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Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle
Dabieshan cattle (DBSC) are a valuable genetic resource for indigenous cattle breeds in China. It is a small to medium-sized breed with slower growth, but with good meat quality and fat deposition. Genetic markers could be used for the estimation of population genetic structure and genetic parameter...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9859230/ https://www.ncbi.nlm.nih.gov/pubmed/36672850 http://dx.doi.org/10.3390/genes14010107 |
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author | Jin, Hai Zhao, Shuanping Jia, Yutang Xu, Lei |
author_facet | Jin, Hai Zhao, Shuanping Jia, Yutang Xu, Lei |
author_sort | Jin, Hai |
collection | PubMed |
description | Dabieshan cattle (DBSC) are a valuable genetic resource for indigenous cattle breeds in China. It is a small to medium-sized breed with slower growth, but with good meat quality and fat deposition. Genetic markers could be used for the estimation of population genetic structure and genetic parameters. In this work, we genotyped the DBSC breeding population (n = 235) with the GeneSeek Genomic Profiler (GGP) 100 k density genomic chip. Genotype data of 222 individuals and 81,579 SNPs were retained after quality control. The average minor allele frequency (MAF) was 0.20 and the average linkage disequilibrium (LD) level (r(2)) was 0.67 at a distance of 0–50 Kb. The estimated relationship coefficient and effective population size (Ne) were 0.023 and 86 for the current generation. In addition, we used genotype data to estimate the genetic parameters of the population’s phenotypic traits. Among them, height at hip cross (HHC) and shin circumference (SC) were rather high heritability traits, with heritability of 0.41 and 0.54, respectively. The results reflected the current cattle population’s extent of inbreeding and history. Through the principal breeding parameters, genomic breeding would significantly improve the genetic progress of breeding. |
format | Online Article Text |
id | pubmed-9859230 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-98592302023-01-21 Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle Jin, Hai Zhao, Shuanping Jia, Yutang Xu, Lei Genes (Basel) Article Dabieshan cattle (DBSC) are a valuable genetic resource for indigenous cattle breeds in China. It is a small to medium-sized breed with slower growth, but with good meat quality and fat deposition. Genetic markers could be used for the estimation of population genetic structure and genetic parameters. In this work, we genotyped the DBSC breeding population (n = 235) with the GeneSeek Genomic Profiler (GGP) 100 k density genomic chip. Genotype data of 222 individuals and 81,579 SNPs were retained after quality control. The average minor allele frequency (MAF) was 0.20 and the average linkage disequilibrium (LD) level (r(2)) was 0.67 at a distance of 0–50 Kb. The estimated relationship coefficient and effective population size (Ne) were 0.023 and 86 for the current generation. In addition, we used genotype data to estimate the genetic parameters of the population’s phenotypic traits. Among them, height at hip cross (HHC) and shin circumference (SC) were rather high heritability traits, with heritability of 0.41 and 0.54, respectively. The results reflected the current cattle population’s extent of inbreeding and history. Through the principal breeding parameters, genomic breeding would significantly improve the genetic progress of breeding. MDPI 2022-12-29 /pmc/articles/PMC9859230/ /pubmed/36672850 http://dx.doi.org/10.3390/genes14010107 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Jin, Hai Zhao, Shuanping Jia, Yutang Xu, Lei Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle |
title | Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle |
title_full | Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle |
title_fullStr | Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle |
title_full_unstemmed | Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle |
title_short | Estimation of Linkage Disequilibrium, Effective Population Size, and Genetic Parameters of Phenotypic Traits in Dabieshan Cattle |
title_sort | estimation of linkage disequilibrium, effective population size, and genetic parameters of phenotypic traits in dabieshan cattle |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9859230/ https://www.ncbi.nlm.nih.gov/pubmed/36672850 http://dx.doi.org/10.3390/genes14010107 |
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