1. Partial genotyping at polymorphic markers can improve heritability estimates in sibling groups
- Author
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J. Gauzere, S. Oddou-Muratorio, L. Gay, E. K. Klein, Ecologie des Forêts Méditerranéennes [Avignon] (URFM 629), Institut National de la Recherche Agronomique (INRA), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), 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), Biostatistique et Processus Spatiaux (BIOSP), ERANet BiodivERsA TipTree project : ANR-12-EBID-0003, metaprogramme Adaptation of Agriculture and Forests to Climate Change (AAFCC) of the French National Institute for Agricultural Research (INRA), MECC project : ANR-13-ADAP-0006, Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (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), Klein, Etienne K., Ecologie des Forêts Méditerranéennes (URFM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), and Biostatistique et Processus Spatiaux (BioSP)
- Subjects
0301 basic medicine ,Genotyping Techniques ,héritabilité ,[SDV]Life Sciences [q-bio] ,Population ,Biology ,heritability ,unequal reproductive success ,modelling ,03 medical and health sciences ,pédigrée ,pedigree-free methods ,marker-based relatednesses ,maternal effects ,breeding ,Statistics ,Genetics ,Animals ,Sibling ,education ,coefficient d'heritabilité ,Ecology, Evolution, Behavior and Systematics ,modélisation ,education.field_of_study ,Chimera ,Reproduction ,Siblings ,Maternal effect ,Selfing ,Heritability ,Mating system ,030104 developmental biology ,Genetics, Population ,marqueur microsatellite ,Inbreeding ,microsatellite repeats ,Biotechnology - Abstract
Agap : équipe GE2pop; Accurate estimates of heritability (h2) are necessary to assess adaptive responses of populations and evolution of fitness-related traits in changing environments. For plants, h2 estimates generally rely on maternal progeny designs, assuming that offspring are either half-sibs or unrelated. However, plant mating systems often depart from half-sib assumptions, this can bias h2 estimates. Here, we investigate how to accurately estimate h2 in non-model species through the analysis of sibling designs with a moderate genotyping effort. We performed simulations to investigate how microsatellite marker information available for only a subset of offspring can improve h2 estimates based on maternal progeny designs in presence of non-random mating, inbreeding in the parental population or maternal effects. We compared the basic family method, considering or not adjustments based on average relatedness coefficients, and methods based on the animal model. The animal model was used with average relatedness information, or with hybrid relatedness information: associating one-generation pedigree and family assumptions, or associating one-generation pedigree and average relatedness coefficients. Our results highlighted that methods using marker-based relatedness coefficients performed as well as pedigree-based methods in presence of non-random mating (i.e. unequal male reproductive contributions, selfing), offering promising prospects to investigate in situ heritabilities in natural populations. In presence of maternal effects, only the use of pairwise relatednesses through pedigree information improved the accuracy of h2 estimates. In that case the amount of father-related offspring in the sibling design is the most critical. Overall, we showed that the method using both one-generation pedigree and average relatedness coefficients was the most robust to various ecological scenarios.
- Published
- 2016