Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences

Abstract

Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2–71.3 Mb), BTA5 (10.0–19.7 Mb), BTA20 (10.0–19.9 and 20.0–22.7 Mb), and BTA25 (0.5–9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.

Taurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle

“…A potential negative side-effect of white-headed cattle, similar to gonadal hypoplasia in KIT -related color-sided cattle (Venhoranta et al, 2013), is an increased susceptibility to infectious bovine keratoconjunctivitis, eye cancer, or squamous cell carcinoma under UV light exposure (Anderson, 1991). However, a peculiar pigmentation around the eyes, which is a moderately to highly heritable trait associated with reduced susceptibility to eye disease, occurs in some white-headed cattle breeds (e.g., Fleckvieh, Simmental, Hereford, Groningen White Headed) and KIT alleles possibly contribute to this pigmentation pattern (Gonzalez-Prendes et al, 2022; Jara et al, 2022; Pausch et al, 2012).…”

Genomic insights into shank and eggshell color in Italian local chickens

“…In Groningen White Headed cattle, the ERCC8 gene is implicated in the pathway of skin pigmentation bringing to the peculiar phenotype of the breed characterized by black or red body and white head. The role of ERCC8 is important for UV protection and this could impact the final colour of shank in chicken ( Gonzalez-Prendes et al, 2022 ). A real interesting region is Z:31376546-32699330 in which the gene Basonuclin 2 ( BNC2 ) has been found; this gene is strongly associated with human different saturation skin pigmentations ( Jacobs et al, 2013 ).…”

Genome-wide scan for runs of homozygosity in South American Camelids

“…In vicugna, overlapping ROHs in DLG1 suggest selection for feeding efficiency in poor pasture quality [ 65 ] while the selection signals found in PDE4D hint the adaptation of the species to UV radiation exposure through the modulation of pigmentation and/or eye-protective phenotypes. Indeed, this gene was recently described as essential in signaling pathways of melanin encompassing signatures of selection for variation in pigmentation in Groningen White Headed cattle [ 66 ] and goat breeds from Southern China [ 67 ]. Potential environmental adaptation was also observed in guanaco as the species showed overlapping ROHs in BCL2L13 , a gene selected for heat stress tolerance [ 68 ].…”