PHENOTYPING COWS NEW TOOLS BY COMBINING MIR-SPECTRA AND DHI-DATA M Kammer 1, J Duda 1, C Baumgartner 2 1 LKV Bayern e.v., 2 MPR Bayern e.v. 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur Martin Kammer
Introduction & Goals Introduction Typical milk parameters (fat, protein and urea content) analyzed using mid-infrared spectra (MIR-spectra) MIR-spectra contain information from all components in milk Goals Determine biological parameters from chemical information in milk Create new management tools for farmers Focus of presentation: pregnancy status of the cow 60 to 160 days in milk Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 2
Overview Partners LKV Bayern e.v. Dairy Health Improvement Association of Bavaria And MPR Bayern e.v. Raw Milk Testing Lab of Bavaria Data Acquisition One raw milk lab - One type of IR-apparatus Currently (09.04.2015) 27,156,877 MIR-spectra from 24,797 farms in database All data accessible from one database: animal and milk recording data from dairy health improvement association and spectra Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 3
Dataset Reference for pregnancy status Calving and insemination dates General constraints Only German Simmental cows 60 160 days in milk 11 70 days after insemination Data in two independent datasets: Calibration - Training Set: 565,632 spectra collected in 2013 Validation - Test Set: 100,946 spectra collected from cows inseminated from January to February 2014 Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 4
Spectra: Pregnant & Non-Pregnant Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 5
Spectra: Pregnant & Non-Pregnant Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 6
Methods MIR-spectra Preprocessing None First Derivative of MIR-spectra Partial Least Squares Regression with 20 components Correction for Day in Milk based on a linear Model: Estimate the MIR-spectrum of the non-pregnant cow Classification Linear Discriminant Analysis Linear Model Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 7
Quality Measures Test Set Non-Pregnant Pregnant Classification Correct Non- Pregnant False Non- Pregnant Correct Pregnant False Pregnant Sensitivity: Percentage of correctly identified records of non-pregnant cows out of all records of non-pregnant cows Specificity: Percentage of correctly identified records of pregnant cows out of all records of pregnant cows Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 8
Results: Preprocessing Sensitivity LDA Specificity LDA Sensitivity Linear Model Specificity Linear Model None 61.46 % 58.64 % 64.45 % 55.22 % 1. derivative 59.31 % 60.63 % 63.13 % 55.74 % PLSR 56.30 % 61.77 % 57.81 % 60.38 % Correction DIM 58.53 % 56.63 % 57.91 % 56.87 % 1. Derivative + Correction DIM 51.60 % 63.38 % 54.12 % 60.15 % Trend: Decrease in sensitivity coupled with increase in specificity Sensitivity: Correct classification of nonpregnancy Specificity: Correct classification of pregnancy Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 9
Results: Additional Animal Data Data directly in model for classification non-pregnant / pregnant Investigated: Fat-protein-ratio Urea content Days in milk Time since last insemination Breeding value for fertility Non-return rate on farm Average milk yield on farm Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 10
Results: Additional Animal Data Only time since last insemination resulted in appreciable improvement! Only MIRspectra MIR-spectra + time since last insemination Sensitivity LDA Specificity LDA Sensitivity Linear Model Specificity Linear Model 61.46 % 58.64 % 64.45 % 55.22 % 67.72 % 67.27 % 67,11 % 67,84 % Almost no difference between LDA and linear model using time since last insemination in addition to MIRspectra Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 11
Results: Additional Data MIR-spectra contain information related to pregnancy status of cows Very small changes in MIR-spectra by pregnancy - not sufficient for practical use Additional animal data improves quality of models Focus on ways to improve models by combining MIRspectra with animal data Phenotyping cows new tools by combining MIR-spectra and DHI-data 16.04.2015 Final OptiMIR Scientific and Expert Meeting Namur M Kammer 12
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