Genome‐wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

Abstract

Runs of homozygosity (ROH) are contiguous homozygous regions of the genome. These regions can be used to identify genes associated with traits of economic interest, as well as inbreeding levels. The aim of the present study was to analyse the length and distribution of ROH islands in Gyr cattle and to identify genes within these regions. A population of 173 animals selected for beef production and a population of 291 animals selected for dairy production were used. Differences in the number of short ROH (ROH1‐2 Mb) were observed between the two populations, while the number of long ROH (ROH>16 Mb) was similar. ROH islands with the highest incidences (>0.50) overlapped in several segments of the genome in the two populations. The genes identified were associated with milk production, growth, reproduction, immune response and resistance traits. Our results contribute to the understanding of how selection can shape the distribution of ROH and ROH islands within the same breed when animals are selected for different purposes such as dairy or beef production.

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

“…In other studies carried out in South America on breeds such as Nelore and Gyr, the genome of these breeds was mainly composed of a large number of short segments that accounted for 78% of all ROH [ 26 ]. For the Gyr population, a proportion of its genome (183.6 Mb), covered by an ROH of a shorter length (ROH1–2 Mb), was also evaluated [ 8 ]. The identification of ROH in the bovine genome provides information on the specific regions that could be related to selection events.…”

“…The database was composed of the genotypes of 127 Creole animals genotyped with the BovineHD BeadChip 777,000 SNPs (Illumina, San Diego, CA, USA). Assuming an MAF < 0.01, the PLINK program was applied for quality control of the genotypes [ 8 , 12 , 16 ], a call rate for SNPs < 0.90, and a call rate for samples < 0.98.…”

“…Genomic analysis of the population structure indicates the proportion of the total genetic variability represented by the associated principal component (PC), obtained by the plink-pca command line of the PLINK program [17]. 0.01, the PLINK program was applied for quality control of the genotypes [8,12,16], a call rate for SNPs < 0.90, and a call rate for samples < 0.98.…”

“…The ROH is a continuous homozygous segment in the genome that is widely used in livestock to characterize population structure and demographic history [ 7 ]. Additionally, ROH analysis can help to reveal the genetic relationships between individuals by measuring genomic inbreeding levels and identifying regions with a high frequency of homozygosity (ROH islands) associated with traits of economic interest [ 8 ]. Several studies involving native breeds from different countries have used ROH to find the history of their genome; for example, a native Chinese breed [ 9 ], the Blanco Orejinegro breed in Colombia [ 10 ], and native Italian dairy breeds [ 11 ].…”

Analysis of the genetic diversity of Ayrshire cattle in Russia. Message 2. Genome analysis based on data on the distribution of ROH patterns in Ayrshire cows

“…Протеин-кодируемые гены DOP1B и ABCG2, ZGPAT, CA6 и ENO1, NT5DC2, LZTS2 могут быть связаны у айрширов с образованием молочного жира и белка в молоке. Ранее их функции были описаны в исследованиях у голштинской породы коров [11,18], яков [22,25], азиатских буйволов [28] и у породы Гир (Bos indicus) [34]. За синтез и секрецию β-казеина отвечают белки, кодируемые группой генов HERC3, HERC5, HERC6, которые изучены в работах V.B.…”