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. 2020 Feb 10;21(1):16.
doi: 10.1186/s12863-020-0824-y.

Genomic Measures of Inbreeding Coefficients and Genome-Wide Scan for Runs of Homozygosity Islands in Iranian River Buffalo, Bubalus Bubalis

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Free PMC article

Genomic Measures of Inbreeding Coefficients and Genome-Wide Scan for Runs of Homozygosity Islands in Iranian River Buffalo, Bubalus Bubalis

Seyed Mohammad Ghoreishifar et al. BMC Genet. .
Free PMC article

Erratum in

Abstract

Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~ 65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies.

Results: In this study, 9102 ROH were identified, with an average number of 21.2 ± 13.1 and 33.2 ± 15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8 ± 120.3 Mb), and in KHZ, 5.96% (149.1 ± 107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P ≤ 0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX).

Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

Keywords: Gene enrichment; Genetic diversity; Inbreeding; River buffalo; Runs of homozygosity; Selection signatures; Water buffalo.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Geographic distribution of Azeri (AZ) and Khuzestani (KHZ) breeds used in this study. The samples of the AZ breed were obtained from the provinces shown in red (located in north and north-western part of Iran i.e. East and West Azerbaijan, Ardabil and Gilan). The samples for the Khuzestani (KHZ) breed were taken from the provinces shown in green (located in the west and south-western part of Iran i.e. Khuzestan and Kermanshah). Reprinted from “A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds,” by Mahdi Mokhber et al., 2018; BMC Genomics., 19(1), 449. Copyright 2018 by the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/). Reprinted with permission
Fig. 2
Fig. 2
Azeri (AZ) and Khuzestani (KHZ) breeds clustered according to principal component (PC) analysis of identical by state (IBS) distance matrix. The first and second PCs explain 7.02 and 5.63% of the total variance, respectively
Fig. 3
Fig. 3
Number of runs of homozygosity (ROH) and the length of the genome covered by ROH in the samples taken from the Azeri (AZ) and Khuzestani (KHZ) breeds
Fig. 4
Fig. 4
Manhattan plot of the distribution of frequently occurring runs of homozygosity (ROH) in Azeri (AZ) and Khuzestani (KHZ) Iranian water buffalo breeds. The X-axis shows the distribution of ROH over the genome, and the Y-axis shows the percentage of ROH shared among animals within each breed. The significance threshold of 20% (less than 1% of all SNPs) shown as a blue line is used for detecting ROH islands (green arrows)

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