Abstract
Background
Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders.
Objective
The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes.
Methods
For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (FROH) and homozygous loci-based inbreeding estimate (FHOM).
Results
A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of FROH, FHOM, and pedigree-based inbreeding estimate (FPED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity.
Conclusions
This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.
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Data availability
The datasets generated and analysed during the current study are available from the corresponding author on reasonable request.
Abbreviations
- ROH:
-
Runs of homozygosity
- LROH :
-
Length of ROH
- LAUTOSOME :
-
Length of autosome
- FROH :
-
Coefficient of inbreeding using ROH/ROH-based inbreeding estimate
- PED:
-
Pedigree
- F PED :
-
Coefficient of inbreeding using pedigree information/pedigree-based inbreeding estimate
- HOM:
-
Homozygous loci
- F HOM :
-
Coefficient of inbreeding using homozygous loci/homozygous loci-based inbreeding estimate
- IBD:
-
Identical by descent
- IBS:
-
Identical by state
- SNP:
-
Single nucleotide polymorphism
- MP:
-
Matrilateral parallel
- MC:
-
Matrilateral cross
- PP:
-
Patrilateral parallel
- PC:
-
Patrilateral cross
- NI:
-
Non-inbred
- Chr:
-
Chromosome
- Mb:
-
Mega bases
- Gbp:
-
Giga base pair
- ANOVA:
-
Analysis of variance
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Acknowledgements
Authors are thankful to the chairperson, Department of Zoology, Aligarh Muslim University, for providing essential facilities. Maulana Azad National Fellowship (MANF-2018-19-UTT-100618) under University Grants Commission (UGC) to the first author is gratefully acknowledged. The authors are also obliged to all the research participants for their cooperation.
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RF: conceptualization; study design; data curation; data analysis; investigation; methodology; resources; original draft; writing—review & editing. WC: data analysis; investigation; conceptualization; writing—review & editing. MA: supervision; study design; validation; visualization: conceptualization; formal analysis.
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Fatma, R., Chauhan, W. & Afzal, M. The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India. Genes Genom 45, 813–825 (2023). https://doi.org/10.1007/s13258-023-01367-9
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DOI: https://doi.org/10.1007/s13258-023-01367-9