POPREP-Population Structure and Pedigree Analysis

POPREP
Population Structure and Pedigree
Analysis
4/13/2015
1
Introduction
 POPREP is a web application (http://poprep.tzv.fal.de)
operating on the principle of uploading data.
 The software is available under the General Public
License (Free Software Foundation, Inc (1991)).
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Methodology
 Convert the pedigree file into input file format ASCII
(American Standard Code for Information Interchange)
 Open user interface which require six inputs
i. Email address to which the results will be sent
ii. Name of the breed
iii. Codes used for males and females
iv. Date format
v. Date separator
vi. Upload of the pedigree file to the website
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3
Methodology…
 Browse and upload the pedigree file
 Data requirements
i.
Animal ID (not null)
ii.
Sire ID (may be null)
iii.
Dam ID (may be null)
iv.
Date of birth of animal (may be null)
v.
Sex of the animal (not null)

The five columns are delimited by pipe sign
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4
Results-Population structure
 Number of breeding males and females by year
 Age structure of the parents by birth year of offspring
 Distribution of parity of dams at birth of offspring
 Generation interval
 Family size
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5
Number of breeding bulls registered in the herd
book
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6
Number of cows registered in the herd book
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7
Number of breeding males and females by year
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8
Age of parents used for breeding over the studied
period
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Generation interval of the Sahiwal breed in Kenya
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Number of progenies per dam
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Number of progenies per sire
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Results-Pedigree analysis
 Pedigree completeness per year
 Inbreeding
 Effective population size
 Average and rate of additive relationships
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Pedigree completeness index
Parameter
Average
pedigree
completeness index (%) for:
1st generation
2nd generation
3rd generation
4th generation
5th generation
6th generation
Longest ancestral path traced
Maximum
generation
equivalents
Average generation equivalents
4/13/2015
Value
75.7
73.8
69.9
64.7
58.3
51.4
16
6.41
2.46
14
Trend of the total number of registered and inbred
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Average inbreeding of the registered and inbred
animals
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Average inbreeding level of sires and dams
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Distribution of inbred animals by inbreeding
classes
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The trend of Ne
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19
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