Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture

Autor: Vincent Migault, Benoît Pallas, Evelyne Costes
Přispěvatelé: Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Architecture et Fonctionnement des Espèces Fruitières [AGAP] (AFEF), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Jazyk: angličtina
Rok vydání: 2017
Předmět:
0106 biological sciences
0301 basic medicine
carte génétique
déterminisme génétique
croissance végétale
organogenesis
Population
pommier
Apple tree
simulation models
Plant Science
temperature effect
ramification sylleptique
Biology
modèle de simulation
01 natural sciences
modèle structure fonction
03 medical and health sciences
genome wide prediction
Statistics
branching
Phyllochron
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Genetic variability
Plant breeding
apple tree
education
Original Research
2. Zero hunger
FSPM
education.field_of_study
Vegetal Biology
architecture de l'arbre
Ecology
Simulation modeling
genêtic determinism
Ideotype
plant growth
15. Life on land
Tree (data structure)
030104 developmental biology
organogénèse
genetic mapping
Biologie végétale
RR-BLUP
010606 plant biology & botany
Zdroj: Frontiers in Plant Science
Frontiers in Plant Science, Frontiers, 2017, 7, ⟨10.3389/fpls.2016.02065⟩
Frontiers in Plant Science (7), . (2017)
ISSN: 1664-462X
DOI: 10.3389/fpls.2016.02065⟩
Popis: UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitières; In crops, optimizing target traits in breeding programs can be fostered by selecting appropriate combinations of architectural traits which determine light interception and carbon acquisition. In apple tree, architectural traits were observed to be under genetic control. However, architectural traits also result from many organogenetic and morphological processes interacting with the environment. The present study aimed at combining a FSPM built for apple tree, MAppleT, with genetic determinisms of architectural traits, previously described in a bi-parental population. We focused on parameters related to organogenesis (phyllochron and immediate branching) and morphogenesis processes (internode length and leaf area) during the first year of tree growth. Two independent datasets collected in 2004 and 2007 on 116 genotypes, issued from a ‘Starkrimson’ × ‘Granny Smith’ cross, were used. The phyllochron was estimated as a function of thermal time and sylleptic branching was modeled subsequently depending on phyllochron. From a genetic map built with SNPs, marker effects were estimated on four MAppleT parameters with rrBLUP, using 2007 data. These effects were then considered in MAppleT to simulate tree development in the two climatic conditions. The genome wide prediction model gave consistent estimations of parameter values with correlation coefficients between observed values and estimated values from SNP markers ranging from 0.79 to 0.96. However, the accuracy of the prediction model following cross validation schemas was lower. Three integrative traits (the number of leaves, trunk length, and number of sylleptic laterals) were considered for validating MAppleT simulations. In 2007 climatic conditions, simulated values were close to observations, highlighting the correct simulation of genetic variability. However, in 2004 conditions which were not used for model calibration, the simulations differed from observations. This study demonstrates the possibility of integrating genome-based information in a FSPM for a perennial fruit tree. It also showed that further improvements are required for improving the prediction ability. Especially temperature effect should be extended and other factors taken into account for modeling GxE interactions. Improvements could also be expected by considering larger populations and by testing other genome wide prediction models. Despite these limitations, this study opens new possibilities for supporting plant breeding by in silico evaluations of the impact of genotypic polymorphisms on plant integrative phenotypes.
Databáze: OpenAIRE
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