Factor analysis of evaluated and linearly scored traits in Swedish Warmblood horses.

Assessment protocols to describe the various aspects of conformation, gait and jumping traits on a linear scale were introduced at young horse tests for Swedish Warmblood horses in 2013. The traits scored on a linear scale are assumed to be less subjective and more easily compared across populations than the traditional evaluated traits that are scored relative to the breeding goal. However, the resulting number of traits is considerable, and several of the traits are correlated. The aim of this study was to investigate the interrelationship between the different evaluated and linearly scored traits in Swedish Warmbloods using factor analysis. In total, 20,935 horses born 1996-2017 had information on evaluated traits, and 5450 of these also had linearly scored trait records assessed since 2014 when the protocol was updated. A factor analysis with varimax rotation was performed separately for evaluated and linearly scored traits using the Psych package in R. Height at withers was included in both analyses. A total of four factors for evaluated traits and 14 factors for linearly scored traits were kept for further analysis. Missing values for individual traits in horses with linearly scored trait records were imputed based on correlated traits before factor scores were calculated using factor loadings. Genetic parameters for, and correlations between, the resulting underlying factors were estimated using multiple-trait animal models in the BLUPF90 package. Heritability estimates were on a similar level as for the traits currently used in the genetic evaluation, ranging from 0.05 for the factor for linearly scored traits named L.behaviour (dominated by traits related to behaviour) to 0.59 for the factor for evaluated traits named E.size (dominated by height at withers and conformation). For both types of traits, separate factors were formed for jumping and gait traits, as well as for body size. High genetic correlations were estimated between such corresponding factors for evaluated traits and factors for linearly scored traits. In conclusion, factor analysis could be used to reduce the number of traits to be included in multiple-trait genetic evaluation or in genomic analysis for warmblood horses. It can also contribute to a better understanding of the interrelationships among the assessed traits and be useful to decide on subgroups of traits to be used in several multiple-trait evaluations on groups of original traits.

Genome-wide association study reveals novel candidate genes for litter size in Markhoz goats.

Introduction: The Markhoz goat is the only breed that can produce high-quality fiber called mohair in Iran; however, the size of its population has faced a dramatic decline during the last decades, mainly due to the reluctance of farmers to rear Markhoz goats caused by a reduction in goat production income. Litter size at birth (LSB) and weaning (LSW) are two economically important reproductive traits for local goat breeders and have the potential of increasing the population growth rate. The present study was aimed to identify possible genomic regions that are associated with LSB and LSW in Markhoz goats using a genome-wide association study (GWAS). Methods: To this end, 136 Markhoz goats with record(s) of kidding were selected for GWAS using the Illumina Caprine 50K bead chip. The individual breeding values (BV) of available LSB and LSW records estimated under an animal mixed model were used as the dependent variable in the GWAS, thereby incorporating repeated categorical variables of litter size. Results: Four SNPs on chromosomes 2, 20 and 21 were identified to be significantly associated (FDR p < 0.05) with LSB after multiple testing correction under a Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model. Least-square analysis was performed to investigate the effects of detected genotypes on LSB. Ultimately, the GWAS results introduced six candidate genes, including GABRA5, AKAP13, SV2B, PPP1R1C, SSFA2 and TRNAS-GCU in a 100 kb adjacent region of the identified SNPs. Previous studies proposed functional roles of GABRA5 and AKAP13 genes in reproductive processes; however, the role of other candidate genes in reproduction is not clear. Conclusion: These findings warrant further investigation for use in marker-assisted selection programs in Markhoz goats.

Genome-Wide Association Studies Identify Candidate Genes for Coat Color and Mohair Traits in the Iranian Markhoz Goat.

The Markhoz goat provides an opportunity to study the genetics underlying coat color and mohair traits of an Angora type goat using genome-wide association studies (GWAS). This indigenous Iranian breed is valued for its quality mohair used in ceremonial garments and has the distinction of exhibiting an array of coat colors including black, brown, and white. Here, we performed 16 GWAS for different fleece (mohair) traits and coat color in 228 Markhoz goats sampled from the Markhoz Goat Research Station in Sanandaj, Kurdistan province, located in western Iran using the Illumina Caprine 50K beadchip. The Efficient Mixed Model Linear analysis was used to identify genomic regions with potential candidate genes contributing to coat color and mohair characteristics while correcting for population structure. Significant associations to coat color were found within or near the ASIP, ITCH, AHCY, and RALY genes on chromosome 13 for black and brown coat color and the KIT and PDGFRA genes on chromosome 6 for white coat color. Individual mohair traits were analyzed for genetic association along with principal components that allowed for a broader perspective of combined traits reflecting overall mohair quality and volume. A multitude of markers demonstrated significant association to mohair traits highlighting potential candidate genes of POU1F1 on chromosome 1 for mohair quality, MREG on chromosome 2 for mohair volume, DUOX1 on chromosome 10 for yearling fleece weight, and ADGRV1 on chromosome 7 for grease percentage. Variation in allele frequencies and haplotypes were identified for coat color and differentiated common markers associated with both brown and black coat color. This demonstrates the potential for genetic markers to be used in future breeding programs to improve selection for coat color and mohair traits. Putative candidate genes, both novel and previously identified in other species or breeds, require further investigation to confirm phenotypic causality and potential epistatic relationships.