Genome‐wide association study for pigmentation traits in Chinese Holstein population

Abstract

With the Illumina BovineSNP50K BeadChip, we performed a genome-wide association study (GWAS) for two pigmentation traits in a Chinese Holstein population: proportion of black (PB) and teat colour (TC). A case-control design was used. Cases were the cows with PB <0.30 (n = 129) and TC <2 points (n = 140); controls were those with PB >0.90 (n = 58) and TC >4 points (n = 281). The RM test of roadtrips (version 1.2) was applied to detect SNPs for the two traits with 42 883 and 42 741 SNPs respectively. A total of nine and 12 genome-wide significant (P < 0.05) SNPs associated with PB and TC respectively were identified. Of these, two SNPs for PB were located within the KIT and IGFBP7 genes, and the other four SNPs were 23~212 kb away from the PDGFRA gene on BTA6; nine SNPs associated with TC were located within or 21~78.8 kb away from known genes on chromosomes 4, 11, 22, 23 and 24. By combing through our GWAS results and the biological functions of the genes, we suggest that the KIT, IGFBP7, PDGFRA, MITF, ING3 and WNT16 genes are promising candidates for PB and TC in Holstein cattle, providing a basis for further investigation on the genetic mechanism of pigmentation formation.

Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds

“…ING3 and WNT16 have been reported to influence teat color in Holstein cattle (Fan et al . ) and were also located in one out of the top 25 windows (Table ). Apart from coat color variation, windows containing genes related to growth ( IGF2 , HRAS , FGFR3 ; De Simoni Gouveia et al .…”

Combined use of principal component analysis and random forests identify population‐informative single nucleotide polymorphisms: application in cattle breeds

“…Olsen et al 2004;Lindholm-Perry et al 2011). In addition, the KIT and PDGFRA genes that may determine important breed-characteristic phenotypes (spotted versus non-spotted phenotypes; Reinsch et al 1999;Fontanesi et al 2010b;Fan et al 2014) that distinguish the Holstein and Simmental breeds from the Brown and Marchigiana cattle are located on this chromosome. Other interesting markers located in QTL regions were selected from other chromosomes (Tables 1 and S3).…”

“…For example, two SNPs on BTA6 (Hapmap31616-BTC-042811 and Hapmap33128-BTC-041916) were within the KIT and PDGFRA genes, respectively. These genes are located in the QTL region for the spotted locus and are associated with spotted phenotypes and proportion of black in Holstein (Reinsch et al 1999;Fontanesi et al 2010b;Fan et al 2014). Markers in the KIT gene have been already proposed for breed traceability (Fontanesi et al 2010a).…”

Genome‐wide association studies for two exterior traits in Chinese Dongxiang spotted pigs

“…We first took a digital photo for each pig from both left and right sides in an upright position. A previously reported digital graphic process was adopted to treat photos (Fan et al., ). Briefly, photos were first treated using PHOTOSHOP CS (Adobe Systems) as follows (Figure ): (1) the body part of each pig was outlined in contrast to background on the digital image using the brush tool; (2) the contour of each pig was extracted out using the extraction tool and was saved as a png file with a transparent background; (3) grayscale or color images were converted to high‐contrast black and white images by adjusting the threshold.…”