ArticleJournal of applied genetics2024
Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle.
Article in Journal of applied genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 13 citations in OpenAlex.
- Imputation in the Wild: Genome-Wide Robustness and Fine-Scale Limitations of Low-Coverage Genomes in Endangered Species.Molecular ecology resources · 2026Article
- Review
- A comprehensive genome-wide analysis for signatures of selection in goat (genus Capra) revealed new candidate genes for environmental adaptation and productive traits.BMC genomics · 2025Article
- Genomic Characterization of the Kazakh Fat-Tailed Coarse-Wool Sheep Breed Using ROH Analysis.Animals : an open access journal from MDPI · 2025Article
- Variation in genetic diversity evaluated under different breeding schemes in Sahiwal herd.Tropical animal health and production · 2025Article
- Genome-wide insights into selection signatures for transcription factor binding sites in cattle ROH regions.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Article
- Genomic insights into adaptation and inbreeding among Sub-Saharan African cattle from pastoral and agropastoral systems.Frontiers in genetics · 2024Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Runs of homozygosity (ROH) are contiguous genomic regions, homozygous across all sites which arise in an individual due to the parents transmitting identical haplotypes to their offspring. The genetic improvement program of Sahiwal cattle after decades of selection needs re-assessment of breeding strategy and population phenomena. Hence, the present study was carried out to optimize input parameters in PLINK for ROH estimates, to explore ROH islands and assessment of pedigree and genome-based inbreeding in Sahiwal cattle. The sliding window approach with parameters standardized to define ROH for the specific population under study was used for the identification of runs. The optimum maximum gap, density, window-snp and window-threshold were 250 Kb, 120 Kb/SNP, 10, 0.05 respectively and ROH patterns were also characterized. ROH islands were defined as the short homozygous genomic regions shared by a large proportion of individuals in a population, containing significantly higher occurrences of ROH than the population specific threshold level. These were identified using the -homozyg-group function of the PLINK v1.9 program. Our results indicated that the Islands of ROH harbor a few candidate genes, ACAD11, RFX4, BANP, UBA5 that are associated with major economic traits. The average F
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