GENETIC ANALYSIS OF FOURIER TRANSFORM INFRARED MILK SPECTRA
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1 GENETIC ANALYSIS OF FOURIER TRANSFORM INFRARED MILK SPECTRA WCGALP 2018 Roos M. Zaalberg, N. Shetty, L. Janss, and A.J. Buitenhuis
2 FT-IR MILK SPECTRA Energy transmitted H H O H H H H O O Energy absorbed
3 FT-IR MILK SPECTRA Fourier Transform Infrared Energy transmitted Mathematical transformation Fast Cheap H H O H H H H O High definition O Energy absorbed
4 APPLICATIONS Prediction Major milk components Energy balance Metabolic diseases Protein Lactose Fat
5 GENETICS Milk spectra heritable Associated to GENOMIC CORRELATIONS? BREED DIFFERENCES? DGAT1 CSN (casein cluster) LGB (β-lactoglobulin)
6 AIMS Estimate heritability of transmittance values for 1,060 individual wavenumbers from the infrared region of 5, cm -1. Estimate genomic correlations between transmittance values of wavenumbers with a high heritability. Analyse breed differences.
7 MATERIALS & METHODS
8 GENOTYPES Danish Holstein (DH) 324 herds 3,278 cows Danish Jersey (DJ) 175 herds 3,426 cows Imputed from 10k to 50k Beagle4
9 PHENOTYPES Danish Holstein (DH) Danish Jersey (DJ) 19,690 Milk samples 10/ / samples per cow 20, days between records DIM
10 PHENOTYPES Danish Holstein (DH) Danish Jersey (DJ) Milk samples 19,690 20,789 FT-IR spectral analysis 5, cm -1 1,060 wavenumbers
11 MODEL Bayesian approach Bayz
12 MODEL Heritability Fixed effects Random effect Uniform distribution Normal distribution # SNPs SNP effects Power LASSO distribution SNP effect size
13 MODEL Genomic correlations Heritability analysis Select Wavenumbers with high heritability
14 MODEL Genomic correlations Bivariate model Fixed effects Random effect SNP effects Uniform distribution Normal distribution Normal distribution
15 MODEL
16 DISCUSSION & RESULTS
17 Lactose Protein Water Fat HERITABILITY Fat Water
18 Lactose Protein Water Fat HERITABILITY Fat Water
19 HERITABILITY Individual wavenumbers moderately heritable. Statistical Highest peaks approach for fat, protein and lactose Breed differences Other studies # SNPs Power Mixture LASSO distribution Similar pattern Low heritability estimates Why? SNP effect size
20 Lactose WAVENUMBER SELECTION Protein Water Fat Fat Water 15 selected wavenumbers
21 GENOMIC CORRELATION Lactose Protein Fat
22 GENOMIC CORRELATION Lactose Protein Fat ,22-0,33-0,87-0,92 0,12-0,92 0,92-0,53 0,84 0,96-0,97 0,96-0,94-0,93 0, ,20 0,91 0,77 0,58 0,71-0,11 0,56-0,37-0,57 0,41-0,53 0,76 0,73-0, ,22 0,94 0,23 0,92-0,81 0,58-0,84-0,94 0,91-0,91 0,95 0,94-0, ,25 0,50 0,97-0,60 0,91-0,64-0,95 0,91-0,96 0,96 0,96-0, ,16 0,63 0,76 0,85 0,84 0,14-0,28 0,03 0,20 0,31 0, ,30-0,48 0,94-0,47-0,94 0,89-0,95 0,96 0,96-0, ,10 0,49 0,94 0,92-0,93 0,91-0,86-0,75 0, ,16 0,39-0,54 0,37-0,67 0,71 0,84-0, ,14 0,88-0,89 0,85-0,83-0,74 0, ,19-0,95 0,97-0,96-0,96 0, ,22-0,96 0,94 0,93-0, ,20-0,96-0,95 0, ,25 0,96-0, ,28-0, ,20
