Abstract
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.
Highlights
Throughout history, goats have played a vital role in the livelihood of humans, being a main source of meat, milk, fiber, and hides, especially in harsh environmental conditions
The release of an improved goat genome assembly (Bickhart et al, 2017) and caprine 50K SNP beadchip have offered more opportunities to examine the genetics of economically important traits in the goat (Tosser-Klopp et al, 2014)
We have identified multiple Quantitative Trait Loci (QTL) and several putative candidate genes associated with coat color and mohair traits through genomewide association that warrant further investigation for causative effect and potential use for genomic selection
Summary
Throughout history, goats have played a vital role in the livelihood of humans, being a main source of meat, milk, fiber, and hides, especially in harsh environmental conditions. Many goat breeds, including the Iranian Markhoz breed, have adapted to climates with extremely high temperatures, low rainfall, and low humidity. It is the mohair or long, silky hair of the Markhoz goat that make this indigenous breed unique. A prominent feature of this breed is the coat color variation, which can be dark to light brown, black, gray, or white. This coat color variation is unique among Angora goats which are predominantly selected for a white coat color (Rashidi et al, 2006). Cross breeding and inbreeding are additional concerns for all local breeds as inbreeding is likely increasing as population sizes diminish and innate characteristics of the indigenous breeds may be lost during admixture with other breeds (Hanotte et al, 2010)
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