Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

DOI: https://doi.org/10.21203/rs.2.17561/v1

Abstract

Background: Consecutive homozygous fragments of the genome inherited from a common ancestor to offspring are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identifying 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 ~65000 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 and/or natural selection.

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tables

 

Table 1. Summary of the detected runs of homozygosity (ROH) grouped according to their length in (Mb).

ROH group 

nROH1

 

Percentage

 

Average length (Mb)

 

Standard deviation (Mb)

 

Percentage of genome coverage

AZ

KHZ

 

AZ

KHZ

 

AZ

KHZ

 

AZ

KHZ

 

AZ

KHZ

ROH1-2

841

629

 

15.71

16.77

 

1.83

1.81

 

0.13

0.15

 

0.06

0.05

ROH2-4

2870

2119

 

53.62

56.51

 

2.70

2.71

 

0.53

0.53

 

0.31

0.23

ROH4-8

855

609

 

15.98

16.24

 

5.44

5.38

 

1.09

1.08

 

0.19

0.13

ROH8-16

484

241

 

9.04

6.42

 

11.23

11.22

 

2.25

2.21

 

0.22

0.11

ROH>16

302

152

 

5.64

4.05

 

26.70

26.19

 

11.06

9.32

 

0.32

0.16

  1. Number of runs of homozygosity segments

 

Table 2. Average inbreeding coefficients (± standard error) estimated using diagonal elements of genomic relationship matrix (FGRM), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI) and runs of homozygosity (ROH) >1 Mb (FROH) in Azeri (AZ) and Khuzestani (KHZ) breeds.

Breed

FGRM

F HOM

FUNI

FROH

AZ

0.026±0.05

0.026±0.0.05

0.026±0.05

0.043±0.05

KHZ

0.019±0.04

0.021±0.06

0.021±0.05

0.059±0.04

  1. FROH: Runs of homozygosity, FHOM: excess of homozygous genotypes, FUNI: correlation between uniting gametes, FGRM: genomic relationship matrix
  2. Inbreeding estimation ± standard deviation

 

 

Table 3. Correlation between inbreeding coefficient calculated using runs of homozygosity (ROH) >1 Mb (FROH) and estimated using diagonal elements of genomic relationship matrix (FGRM), excess of homozygosity (FHOM), and correlation between uniting gametes (FUNI) in Azeri (AZ) and Khuzestani (KHZ) breeds.

Breed

Correlation coefficient

 

 

FGRM -FROH

 

 

FHOM-FROH

 

FUNI-FROH

AZ

 

 

0.88

   

0.92

 

0.98

KHZ

 

 

0.78

   

0.93

 

0.94