phase-2piloted the construct validity and reliability of the Student-SERM in 242 undergraduates, who also completed Depression, Anxiety, and Stress Scale (DASS-21). Phase-3, as a cross-validation study, investigated 487 undergraduates, who completed the refined Student-SERM, HospitalAnxiety and Depression Scale (HADS), and three indices screening academic performance, loneliness, and suicide acceptability. Exploratory factor analysis (EFA) and confirmatory factor analysis (CFA), Pearson's correlation, and Cronbach's alpha were performed. Results: Phase-1 yielded nine items for USS. In phase-2, EFA indicated the construct validity of the main 20-item measure (RMSEA=0.06 and SRMR=0.04) and the nine-item USS (RMSEA=0.07and SRMR =0.04), and the reliability and convergent/divergent validity were confirmed. In phase-3, EFA (RMSEA=0.07 and SRMR=0.04) and CFA (RMSEA=0.07, CFI=0.89, TLI=0.87,and SRMR=0.07) in two separate subsamples and CFA (RMSEA=0.06, CFI=0.92, TLI=0.90,and SRMR=0.06) in the total sample indicated the construct validity of the refined Student-SERM, including family, peer, culture, growth, and USS subscales. The reliability and convergent/divergent validity were also reconfirmed. Conclusion: The Student-SERM incorporates ecological resources, accounting for the students'resilience. Since the resilience process involves a return to healthy functioning after adversity, further research can examine the application of Student-SERM in high-risk student populations.

An Independent Locus Upstream of ASIP Controls Variation in the Shade of the Bay Coat Colour in Horses.

Novel coat colour phenotypes often emerge during domestication, and there is strong evidence of genetic selection for the two main genes that control base coat colour in horses-ASIP and MC1R. These genes direct the type of pigment produced, red pheomelanin (MC1R) or black eumelanin (ASIP), as well as the relative concentration and the temporal-spatial distribution of melanin pigment deposits in the skin and hair coat. Here, we describe a genome-wide association study (GWAS) to identify novel genic regions involved in the determination of the shade of bay. In total, 126 horses from five different breeds were ranked according to the extent of the distribution of eumelanin: spanning variation in phenotype from black colour restricted only to the extremities to the presence of some black pigment across nearly all the body surface. We identified a single region associated with the shade of bay ranking spanning approximately 0.5 MB on ECA22, just upstream of the ASIP gene (p = 9.76 × 10-15). This candidate region encompasses the distal 5' end of the ASIP transcript (as predicted from other species) as well as the RALY gene. Both loci are viable candidates based on the presence of similar alleles in other species. These results contribute to the growing understanding of coat colour genetics in the horse and to the mapping of genetic determinants of pigmentation on a molecular level. Given pleiotropic phenotypes in behaviour and obesity for ASIP alleles, especially those in the 5' regulatory region, improved understanding of this new Shade allele may have implications for health management in the horse.

Genome Diversity and the Origin of the Arabian Horse.

The Arabian horse, one of the world's oldest breeds of any domesticated animal, is characterized by natural beauty, graceful movement, athletic endurance, and, as a result of its development in the arid Middle East, the ability to thrive in a hot, dry environment. Here we studied 378 Arabian horses from 12 countries using equine single nucleotide polymorphism (SNP) arrays and whole-genome re-sequencing to examine hypotheses about genomic diversity, population structure, and the relationship of the Arabian to other horse breeds. We identified a high degree of genetic variation and complex ancestry in Arabian horses from the Middle East region. Also, contrary to popular belief, we could detect no significant genomic contribution of the Arabian breed to the Thoroughbred racehorse, including Y chromosome ancestry. However, we found strong evidence for recent interbreeding of Thoroughbreds with Arabians used for flat-racing competitions. Genetic signatures suggestive of selective sweeps across the Arabian breed contain candidate genes for combating oxidative damage during exercise, and within the "Straight Egyptian" subgroup, for facial morphology. Overall, our data support an origin of the Arabian horse in the Middle East, no evidence for reduced global genetic diversity across the breed, and unique genetic adaptations for both physiology and conformation.