Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data

The objective of this study was to calculate the extent and decay of linkage disequilibrium (LD) in 96 crossbred Vrindavani cattle genotyped with Bovine SNP50K Bead Chip. After filtering, 43,821 SNPs were retained for final analysis, across 2500.3 Mb of autosome. A significant percentage of SNPs was...

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Autores principales:	Akansha Singh, Amit Kumar, Arnav Mehrotra, Karthikeyan A., Ashwni Kumar Pandey, B. P. Mishra, Triveni Dutt
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3104a8993344450ba5665c3b7539b603
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spelling	oai:doaj.org-article:3104a8993344450ba5665c3b7539b6032021-11-18T08:14:36ZEstimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data1932-6203https://doaj.org/article/3104a8993344450ba5665c3b7539b6032021-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8584695/?tool=EBIhttps://doaj.org/toc/1932-6203The objective of this study was to calculate the extent and decay of linkage disequilibrium (LD) in 96 crossbred Vrindavani cattle genotyped with Bovine SNP50K Bead Chip. After filtering, 43,821 SNPs were retained for final analysis, across 2500.3 Mb of autosome. A significant percentage of SNPs was having minor allele frequency of less than 0.20. The extent of LD between autosomal SNPs up to 10 Mb apart across the genome was measured using r2 statistic. The mean r2 value was 0.43, if pairwise distance of marker was less than10 kb and it decreased further to 0.21 for 25–50 kb markers distance. Further, the effect of minor allele frequency and sample size on LD estimate was investigated. The LD value decreased with the increase in inter-marker distance, and increased with the increase of minor allelic frequency. The estimated inbreeding coefficient and effective population size were 0.04, and 46 for present generation, which indicated small and unstable population of Vrindavani cattle. These findings suggested that a denser or breed specific SNP panel would be required to cover all genome of Vrindavani cattle for genome wide association studies (GWAS).Akansha SinghAmit KumarArnav MehrotraKarthikeyan A.Ashwni Kumar PandeyB. P. MishraTriveni DuttPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Akansha Singh Amit Kumar Arnav Mehrotra Karthikeyan A. Ashwni Kumar Pandey B. P. Mishra Triveni Dutt Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data
description	The objective of this study was to calculate the extent and decay of linkage disequilibrium (LD) in 96 crossbred Vrindavani cattle genotyped with Bovine SNP50K Bead Chip. After filtering, 43,821 SNPs were retained for final analysis, across 2500.3 Mb of autosome. A significant percentage of SNPs was having minor allele frequency of less than 0.20. The extent of LD between autosomal SNPs up to 10 Mb apart across the genome was measured using r2 statistic. The mean r2 value was 0.43, if pairwise distance of marker was less than10 kb and it decreased further to 0.21 for 25–50 kb markers distance. Further, the effect of minor allele frequency and sample size on LD estimate was investigated. The LD value decreased with the increase in inter-marker distance, and increased with the increase of minor allelic frequency. The estimated inbreeding coefficient and effective population size were 0.04, and 46 for present generation, which indicated small and unstable population of Vrindavani cattle. These findings suggested that a denser or breed specific SNP panel would be required to cover all genome of Vrindavani cattle for genome wide association studies (GWAS).
format	article
author	Akansha Singh Amit Kumar Arnav Mehrotra Karthikeyan A. Ashwni Kumar Pandey B. P. Mishra Triveni Dutt
author_facet	Akansha Singh Amit Kumar Arnav Mehrotra Karthikeyan A. Ashwni Kumar Pandey B. P. Mishra Triveni Dutt
author_sort	Akansha Singh
title	Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data
title_short	Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data
title_full	Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data
title_fullStr	Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data
title_full_unstemmed	Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data
title_sort	estimation of linkage disequilibrium levels and allele frequency distribution in crossbred vrindavani cattle using 50k snp data
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/3104a8993344450ba5665c3b7539b603
work_keys_str_mv	AT akanshasingh estimationoflinkagedisequilibriumlevelsandallelefrequencydistributionincrossbredvrindavanicattleusing50ksnpdata AT amitkumar estimationoflinkagedisequilibriumlevelsandallelefrequencydistributionincrossbredvrindavanicattleusing50ksnpdata AT arnavmehrotra estimationoflinkagedisequilibriumlevelsandallelefrequencydistributionincrossbredvrindavanicattleusing50ksnpdata AT karthikeyana estimationoflinkagedisequilibriumlevelsandallelefrequencydistributionincrossbredvrindavanicattleusing50ksnpdata AT ashwnikumarpandey estimationoflinkagedisequilibriumlevelsandallelefrequencydistributionincrossbredvrindavanicattleusing50ksnpdata AT bpmishra estimationoflinkagedisequilibriumlevelsandallelefrequencydistributionincrossbredvrindavanicattleusing50ksnpdata AT trivenidutt estimationoflinkagedisequilibriumlevelsandallelefrequencydistributionincrossbredvrindavanicattleusing50ksnpdata
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Estimation of linkage disequilibrium levels and allele frequency distribution in crossbred Vrindavani cattle using 50K SNP data

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