A 17-bp InDel (rs668420586) within goat CHCHD7 gene located in growth-related QTL affecting body measurement traits

The Coiled-Coil-Helix-Coiled-Coil-Helix Domain Containing 7 (CHCHD7) gene was located in a growth-related major QTL that participated in the process of bone cells metabolism in animals by regulating mitochondrial copper homeostasis and cytochrome C oxidase assembly. Therefore, we speculated that CHCHD7 gene might be involved in animal growth and body size. Herein, we discovered a 17-bp insertion/deletion (indel) within the goat CHCHD7 gene. Then, we detected this variation in Shaanbei White Cashmere (SBWC, n = 1055) goats and Inner Mongolia White Cashmere (IMWC, n = 743) goats (Alathai type) using the mathematical expectation (ME) method. We then analyzed the correlation between these genotypes and goat body measurement traits. The results showed that the minor allelic frequency (MAF) was 0.011 in SBWC, and 0.048 in IMWC. In SBWC and IMWC, the reaction time by ME method was reduced by 36.78% and 27.59%, respectively, compared to the traditional method of screening samples one by one. Moreover, in SBWC goats, the 17-bp indel was significantly associated with body measurement traits (e.g. body height, and body length) in adults. In IMWC goats, the 17-bp indel was correlated with body measurement traits (e.g. body height) in weaners. In SBWC and IMWC goat populations, the body measurement traits of the individuals homozygous for 17-bp indel were higher than those in heterozygous individuals, except for the case of cannon circumference in IMWC weaners. These findings showed that the 17-bp insertion mutation within the goat CHCHD7 gene significantly affected body morphometric traits, and could provide a basis for marker-assisted selection (MAS) breeding of cashmere goats.