Selection signatures in Canchim beef cattle
Background: Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel. Results: A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS>5, with 39 and nine statistically significant SNPs (P<0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development. Conclusions: The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization.
Main Authors: | , , , , , , , , |
---|---|
Other Authors: | |
Format: | Artigo de periódico biblioteca |
Language: | English eng |
Published: |
2017-01-23
|
Subjects: | Genômica, Polimorfismo de nucleotídeo único, Extended haplotype homozygosity, Gado de corte, Composite breeds, Genomics, Single nucleotide polymorphism, Beef cattle, Quantitative trait loci, |
Online Access: | http://www.alice.cnptia.embrapa.br/alice/handle/doc/1061492 |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-alice-doc-1061492 |
---|---|
record_format |
koha |
spelling |
dig-alice-doc-10614922017-08-16T04:04:57Z Selection signatures in Canchim beef cattle URBINATI, I. STAFUZZA, N. B. OLIVEIRA, M. T. CHUD, T. C. S. HIGA, R. H. REGITANO, L. C. de A. ALENCAR, M. M. de BUZANSKAS, M. E. MUNARI, D. P. ISMAEL URBINATI, Unesp Jaboticabal; NEDENIA BONVINO STAFUZZA, Unesp Jaboticabal; MARCOS TÚLIO OLIVEIRA, Unesp Jaboticabal; TATIANE CRISTINA SELEGUIM CHUD, Unesp Jaboticabal; ROBERTO HIROSHI HIGA, CNPTIA; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; MAURICIO MELLO DE ALENCAR, CPPSE; MARCOS ELI BUZANSKAS, Unesp Jaboticabal; DANÍSIO PRADO MUNARI, Unesp Jaboticabal. Genômica Polimorfismo de nucleotídeo único Extended haplotype homozygosity Gado de corte Composite breeds Genomics Single nucleotide polymorphism Beef cattle Quantitative trait loci Background: Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel. Results: A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS>5, with 39 and nine statistically significant SNPs (P<0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development. Conclusions: The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization. Na publicação: Luciana Correia de Almeida Regitano. 2017-01-23T11:11:11Z 2017-01-23T11:11:11Z 2017-01-23 2016 2017-03-20T11:11:11Z Artigo de periódico Journal of Animal Science and Biotechnology, v. 7, p. 1-9, 2016. http://www.alice.cnptia.embrapa.br/alice/handle/doc/1061492 10.1186/s40104-016-0089-5 en eng openAccess |
institution |
EMBRAPA |
collection |
DSpace |
country |
Brasil |
countrycode |
BR |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-alice |
tag |
biblioteca |
region |
America del Sur |
libraryname |
Sistema de bibliotecas de EMBRAPA |
language |
English eng |
topic |
Genômica Polimorfismo de nucleotídeo único Extended haplotype homozygosity Gado de corte Composite breeds Genomics Single nucleotide polymorphism Beef cattle Quantitative trait loci Genômica Polimorfismo de nucleotídeo único Extended haplotype homozygosity Gado de corte Composite breeds Genomics Single nucleotide polymorphism Beef cattle Quantitative trait loci |
spellingShingle |
Genômica Polimorfismo de nucleotídeo único Extended haplotype homozygosity Gado de corte Composite breeds Genomics Single nucleotide polymorphism Beef cattle Quantitative trait loci Genômica Polimorfismo de nucleotídeo único Extended haplotype homozygosity Gado de corte Composite breeds Genomics Single nucleotide polymorphism Beef cattle Quantitative trait loci URBINATI, I. STAFUZZA, N. B. OLIVEIRA, M. T. CHUD, T. C. S. HIGA, R. H. REGITANO, L. C. de A. ALENCAR, M. M. de BUZANSKAS, M. E. MUNARI, D. P. Selection signatures in Canchim beef cattle |
description |
Background: Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel. Results: A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS>5, with 39 and nine statistically significant SNPs (P<0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development. Conclusions: The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization. |
author2 |
ISMAEL URBINATI, Unesp Jaboticabal; NEDENIA BONVINO STAFUZZA, Unesp Jaboticabal; MARCOS TÚLIO OLIVEIRA, Unesp Jaboticabal; TATIANE CRISTINA SELEGUIM CHUD, Unesp Jaboticabal; ROBERTO HIROSHI HIGA, CNPTIA; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; MAURICIO MELLO DE ALENCAR, CPPSE; MARCOS ELI BUZANSKAS, Unesp Jaboticabal; DANÍSIO PRADO MUNARI, Unesp Jaboticabal. |
author_facet |
ISMAEL URBINATI, Unesp Jaboticabal; NEDENIA BONVINO STAFUZZA, Unesp Jaboticabal; MARCOS TÚLIO OLIVEIRA, Unesp Jaboticabal; TATIANE CRISTINA SELEGUIM CHUD, Unesp Jaboticabal; ROBERTO HIROSHI HIGA, CNPTIA; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; MAURICIO MELLO DE ALENCAR, CPPSE; MARCOS ELI BUZANSKAS, Unesp Jaboticabal; DANÍSIO PRADO MUNARI, Unesp Jaboticabal. URBINATI, I. STAFUZZA, N. B. OLIVEIRA, M. T. CHUD, T. C. S. HIGA, R. H. REGITANO, L. C. de A. ALENCAR, M. M. de BUZANSKAS, M. E. MUNARI, D. P. |
format |
Artigo de periódico |
topic_facet |
Genômica Polimorfismo de nucleotídeo único Extended haplotype homozygosity Gado de corte Composite breeds Genomics Single nucleotide polymorphism Beef cattle Quantitative trait loci |
author |
URBINATI, I. STAFUZZA, N. B. OLIVEIRA, M. T. CHUD, T. C. S. HIGA, R. H. REGITANO, L. C. de A. ALENCAR, M. M. de BUZANSKAS, M. E. MUNARI, D. P. |
author_sort |
URBINATI, I. |
title |
Selection signatures in Canchim beef cattle |
title_short |
Selection signatures in Canchim beef cattle |
title_full |
Selection signatures in Canchim beef cattle |
title_fullStr |
Selection signatures in Canchim beef cattle |
title_full_unstemmed |
Selection signatures in Canchim beef cattle |
title_sort |
selection signatures in canchim beef cattle |
publishDate |
2017-01-23 |
url |
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1061492 |
work_keys_str_mv |
AT urbinatii selectionsignaturesincanchimbeefcattle AT stafuzzanb selectionsignaturesincanchimbeefcattle AT oliveiramt selectionsignaturesincanchimbeefcattle AT chudtcs selectionsignaturesincanchimbeefcattle AT higarh selectionsignaturesincanchimbeefcattle AT regitanolcdea selectionsignaturesincanchimbeefcattle AT alencarmmde selectionsignaturesincanchimbeefcattle AT buzanskasme selectionsignaturesincanchimbeefcattle AT munaridp selectionsignaturesincanchimbeefcattle |
_version_ |
1756023067605204992 |