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. 2023 Jan 3:101:skad061.
doi: 10.1093/jas/skad061.

Analysis of runs of homozygosity of cattle living in different climate zones

Laura Falchi  1 , Alberto Cesarani  1   2 , Salvatore Mastrangelo  3 , Gabriele Senczuk  4 , Baldassare Portolano  3 , Fabio Pilla  4 , Nicolò P P Macciotta  1
Affiliations

Analysis of runs of homozygosity of cattle living in different climate zones

Laura Falchi et al. J Anim Sci. .

Abstract

Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.

Keywords: cattle breeds; environmental adaptation, hybrid; indicus; runs of homozygosity; taurus.

Plain language summary

Domestication and evolution of cattle originated different modern breeds in different places worldwide. The interaction between natural and artificial selection and the adaptation to environment shaped the genome, and the three different types of cattle here considered (taurus, indicus, and composite) may harbor different selection signatures. To study the difference among types and region of origin (tropics, temperate, and continental zones), Regions of Homozygosity (ROH) were used. ROH are continuous homozygous chromosomal segments identical by descendent, which characteristics can give information about inbreeding occurrence and natural and artificial selection. Moreover, it had been investigated which genes were mapped in these regions, and if interesting differences pertaining to environmental adaptation or fitness in general, could be observed.

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Conflict of interest statement

The authors declare no real or perceived conflicts of interest.

Figures

Figure 1.
Figure 1.
Plot of the first 2 principal components extracted from the genomic relationship matrix (GRM).
Figure 2.
Figure 2.
Manhattan plot of SNPROH computed for all markers within Type and Zone. The green dots represent SNP exceeding the 99th percentile of the SNPROH distribution.
See this image and copyright information in PMC

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