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.

Conformation has long been a driving force in horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlated positively with PC1, indicating that PC1 describes overall body size. We genotyped 109 horses using the EquineSNP70 bead chip and marker association assessed the data using PC1 scores as a phenotype. Mixed-model linear analysis (EMMAX) revealed a well-documented candidate locus on ECA3 (raw P = 3.86 × 10⁻⁹) near the LCORL gene. A custom genotyping panel enabled fine-mapping of the PC1 body-size trait to the 3′-end of the LCORL gene ( P = 7.09 × 10⁻¹⁰). This position differs from other reports suggesting single nucleotide polymorphisms (SNPs) upstream of the LCORL coding sequence regulate expression of the gene and, therefore, body size in horses. Fluorescent in situ hybridization analysis defined the position of a highly homologous 5 kb retrogene copy of LCORL (assigned to unplaced contigs of the EquCab 2.0 assembly) at ECA9 q12-q13. This is the first study to identify putative causative SNPs within the LCORL transcript itself, which are associated with skeletal size variation in horses.

A coat color dilution, called lilac, was observed within the Jacob sheep breed. This dilution results in sheep appearing gray, where black would normally occur. Pedigree analysis suggested an autosomal recessive inheritance. Whole-genome sequencing of a dilute case, a known carrier, and sixteen non-dilute sheep was used to identify the molecular variant responsible for the coat color change. Through investigation of the genes MLPH, MYO5A, and RAB27A, we discovered a nonsynonymous mutation within MLPH, which appeared to match the reported autosomal recessive nature of the lilac dilution. This mutation (NC_019458.2:g.3451931C>A) results in a premature stop codon being introduced early in the protein (NP_001139743.1:p.Glu14*), likely losing its function. Validation testing of additional lilac Jacob sheep and known carriers, unrelated to the original case, showed a complete concordance between the mutation and the dilution. This stop-gain mutation is likely the causative mutation for dilution within Jacob sheep.

The objectives of our study were to expand phenotypic characterization of digital cushion thickness (DCT) to the Jersey breed and include mature bulls and to identify breed-specific quantitative trait loci (QTL) for DCT within the Jersey or Holstein breeds and common QTL across breeds and sexes to better understand biological regulation and guide future use of marker-assisted selection. In a cohort of 698 cows and 85 bulls (Holstein and Jersey) from 8 farms in New York State, data were collected on DCT, body condition score (BCS), withers height, and sacral height. All animals underwent sonographic examination of the digital cushion evaluated at the sole ulcer site for the right front and hind feet. Linear mixed models were conducted on DCT separately for cows and bulls with fixed effects of time point, breed, age, digit, arid BCS group. The models included random effects to control for the random subset of animals per farm, repeated measures, and multiple measurements from each animal. The phenotypic results indicated that DCT varied by time point, breed, age, digit, and BCS group for cows and by breed, age, digit, and BCS group for bulls. For the genotypic study, 616 cow DNA samples were genotyped on the Illumina BovineHD 777K BeadChip (Illumina Inc., San Diego, CA), whereas 76 bull DNA samples were genotyped on different platforms ranging from 5K to 150K. Multiple genome-wide association studies were conducted to highlight pertinent pheriotyping parameters and genetic markers for genomic selection. Data were separated into 8 data sets based on different combinations of breed and sex. Each data set was assessed for quality of markers and samples before conducting genome-wide association studies for DCT, testing the inheritance models and genetic variation of digit, foot, and average thickness. Ten markers passed the Bonferroni correction threshold and 9 passed false discovery rate from 10 genome-wide association studies using a combination of the covariates breed, sex, genotyping batch plate, age, BCS, withers height, and sacral height. Of the 43 candidate genes, 8 novel biologically plausible genes were identified on Bos taurus autosornes 3, 4, 7, and 9: SFRS18 and LRRFIP1 function in fat deposition, whereas AHR, BZW2, EFNA5, USP45, and VAVS effect bone growth, and SOSTDC1 is related to epidermal keratinocyte function. The genetic markers associated with DCT in this study were explored for variation between cows and bulls within and across breeds for their potential use in marker-assisted selection.