Signatures of selection are present in the genome of two close autochthonous cattle breeds raised in the North of Italy and mainly distinguished for their coat colours

Abstract

Autochthonous cattle breeds are genetic resources that, in many cases, have been fixed for inheritable exterior phenotypes useful to understand the genetic mechanisms affecting these breed-specific traits. Reggiana and Modenese are two closely related autochthonous cattle breeds mainly raised in the production area of the well-known Protected Designation of Origin Parmigiano-Reggiano cheese, in the North of Italy. These breeds can be mainly distinguished for their standard coat colour: solid red in Reggiana and solid white with pale shades of grey in Modenese. In this study we genotyped with the GeneSeek GGP Bovine 150k single nucleotide polymorphism (SNP) chip almost half of the extant cattle populations of Reggiana (n = 1109 and Modenese (n = 326) and used genome-wide information in comparative F_ST analyses to detect signatures of selection that diverge between these two autochthonous breeds. The two breeds could be clearly distinguished using multidimensional scaling plots and admixture analysis. Considering the top 0.0005% F_ST values, a total of 64 markers were detected in the single-marker analysis. The top F_ST value was detected for the melanocortin 1 receptor (MC1R) gene mutation, which determines the red coat colour of the Reggiana breed. Another coat colour gene, agouti signalling protein (ASIP), emerged amongst this list of top SNPs. These results were also confirmed with the window-based analyses, which included 0.5-Mb or 1-Mb genome regions. As variability affecting ASIP has been associated with white coat colour in sheep and goats, these results highlighted this gene as a strong candidate affecting coat colour in Modenese breed. This study demonstrates how population genomic approaches designed to take advantage from the diversity between local genetic resources could provide interesting hints to explain exterior traits not yet completely investigated in cattle.

Keywords: Bos taurus; coat colour; genetic resource; genome; population genomics.

FIGURE 1

Pictures of Reggiana (a) and Modenese (b) sires [Colour figure can be viewed at wileyonlinelibrary.com]

FIGURE 2

Multidimensional scaling plots produced using genotyping information from each investigated cattle of the Reggiana (red dots) and Modenese (blue dots) breeds. Different components (C) are considered in the plots [Colour figure can be viewed at wileyonlinelibrary.com]

FIGURE 3

Results of the ADMIXTURE analysis. a) Cross validation (CV) error with K from 1 to 39. b) Plot distribution with K = 2. c) Plot distribution with K = 4. For the last two plots, putative subpopulations (therefore, 2 for K = 2 and 4 for K = 4) are labelled with a different colour [Colour figure can be viewed at wileyonlinelibrary.com]

FIGURE 4

Population genomic parameters represented in the Reggiana (red points and lines) and in Modenese (blue points and lines) breeds: (a) linkage disequilibrium (LD) decay over distance; (b) average LD calculated for all autosomes; (c) effective population size (Ne) over the past generations [Colour figure can be viewed at wileyonlinelibrary.com]

FIGURE 5

Manhattan plots obtained in the single‐marker (a) and window‐based F_ST analyses using windows of 0.5 Mb (b) or windows of 1 Mb (c), in which the y axis reports the mean F_ST values (mF_ST). In the single‐marker analysis, the top 20 markers have been annotated, including two markers within the top 64 list, which are close to genes (in blue) that have been also contained in windows detected with the window‐based approaches. The regions detected with the window‐based approaches (b and c) are annotated with the genes close to SNPs reported in the single‐marker analysis. The two main coat colour genes are indicated in red. A few genes in the ASIP region on BTA13 identified in the window‐based analyses are annotated. The threshold lines are defined according to the percentiles reported in Materials and methods [Colour figure can be viewed at wileyonlinelibrary.com]