23 GENOMIC CORRELATION 1 Lactose Protein Fat ,22-0,33-0,87-0,92 0,12-0,92 0,92-0,53 0,84 0,96-0,97 0,96-0,94-0,93 0, ,20 0,91 0,77 0,58 0,71-0,11 0,56-0,37-0,57 0,41-0,53 0,76 0,73-0, ,22 0,94 0,23 0,92-0,81 0,58-0,84-0,94 0,91-0,91 0,95 0,94-0, ,25 0,50 0,97-0,60 0,91-0,64-0,95 0,91-0,96 0,96 0,96-0, ,16 0,63 0,76 0,85 0,84 0,14-0,28 0,03 0,20 0,31 0, ,30-0,48 0,94-0,47-0,94 0,89-0,95 0,96 0,96-0, ,10 0,49 0,94 0,92-0,93 0,91-0,86-0,75 0, ,16 0,39-0,54 0,37-0,67 0,71 0,84-0,23 Genomic correlation > 0.8 or < ,14 0,88-0,89 0,85-0,83-0,74 0, ,19-0,95 0,97-0,96-0,96 0, ,22-0,96 0,94 0,93-0,96 Why so many? ,20-0,96-0,95 0, ,25 0,96-0,92 Fat molecules interact with many wavenumbers! ,28-0, ,20
24 GENOMIC CORRELATION 2 Lactose Protein Fat ,22-0,33-0,87-0,92 0,12-0,92 0,92-0,53 0,84 0,96-0,97 0,96-0,94-0,93 0, ,20 0,91 0,77 0,58 0,71-0,11 0,56-0,37-0,57 0,41-0,53 0,76 0,73-0, ,22 0,94 0,23 0,92-0,81 0,58-0,84-0,94 0,91-0,91 0,95 0,94-0, ,25 0,50 0,97-0,60 0,91-0,64-0,95 0,91-0,96 0,96 0,96-0, ,16 0,63 0,76 0,85 0,84 0,14-0,28 0,03 0,20 0,31 0, ,30-0,48 0,94-0,47-0,94 0,89-0,95 0,96 0,96-0, ,10 0,49 0,94 0,92-0,93 0,91-0,86-0,75 0, ,16 0,39-0,54 0,37-0,67 0,71 0,84-0,23 Two groups within selection ,14 0,88-0,89 0,85-0,83-0,74 0, ,19-0,95 0,97-0,96-0,96 0,96 Within group Blue ,22-0,96 0,94 0,93-0, ,20-0,96-0,95 0, ,25 0,96-0, ,28-0, ,20
25 GENOMIC CORRELATION 2 Lactose Protein Fat ,22-0,33-0,87-0,92 0,12-0,92 0,92-0,53 0,84 0,96-0,97 0,96-0,94-0,93 0, ,20 0,91 0,77 0,58 0,71-0,11 0,56-0,37-0,57 0,41-0,53 0,76 0,73-0, ,22 0,94 0,23 0,92-0,81 0,58-0,84-0,94 0,91-0,91 0,95 0,94-0, ,25 0,50 0,97-0,60 0,91-0,64-0,95 0,91-0,96 0,96 0,96-0, ,16 0,63 0,76 0,85 0,84 0,14-0,28 0,03 0,20 0,31 0, ,30-0,48 0,94-0,47-0,94 0,89-0,95 0,96 0,96-0, ,10 0,49 0,94 0,92-0,93 0,91-0,86-0,75 0, ,16 0,39-0,54 0,37-0,67 0,71 0,84-0,23 Two groups within selection ,14 0,88-0,89 0,85-0,83-0,74 0, ,19-0,95 0,97-0,96-0,96 0,96 Within group Blue ,22-0,96 0,94 0,93-0,96 Within group Orange +/ ,20-0,96-0,95 0, ,25 0,96-0, ,28-0, ,20
26 GENOMIC CORRELATION 2 Lactose Protein Fat ,22-0,33-0,87-0,92 0,12-0,92 0,92-0,53 0,84 0,96-0,97 0,96-0,94-0,93 0, ,20 0,91 0,77 0,58 0,71-0,11 0,56-0,37-0,57 0,41-0,53 0,76 0,73-0, ,22 0,94 0,23 0,92-0,81 0,58-0,84-0,94 0,91-0,91 0,95 0,94-0, ,25 0,50 0,97-0,60 0,91-0,64-0,95 0,91-0,96 0,96 0,96-0, ,16 0,63 0,76 0,85 0,84 0,14-0,28 0,03 0,20 0,31 0, ,30-0,48 0,94-0,47-0,94 0,89-0,95 0,96 0,96-0, ,10 0,49 0,94 0,92-0,93 0,91-0,86-0,75 0, ,16 0,39-0,54 0,37-0,67 0,71 0,84-0,23 Two groups within selection ,14 0,88-0,89 0,85-0,83-0,74 0, ,19-0,95 0,97-0,96-0,96 0,96 Within group Blue ,22-0,96 0,94 0,93-0,96 Within group Orange +/ ,20-0,96-0,95 0, ,25 0,96-0,92 Between group Blue and Orange -/--! ,28-0, ,20
