Repositorio Institucional
Repositorio Institucional
CONICET Digital
  • Inicio
  • EXPLORAR
    • AUTORES
    • DISCIPLINAS
    • COMUNIDADES
  • Estadísticas
  • Novedades
    • Noticias
    • Boletines
  • Ayuda
    • General
    • Datos de investigación
  • Acerca de
    • CONICET Digital
    • Equipo
    • Red Federal
  • Contacto
JavaScript is disabled for your browser. Some features of this site may not work without it.
  • INFORMACIÓN GENERAL
  • RESUMEN
  • ESTADISTICAS
 
Artículo

Genotype imputation accuracy in a F2 pig population using high density and low density SNP panels

Gualdron Duarte, Jose LuisIcon ; Bates, Ronald O.; Ernst, Catherine W.; Raney, Nancy E.; Cantet, Rodolfo Juan CarlosIcon ; Steibel, Juan P.
Fecha de publicación: 05/2013
Editorial: BioMed Central
Revista: BMC Genetics
ISSN: 1471-2156
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
Otras Producción Animal y Lechería

Resumen

Background: F2 resource populations have been used extensively to map QTL segregating between pig breeds. A limitation associated with the use of these resource populations for fine mapping of QTL is the reduced number of founding individuals and recombinations of founding haplotypes occurring in the population. These limitations, however, become advantageous when attempting to impute unobserved genotypes using within family segregation information. A trade-off would be to re-type F2 populations using high density SNP panels for founding individuals and low density panels (tagSNP) in F2 individuals followed by imputation. Subsequently a combined meta-analysis of several populations would provide adequate power and resolution for QTL mapping, and could be achieved at relatively low cost. Such a strategy allows the wealth of phenotypic information that has previously been obtained on experimental resource populations to be further mined for QTL identification. In this study we used experimental and simulated high density genotypes (HD-60K) from an F2 cross to estimate imputation accuracy under several genotyping scenarios. Results: Selection of tagSNP using physical distance or linkage disequilibrium information produced similar imputation accuracies. In particular, tagSNP sets averaging 1 SNP every 2.1 Mb (1,200 SNP genome-wide) yielded imputation accuracies (IA) close to 0.97. If instead of using custom panels, the commercially available 9K chip is used in the F2, IA reaches 0.99. In order to attain such high imputation accuracy the F0 and F1 generations should be genotyped at high density. Alternatively, when only the F0 is genotyped at HD, while F1 and F2 are genotyped with a 9K panel, IA drops to 0.90. Conclusions: Combining 60K and 9K panels with imputation in F2 populations is an appealing strategy to re-genotype existing populations at a fraction of the cost.
Palabras clave: Genotype Imputation , Tag Snps , Pigs
Ver el registro completo
 
Archivos asociados
Thumbnail
 
Tamaño: 1.873Mb
Formato: PDF
.
Descargar
Licencia
info:eu-repo/semantics/openAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
Identificadores
URI: http://hdl.handle.net/11336/26192
DOI: http://dx.doi.org/10.1186/1471-2156-14-38
URL: https://bmcgenet.biomedcentral.com/articles/10.1186/1471-2156-14-38
Colecciones
Articulos(OCA PQUE. CENTENARIO)
Articulos de OFICINA DE COORDINACION ADMINISTRATIVA PQUE. CENTENARIO
Citación
Gualdron Duarte, Jose Luis; Bates, Ronald O.; Ernst, Catherine W.; Raney, Nancy E.; Cantet, Rodolfo Juan Carlos; et al.; Genotype imputation accuracy in a F2 pig population using high density and low density SNP panels; BioMed Central; BMC Genetics; 14; 5-2013; 38-51
Compartir
Altmétricas
 

Enviar por e-mail
Separar cada destinatario (hasta 5) con punto y coma.
  • Facebook
  • X Conicet Digital
  • Instagram
  • YouTube
  • Sound Cloud
  • LinkedIn

Los contenidos del CONICET están licenciados bajo Creative Commons Reconocimiento 2.5 Argentina License

https://www.conicet.gov.ar/ - CONICET

Inicio

Explorar

  • Autores
  • Disciplinas
  • Comunidades

Estadísticas

Novedades

  • Noticias
  • Boletines

Ayuda

Acerca de

  • CONICET Digital
  • Equipo
  • Red Federal

Contacto

Godoy Cruz 2290 (C1425FQB) CABA – República Argentina – Tel: +5411 4899-5400 repositorio@conicet.gov.ar
TÉRMINOS Y CONDICIONES