POPREP Population Structure and Pedigree Analysis 12/5/20151.

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Presentation transcript:

POPREP Population Structure and Pedigree Analysis 12/5/20151

Introduction  POPREP is a web application ( operating on the principle of uploading data.  The software is available under the General Public License (Free Software Foundation, Inc (1991)). 12/5/20152

Methodology  Convert the pedigree file into input file format ASCII (American Standard Code for Information Interchange)  Open user interface which require six inputs i. 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 12/5/20153

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 12/5/20154

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 12/5/20155

Number of breeding bulls registered in the herd book 12/5/20156

Number of cows registered in the herd book 12/5/20157

Number of breeding males and females by year 12/5/20158

Age of parents used for breeding over the studied period 12/5/20159

Generation interval of the Sahiwal breed in Kenya 12/5/201510

Number of progenies per dam 12/5/201511

Number of progenies per sire 12/5/201512

Results-Pedigree analysis  Pedigree completeness per year  Inbreeding  Effective population size  Average and rate of additive relationships 12/5/201513

Pedigree completeness index 12/5/ ParameterValue Average pedigree completeness index (%) for: 1 st generation 2 nd generation 3 rd generation 4 th generation 5 th generation 6 th generation Longest ancestral path traced16 Maximum generation equivalents 6.41 Average generation equivalents2.46

Trend of the total number of registered and inbred 12/5/201515

Average inbreeding of the registered and inbred animals 12/5/201516

Average inbreeding level of sires and dams 12/5/201517

Distribution of inbred animals by inbreeding classes 12/5/201518

The trend of Ne 12/5/201519