title: Genome-wide patterns of recombination, linkage disequilibrium and nucleotide diversity from pooled resequencing and single nucleotide polymorphism genotyping unlock the evolutionary history of Eucalyptus grandis.
abstract: We used high-density single nucleotide polymorphism (SNP) data and whole-genome pooled resequencing to examine the landscape of population recombination (ρ) and nucleotide diversity (ϴw ), assess the extent of linkage disequilibrium (r(2) ) and build the highest density linkage maps for Eucalyptus. At the genome-wide level, linkage disequilibrium (LD) decayed within c. 4-6 kb, slower than previously reported from candidate gene studies, but showing considerable variation from absence to complete LD up to 50 kb. A sharp decrease in the estimate of ρ was seen when going from short to genome-wide inter-SNP distances, highlighting the dependence of this parameter on the scale of observation adopted. Recombination was correlated with nucleotide diversity, gene density and distance from the centromere, with hotspots of recombination enriched for genes involved in chemical reactions and pathways of the normal metabolic processes. The high nucleotide diversity (ϴw = 0.022) of E. grandis revealed that mutation is more important than recombination in shaping its genomic diversity (ρ/ϴw = 0.645). Chromosome-wide ancestral recombination graphs allowed us to date the split of E. grandis (1.7-4.8 million yr ago) and identify a scenario for the recent demographic history of the species. Our results have considerable practical importance to Genome Wide Association Studies (GWAS), while indicating bright prospects for genomic prediction of complex phenotypes in eucalypt breeding.
authors.affiliation: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, Brasilia, 70770-970, DF, Brazil.|Laboratório de Bioinformática, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, Brasilia, DF, 70770-970, Brazil.|Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916, Brasilia, DF, 70790-160, Brazil.
authors.forename: Orzenil B
authors.initials: OB
authors.lastname: Silva-Junior
authors.affiliation: Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, Brasilia, 70770-970, DF, Brazil.|Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916, Brasilia, DF, 70790-160, Brazil.
authors.forename: Dario
authors.initials: D
authors.lastname: Grattapaglia
mesh_terms: D005052:Eucalyptus / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D060005:Genotyping Techniques; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic
keywords: Eucalyptus; ancestral recombination graphs; effective population size; linkage disequilibrium (LD); mutation rate; nucleotide diversity; population recombination rate; whole-genome pooled resequencing