Heritability estimates from genomewide relatedness matrices in wild populations: Application to a passerine, using a small sample size

• Published in: Molecular ecology resources Vol. 18; no. 4; pp. 838 - 853
• Main Authors: Perrier, C., Delahaie, B., Charmantier, A.
• Format: Journal Article
• Language: English
• Published: England Wiley Subscription Services, Inc 01.07.2018; Wiley/Blackwell
• Subjects: Animals; Biodiversity; blue tit; Body mass; Chromosomes; Correlation analysis; Cyanistes caeruleus; Data processing; Extra-pair paternity; Genetic Association Studies - methods; genetic correlation; Genome; genomewide relatedness matrices; Heritability; Life Sciences; Natural populations; Partitioning; Passeriformes - anatomy & histology; Passeriformes - genetics; Pedigree; phenotype; Polymorphism, Single Nucleotide; Populations; Populations and Evolution; Quantitative genetics; Quantitative Trait Loci; RAD‐sequencing; Sequence Analysis, DNA; Single-nucleotide polymorphism; SNP; pedigree; phenotype; RAD-sequencing; blue tit; SNP; genomewide relatedness matrices; Cyanistes caeruleus; partitioning; genetic correlation; heritability
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.12886

Genomic developments have empowered the investigation of heritability in wild populations directly from genomewide relatedness matrices (GRM). Such GRM‐based approaches can in particular be used to improve or substitute approaches based on social pedigree (PED‐social). However, measuring heritability from GRM in the wild has not been widely applied yet, especially using small samples and in nonmodel species. Here, we estimated heritability for four quantitative traits (tarsus length, wing length, bill length and body mass), using PED‐social, a pedigree corrected by genetic data (PED‐corrected) and a GRM from a small sample (n = 494) of blue tits from natural populations in Corsica genotyped at nearly 50,000 filtered SNPs derived from RAD‐seq. We also measured genetic correlations among traits, and we performed chromosome partitioning. Heritability estimates were slightly higher when using GRM compared to PED‐social, and PED‐corrected yielded intermediate values, suggesting a minor underestimation of heritability in PED‐social due to incorrect pedigree links, including extra‐pair paternity, and to lower information content than the GRM. Genetic correlations among traits were similar between PED‐social and GRM but credible intervals were very large in both cases, suggesting a lack of power for this small data set. Although a positive linear relationship was found between the number of genes per chromosome and the chromosome heritability for tarsus length, chromosome partitioning similarly showed a lack of power for the three other traits. We discuss the usefulness and limitations of the quantitative genetic inferences based on genomic data in small samples from wild populations.