Genome-Wiide estimates of coancestry, in breeding and effective population size in the Spanish Holstein population

Rodríguez Ramilo, Silvia Teresa and Fernández Diezma, Jesús and Toro Ibañez, Miguel Angel and Hernández, Delfino and Villanueva Cajide, Beatriz (2015). Genome-Wiide estimates of coancestry, in breeding and effective population size in the Spanish Holstein population. "Plos One" ; pp. 1-11. ISSN 1932-6203. https://doi.org/10.1371/journal.pone.0124157.

Description

Title: Genome-Wiide estimates of coancestry, in breeding and effective population size in the Spanish Holstein population
Author/s:
  • Rodríguez Ramilo, Silvia Teresa
  • Fernández Diezma, Jesús
  • Toro Ibañez, Miguel Angel
  • Hernández, Delfino
  • Villanueva Cajide, Beatriz
Item Type: Article
Título de Revista/Publicación: Plos One
Date: 2015
Subjects:
Faculty: E.T.S.I. Agrónomos (UPM) [antigua denominación]
Department: Producción Agraria
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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Abstract

Estimates of effective population size in the Holstein cattle breed have usually been low despite the large number of animals that constitute this breed. Effective population size is inversely related to the rates at which coancestry and inbreeding increase and these rates have been high as a consequence of intense and accurate selection. Traditionally, coancestry and inbreeding coefficients have been calculated from pedigree data. However, the development of genome-wide single nucleotide polymorphisms has increased the interest of calculating these coefficients from molecular data in order to improve their accuracy. In this study, genomic estimates of coancestry, inbreeding and effective population size were obtained in the Spanish Holstein population and then compared with pedigree-based estimates. A total of 11,135 animals genotyped with the Illumina BovineSNP50 BeadChip were available for the study. After applying filtering criteria, the final genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Pedigree data from those genotyped animals included 31,203 animals. These individuals represented only the last five generations in order to homogenise the amount of pedigree information across animals. Genomic estimates of coancestry and inbreeding were obtained from identity by descent segments (coancestry) or runs of homozygosity (inbreeding). The results indicate that the percentage of variance of pedigree-based coancestry estimates explained by genomic coancestry estimates was higher than that for inbreeding. Estimates of effective population size obtained from genome-wide and pedigree information were consistent and ranged from about 66 to 79. These low values emphasize the need of controlling the rate of increase of coancestry and inbreeding in Holstein selection programmes.

More information

Item ID: 40901
DC Identifier: http://oa.upm.es/40901/
OAI Identifier: oai:oa.upm.es:40901
DOI: 10.1371/journal.pone.0124157
Official URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124157
Deposited by: Memoria Investigacion
Deposited on: 08 Jul 2016 15:21
Last Modified: 08 Jul 2016 15:21
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