Assessing effective population size, coancestry and inbreeding effects on litter size using the pedigree and SNP data in closed lines of the Iberian pig breed

2015 ◽  
Vol 133 (2) ◽  
pp. 145-154 ◽  
Author(s):  
L. Silió ◽  
C. Barragán ◽  
A.I. Fernández ◽  
J. García-Casco ◽  
M.C. Rodríguez
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Litter Size ◽  
Effective Population ◽  
Snp Data ◽  
Iberian Pig

scholarly journals Genetic Diversity in the Italian Holstein Dairy Cattle Based on Pedigree and SNP Data Prior and After Genomic Selection

2022 ◽  
Vol 8 ◽  
Author(s):  
Michela Ablondi ◽  
Alberto Sabbioni ◽  
Giorgia Stocco ◽  
Claudio Cipolat-Gotet ◽  
Christos Dadousis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dairy Cattle ◽  
Population Size ◽  
Genomic Selection ◽  
Effective Population Size ◽  
Genomic Data ◽  
Future Market ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Snp Data

Genetic diversity has become an urgent matter not only in small local breeds but also in more specialized ones. While the use of genomic data in livestock breeding programs increased genetic gain, there is increasing evidence that this benefit may be counterbalanced by the potential loss of genetic variability. Thus, in this study, we aimed to investigate the genetic diversity in the Italian Holstein dairy cattle using pedigree and genomic data from cows born between 2002 and 2020. We estimated variation in inbreeding, effective population size, and generation interval and compared those aspects prior to and after the introduction of genomic selection in the breed. The dataset contained 84,443 single-nucleotide polymorphisms (SNPs), and 74,485 cows were analyzed. Pedigree depth based on complete generation equivalent was equal to 10.67. A run of homozygosity (ROH) analysis was adopted to estimate SNP-based inbreeding (FROH). The average pedigree inbreeding was 0.07, while the average FROH was more than double, being equal to 0.17. The pattern of the effective population size based on pedigree and SNP data was similar although different in scale, with a constant decrease within the last five generations. The overall inbreeding rate (ΔF) per year was equal to +0.27% and +0.44% for Fped and FROH throughout the studied period, which corresponded to about +1.35% and +2.2% per generation, respectively. A significant increase in the ΔF was found since the introduction of genomic selection in the breed. This study in the Italian Holstein dairy cattle showed the importance of controlling the loss of genetic diversity to ensure the long-term sustainability of this breed, as well as to guarantee future market demands.

scholarly journals EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON CORRELATED RESPONSES TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽  
1973 ◽  
Vol 74 (1) ◽  
pp. 157-170
Author(s):  
E J Eisen ◽  
J P Hanrahan ◽  
J E Legates
Keyword(s):  
Body Weight ◽  
Population Size ◽  
Effective Population Size ◽  
Litter Size ◽  
The Body ◽  
Selection Intensity ◽  
Correlated Responses ◽  
Effective Population ◽  
Population Sizes ◽  
Selection For

ABSTRACT Correlated responses to selection for postweaning gain in mice were studied to determine the influence of population size and selection intensity. Correlated traits measured were three-, six- and eight-week body weights, litter size, twelve-day litter weight, proportion infertile matings and two indexes of reproductive performance. In general, the results agreed with observations made on direct response: correlated responses in the body weight traits and litter size increased as (1) selection intensity increased and (2) effective population size increased. Correlated responses in the body weight traits and litter size were positive in the large population size lines (16 pairs), as expected from the positive genetic correlation between these traits and postweaning gain. However, several negative correlated responses were observed at small population sizes (one and two pairs). Within each level of selection intensity, traits generally associated with fitness tended to decline most in the very small populations (one and two pairs) and in the large populations (16 pairs) for apparently different reasons. The fitness decline at the small effective population sizes was attributable to inbreeding depression. In contrast, it was postulated that the fitness decline at the large effective population size was due to selection moving the population mean for body weight and a trait positively correlated genetically with body weight (i.e., percent body fat) away from an optimum

scholarly journals The Analysis of Czech Genetic Resources of Nutrias (Myocastor coypus)

2018 ◽  
Vol 49 (2) ◽  
pp. 93-97
Author(s):  
T. Němeček ◽  
E. Tůmová
Keyword(s):  
Genetic Resources ◽  
Population Size ◽  
Effective Population Size ◽  
Litter Size ◽  
Biodiversity Loss ◽  
Effective Population ◽  
Myocastor Coypus ◽  
Colour Type

Abstract The aim of this study is to evaluate the effective population size and fertility in the Czech Genetic Resources of nutrias during the last ten years. This study includes three Czech colour types of nutrias: Czech Type of Standard (ST), Moravian Silver (MS), and Prestice Multicolour (PM). The effective population size of ST shows that this colour type is endangered, while MS and PM are critical. The average number of pregnancy was the highest (P ≤ 0.004) in ST (1.7 pregnancy) and the lowest in PM (1.3 pregnancy). ST and MS nutrias had the significantly biggest litter size (P ≤ 0.004). For the number of kits born per female in a year (P < 0.001) the significantly lowest value was in PM (5.1 kits). For weaned kits the highest value (P ≤ 0.006) was in ST (4.8 kits). The results showed that the population size of MS and PM is low and there is a risk of biodiversity loss in these colour types.

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