Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data

Despite the importance of mutation rate, some difficulties exist in estimating it. Next-generation sequencing (NGS) data yields large numbers of single-nucleotide polymorphisms, which can make it feasible to estimate substitution rates. The genetic substitution rates of Hanwoo and Holstein cattle we...

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Main Authors: Young-Sup Lee, Donghyun Shin
Format: Article
Language:English
Published: BioMed Central 2018-03-01
Series:Genomics & Informatics
Subjects:
Online Access:http://genominfo.org/upload/pdf/gi-2018-16-1-14.pdf
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author Young-Sup Lee
Donghyun Shin
author_facet Young-Sup Lee
Donghyun Shin
author_sort Young-Sup Lee
collection DOAJ
description Despite the importance of mutation rate, some difficulties exist in estimating it. Next-generation sequencing (NGS) data yields large numbers of single-nucleotide polymorphisms, which can make it feasible to estimate substitution rates. The genetic substitution rates of Hanwoo and Holstein cattle were estimated using NGS data. Our main findings was to calculate the gene’s substitution rates. Through estimation of genetic substitution rates, we found: diving region of altered substitution density exists. This region may indicate a boundary between protected and unprotected genes. The protected region is mainly associated with the gene ontology terms of regulatory genes. The genes that distinguish Hanwoo from Holstein in terms of substitution rate predominantly have gene ontology terms related to blood and circulatory system. This might imply that Hanwoo and Holstein evolved with dissimilar mutation rates and processes after domestication. The difference in meat quality between Hanwoo and Holstein could originate from differential evolution of the genes related to these blood and circulatory system ontology terms.
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institution Kabale University
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spelling doaj-art-92d98e2724b7412d974f50de31fac8fa2025-02-02T23:39:17ZengBioMed CentralGenomics & Informatics2234-07422018-03-01161142010.5808/GI.2018.16.1.14506Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing DataYoung-Sup LeeDonghyun ShinDespite the importance of mutation rate, some difficulties exist in estimating it. Next-generation sequencing (NGS) data yields large numbers of single-nucleotide polymorphisms, which can make it feasible to estimate substitution rates. The genetic substitution rates of Hanwoo and Holstein cattle were estimated using NGS data. Our main findings was to calculate the gene’s substitution rates. Through estimation of genetic substitution rates, we found: diving region of altered substitution density exists. This region may indicate a boundary between protected and unprotected genes. The protected region is mainly associated with the gene ontology terms of regulatory genes. The genes that distinguish Hanwoo from Holstein in terms of substitution rate predominantly have gene ontology terms related to blood and circulatory system. This might imply that Hanwoo and Holstein evolved with dissimilar mutation rates and processes after domestication. The difference in meat quality between Hanwoo and Holstein could originate from differential evolution of the genes related to these blood and circulatory system ontology terms.http://genominfo.org/upload/pdf/gi-2018-16-1-14.pdfgenetic substitution rateHanwoohidden substitution factorHolsteinwhole genome sequencing
spellingShingle Young-Sup Lee
Donghyun Shin
Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data
Genomics & Informatics
genetic substitution rate
Hanwoo
hidden substitution factor
Holstein
whole genome sequencing
title Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data
title_full Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data
title_fullStr Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data
title_full_unstemmed Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data
title_short Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data
title_sort estimation of the genetic substitution rate of hanwoo and holstein cattle using whole genome sequencing data
topic genetic substitution rate
Hanwoo
hidden substitution factor
Holstein
whole genome sequencing
url http://genominfo.org/upload/pdf/gi-2018-16-1-14.pdf
work_keys_str_mv AT youngsuplee estimationofthegeneticsubstitutionrateofhanwooandholsteincattleusingwholegenomesequencingdata
AT donghyunshin estimationofthegeneticsubstitutionrateofhanwooandholsteincattleusingwholegenomesequencingdata