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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BioMed Central
2018-03-01
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| Series: | Genomics & Informatics |
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| 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. |
| format | Article |
| id | doaj-art-92d98e2724b7412d974f50de31fac8fa |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-03-01 |
| publisher | BioMed Central |
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| series | Genomics & Informatics |
| 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 |