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KMID : 0381120230450060813
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Genes and Genomics
2023 Volume.45 No. 6 p.813 ~ p.825
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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
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Rafat Fatma
Waseem Chauhan
Mohammad Afzal
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Abstract
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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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KEYWORD
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Runs of homozygosity, Pedigree-based inbreeding estimate, Genomic inbreeding estimate, Illumina Global Screening Array, PLINK
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