27 GENOMIC CORRELATION 2 Lactose Protein Fat ,22-0,33-0,87-0,92 0,12-0,92 0,92-0,53 0,84 0,96-0,97 0,96-0,94-0,93 0, ,20 0,91 0,77 0,58 0,71-0,11 0,56-0,37-0,57 0,41-0,53 0,76 0,73-0, ,22 0,94 0,23 0,92-0,81 0,58-0,84-0,94 0,91-0,91 0,95 0,94-0, ,25 0,50 0,97-0,60 0,91-0,64-0,95 0,91-0,96 0,96 0,96-0, ,16 0,63 0,76 0,85 0,84 0,14-0,28 0,03 0,20 0,31 0, ,30-0,48 0,94-0,47-0,94 0,89-0,95 0,96 0,96-0, ,10 0,49 0,94 0,92-0,93 0,91-0,86-0,75 0, ,16 0,39-0,54 0,37-0,67 0,71 0,84-0, ,14 0,88-0,89 0,85-0,83-0,74 0, ,19-0,95 0,97-0,96-0,96 0, ,22-0,96 0,94 0,93-0, ,20-0,96-0,95 0, ,25 0,96-0, ,28-0, ,20
28 GENOMIC CORRELATION 2 Lactose Protein Fat ,22-0,33-0,87-0,92 0,12-0,92 0,92-0,53 0,84 0,96-0,97 0,96-0,94-0,93 0, ,20 0,91 0,77 0,58 0,71-0,11 0,56-0,37-0,57 0,41-0,53 0,76 0,73-0, ,22 0,94 0,23 0,92-0,81 0,58-0,84-0,94 0,91-0,91 0,95 0,94-0, ,25 0,50 0,97-0,60 0,91-0,64-0,95 0,91-0,96 0,96 0,96-0, ,16 0,63 0,76 0,85 0,84 0,14-0,28 0,03 0,20 0,31 0, ,30-0,48 0,94-0,47-0,94 0,89-0,95 0,96 0,96-0, ,10 0,49 0,94 0,92-0,93 0,91-0,86-0,75 0, ,16 0,39-0,54 0,37-0,67 0,71 0,84-0,23 What causes this division? ,14 0,88-0,89 0,85-0,83-0,74 0, ,19-0,95 0,97-0,96-0,96 0,96 Lactation stage dependent fatty acids ,22-0,96 0,94 0,93-0, ,20-0,96-0,95 0,95 Early lactation Body fat mobilization ,25 0,96-0,92 Mid-late lactation De novo synthesis ,28-0, ,20
29 PREDICTION Milk fat % Early lactation Whole lactation Mid-late lactation Days in milk (DIM) Early lactation Body fat mobilization Mid-late lactation De novo synthesis
30 CONCLUSIONS
31 Individual wavenumbers moderately heritable. Strong genomic correlations between wavenumbers interacting with fat. Genomic correlations suggest division of wavenumbers into two groups. Breed differences present, but small.
32 Thank you. Graduate School of Science and Technology REFFICO FT-IR SPEKTRE I MÆLK: GENETISK VARIATION OG EFFEKT PÅ SUNDHED, FRUGTBARHED OG
33 Extra slides
34 Genomic correlation 21 Lactose LGB ProteinNot to DGAT Fat ,22-0,33-0,87-0,92 0,12-0,92 0,92-0,53 0,84 0,96-0,97 0,96-0,94-0,93 0, ,20 0,91 0,77 0,58 0,71-0,11 0,56-0,37-0,57 0,41-0,53 0,76 0,73-0, ,22 0,94 0,23 0,92-0,81 0,58-0,84-0,94 0,91-0,91 0,95 0,94-0, ,25 0,50 0,97-0,60 0,91-0,64-0,95 0,91-0,96 0,96 0,96-0, ,16 0,63 0,76 0,85 0,84 0,14-0,28 0,03 0,20 0,31 0, ,30-0,48 0,94-0,47-0,94 0,89-0,95 0,96 0,96-0, ,10 0,49 0,94 0,92-0,93 0,91-0,86-0,75 0, ,16 0,39-0,54 0,37-0,67 0,71 0,84-0,23 Genomic Three wavenumbers correlation > exluded 0.8 from high correlation < party ,14 0,88-0,89 0,85-0,83-0,74 0, ,19-0,95 0,97-0,96-0,96 0, ,22-0,96 0,94 0,93-0,96 Strong Why so association many? to Lactose ,20-0,96-0,95 0,95 Strong association to LGB Fat molecules interact with many wavenumbers! No association to DGAT ,25 0,96-0, ,28-0, ,20
35 FT-IR milk spectra Super zoom Accurate Fourier transform infrared Fast FT-IR Milk spectra Transmittance Wavenumber
36 Phenotypic correlations DH
37 Phenotypic correlations DJ
38 Genetic PCA
39 Infrared spectra
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