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Estimation of genome-wide patterns of homozygosity, heterozygosity and inbreeding in crossbred dairy cattle population in Pakistan

The present study aimed to explore runs of homozygosity (ROH), Heterozygosity Enriched Regions (HER) using the sliding window approach in both PLINK and detectRUNS, as well as the consecutive SNP approach in detectRUNS and their association with important economic traits. Genomic inbreeding coeffici...

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Main Authors: Un Nisa, F., Usman, M., Ali, A., Ali, M.B., Kaul, H., Asif, M., Mrode, Raphael A., Mukhtar, Z.
Format: Journal Article
Language:Inglés
Published: Springer 2025
Subjects:
cattle
dairying
genomics
inbreeding
Online Access:https://hdl.handle.net/10568/176890
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author Un Nisa, F.
Usman, M.
Ali, A.
Ali, M.B.
Kaul, H.
Asif, M.
Mrode, Raphael A.
Mukhtar, Z.
author_browse Ali, A.
Ali, M.B.
Asif, M.
Kaul, H.
Mrode, Raphael A.
Mukhtar, Z.
Un Nisa, F.
Usman, M.
author_facet Un Nisa, F.
Usman, M.
Ali, A.
Ali, M.B.
Kaul, H.
Asif, M.
Mrode, Raphael A.
Mukhtar, Z.
author_sort Un Nisa, F.
collection Repository of Agricultural Research Outputs (CGSpace)
description The present study aimed to explore runs of homozygosity (ROH), Heterozygosity Enriched Regions (HER) using the sliding window approach in both PLINK and detectRUNS, as well as the consecutive SNP approach in detectRUNS and their association with important economic traits. Genomic inbreeding coefficient based on ROH and heterosis coefficient based on HER were also estimated among crossbred (n = 81) by using GGP_HDv3_C genotyping assay. Total ROH varied from around 600 in the sliding window approach and almost double in the Consecutive SNP approach of detectRUNS. Similarly, the HER are 756 in the sliding window and 771 in the Consecutive SNP method. The mean inbreeding coefficient range varied in different approaches, i.e., 0.016–0.022 is observed based on ROH (Froh), and the heterosis coefficient based on HER (Frohet) is 0.0019. Top ROH and HER regions contain important genes related to dairy (<i>EHHADH, CACNA1C, MICALL1, EIF3L, GTPBP1, SYNGR1, ATF4, GRAP2, FAM83F, ACO2</i>), immunity (<i>LIPH, TMEM41A, PEX26, CDC42EPI, CXXC5, PSD2, PURA, CYSTM1, RNF14</i>), growth and carcass (<i>MAGEF1, TGS1, LYN, CHCHD7, FAM110B, SDCBP, SH3BP1, GGA1, TRIOBP, PICK1, MAFF, TOMM22, MGAT3, TNRC6B, ADSL, EP300, SMDT1, MATR3</i>) traits. These findings may provide valuable insights into the understanding of genome-wide homozygosity and heterozygosity patterns and genetic architecture of the Pakistani crossbred cattle.
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language Inglés
publishDate 2025
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spelling CGSpace1768902025-10-26T12:56:54Z Estimation of genome-wide patterns of homozygosity, heterozygosity and inbreeding in crossbred dairy cattle population in Pakistan Un Nisa, F. Usman, M. Ali, A. Ali, M.B. Kaul, H. Asif, M. Mrode, Raphael A. Mukhtar, Z. cattle dairying genomics inbreeding The present study aimed to explore runs of homozygosity (ROH), Heterozygosity Enriched Regions (HER) using the sliding window approach in both PLINK and detectRUNS, as well as the consecutive SNP approach in detectRUNS and their association with important economic traits. Genomic inbreeding coefficient based on ROH and heterosis coefficient based on HER were also estimated among crossbred (n = 81) by using GGP_HDv3_C genotyping assay. Total ROH varied from around 600 in the sliding window approach and almost double in the Consecutive SNP approach of detectRUNS. Similarly, the HER are 756 in the sliding window and 771 in the Consecutive SNP method. The mean inbreeding coefficient range varied in different approaches, i.e., 0.016–0.022 is observed based on ROH (Froh), and the heterosis coefficient based on HER (Frohet) is 0.0019. Top ROH and HER regions contain important genes related to dairy (<i>EHHADH, CACNA1C, MICALL1, EIF3L, GTPBP1, SYNGR1, ATF4, GRAP2, FAM83F, ACO2</i>), immunity (<i>LIPH, TMEM41A, PEX26, CDC42EPI, CXXC5, PSD2, PURA, CYSTM1, RNF14</i>), growth and carcass (<i>MAGEF1, TGS1, LYN, CHCHD7, FAM110B, SDCBP, SH3BP1, GGA1, TRIOBP, PICK1, MAFF, TOMM22, MGAT3, TNRC6B, ADSL, EP300, SMDT1, MATR3</i>) traits. These findings may provide valuable insights into the understanding of genome-wide homozygosity and heterozygosity patterns and genetic architecture of the Pakistani crossbred cattle. 2025-11 2025-10-08T13:17:36Z 2025-10-08T13:17:36Z Journal Article https://hdl.handle.net/10568/176890 en Limited Access Springer Un Nisa, F., Usman, M., Ali, A., Ali, M.B., Kaul, H., Asif, M., Mrode, R. and Mukhtar, Z. 2025. Estimation of genome-wide patterns of homozygosity, heterozygosity and inbreeding in crossbred dairy cattle population in Pakistan. Tropical Animal Health and Production 57(8): 396.
spellingShingle cattle
dairying
genomics
inbreeding
Un Nisa, F.
Usman, M.
Ali, A.
Ali, M.B.
Kaul, H.
Asif, M.
Mrode, Raphael A.
Mukhtar, Z.
Estimation of genome-wide patterns of homozygosity, heterozygosity and inbreeding in crossbred dairy cattle population in Pakistan
title Estimation of genome-wide patterns of homozygosity, heterozygosity and inbreeding in crossbred dairy cattle population in Pakistan
title_full Estimation of genome-wide patterns of homozygosity, heterozygosity and inbreeding in crossbred dairy cattle population in Pakistan
title_fullStr Estimation of genome-wide patterns of homozygosity, heterozygosity and inbreeding in crossbred dairy cattle population in Pakistan
title_full_unstemmed Estimation of genome-wide patterns of homozygosity, heterozygosity and inbreeding in crossbred dairy cattle population in Pakistan
title_short Estimation of genome-wide patterns of homozygosity, heterozygosity and inbreeding in crossbred dairy cattle population in Pakistan
title_sort estimation of genome wide patterns of homozygosity heterozygosity and inbreeding in crossbred dairy cattle population in pakistan
topic cattle
dairying
genomics
inbreeding
url https://hdl.handle.net/10568/176890
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AT alia estimationofgenomewidepatternsofhomozygosityheterozygosityandinbreedingincrossbreddairycattlepopulationinpakistan
AT alimb estimationofgenomewidepatternsofhomozygosityheterozygosityandinbreedingincrossbreddairycattlepopulationinpakistan
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AT mroderaphaela estimationofgenomewidepatternsofhomozygosityheterozygosityandinbreedingincrossbreddairycattlepopulationinpakistan
AT mukhtarz estimationofgenomewidepatternsofhomozygosityheterozygosityandinbreedingincrossbreddairycattlepopulationinpakistan

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