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Mateus Freua
Faculdade de Zootecnia e Engenharia de Alimentos,
Universidade de São Paulo
Seminário – Tópicos Avançados em Biologia Celular e Molecular e Genética Animal, 2014
G2P
Integração genômica a modelos para predição do fenótipo
Mateus Freua
IntroductionG2P
Working exampleNovel approach
Final remarks
Consegue observar a diferença?
G2PMateus Freua
IntroductionG2P
Working exampleNovel approach
Final remarks
2/20
Variabilidade percebida
G2PMateus Freua
IntroductionG2P
Working exampleNovel approach
Final remarks
Qual o nível de variabilidade percebido pelo produtor na formação de lotes?
Como direciona lotes para mercados específicos?
Uso de modelos matemáticos nutricionais
• Frame, BCS, peso na entrada do confinamento como inputs
3/20
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ti
ti
KGene
Cromossomo
Indivíduo
GMDPopulação
Entender variação em todos os níveis
G2PMateus Freua
Genótipo Fenótipo
IntroductionG2P
Working exampleNovel approach
Final remarks
4/20
Genotype-to-phenotype (G2P)
G2PMateus Freua
“Dissection” of complex trait into component traits, with explicit modeling of their mutual interactions and their interactions with the environment
Implications
• missing h2
• no need to phenotype anymore
• plan for crosses/breeding(!?) // under Climate Change scenarios
IntroductionG2P
Working exampleNovel approach
Final remarks
5/20
e.g. Total shoot biomass QTL mapping
G2PMateus Freua
A.M. Wubs et al. (2012) Proc. IVth IS on HortiModel
1st: Total shoot biomass (i.e. stem + leaves + fruits)
IntroductionG2P
Working exampleNovel approach
Final remarks
6/20
e.g. Total shoot biomass QTL mapping
G2PMateus Freua
Data
20094 experiments 2 locations2 seasons
149 genotypes of Capsicum annuum RILs4 compartments (12 x 12m), 44 plots1 plot = 8 plants of the same genotypeObservations: environment and biomass
IntroductionG2P
Working exampleNovel approach
Final remarks
7/20
e.g. Total shoot biomass QTL mapping
G2PMateus Freua
Description of simulation model
Shoott, g total shoot biomass/m2 at day tIt, radiation at day tk = extinction coefficient, 0.7 for all genotypes LAIt = leaf area index at day tLUE = light use efficiency, g biomass/MJ of intercepted radiation
)1(** 1*
1
tLAIk
ttt eILUEShootShoot
ti
i
biratet TTLAILAILAI0
0 )(*
IntroductionG2P
Working exampleNovel approach
Final remarks
8/20
e.g. Total shoot biomass QTL mapping
G2PMateus Freua
Derivation of crop parameters
fi
i
bi
f
rate
TT
LAILAILAI
0
0
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fi
i
LAIk
i
f
ieI
ShootShootLUE
0
*
0
)1(*
)(
IntroductionG2P
Working exampleNovel approach
Final remarks
9/20
e.g. Total shoot biomass QTL mapping
G2PMateus Freua
Calculations
Genotypic means
h2
QTL analysis
IntroductionG2P
Working exampleNovel approach
Final remarks
10/20
e.g. Total shoot biomass QTL mapping
G2PMateus Freua
IntroductionG2P
Working exampleNovel approach
Final remarks
11/20
e.g. Total shoot biomass QTL mapping
G2PMateus Freua
Simulations
1. with genotypic means for LAIrate and LUE from observations (“control”)
2. with values from QTL analysis on LAIrate and LUE
IntroductionG2P
Working exampleNovel approach
Final remarks
12/20
e.g. Total shoot biomass QTL mapping
G2PMateus Freua
IntroductionG2P
Working exampleNovel approach
Final remarks
13/20
e.g. Total shoot biomass QTL mapping
G2PMateus Freua
Simulation using LAIrate/LUE-QTL fitted values explained on average more of the variation in observed shoot biomass
… in GMDi(t)
QTL-fitted
Direct QTL on Shoot
40
30
43
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27
34
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37
N1 N2 S1 S2
Explained variance (%)
IntroductionG2P
Working exampleNovel approach
Final remarks
14/20
Final remarks
G2PMateus Freua
New phenotyping tools, new experimental designs
Method suitable for many other topics and models
IntroductionG2P
Working exampleNovel approach
Final remarks
19/20