Genetic diversity and relatedness of accessions for coconut growing in Colombia was unknown until this study. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on Genotyping by Sequencing (GBS) with the goal of analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diverse coconut panel consisting of 112 coconut accessions from the Atlantic and Pacific coasts of Colombia. A comprehensive catalog of approximately 40,000 SNPs with a minor allele frequency (MAF) of > 0.05 is presented. A total of 40,614 SNPs were found but only 19,414 anchored to chromosomes. Of these, 10,338 and 4606 were exclusive to the Atlantic and Pacific gene pools, respectively, and 3432 SNPs could differentiate both gene pools. A filtered subset of unlinked and anchored SNPs (1271) showed a population structure at K = 4, separating accessions from the Pacific and Atlantic coasts that can also be distinguished by palm height, as found in previous studies. The Pacific groups had a slow LD decay, low Fixation Index (Fst) and low nucleotide diversity (π), while the Atlantic group had slightly higher genetic diversity and faster LD decay. Genome-wide diversity analyses are of importance to promote germplasm conservation and breeding programs aimed at developing new cultivars better adapted to the region.
Wasps from the arboreal vegetation in Gorgona National Natural Park, Colombian Pacific. Studies of Colombian Hymenoptera are incipient, fragmented and there is no comprehensive study about its size and composition. We know that the guild of hymenopteran parasitoids is the richest in species and that they are common and abundant in all terrestrial ecosystems, acting as regulators of populations of other insects. Studies in Gorgona National Natural Park have mostly focused on the natural history and identification of Formicidae and Apidae. This work was directed toward the identification of other hymenopteran species associated with its tropical rain forest. in November 2007, 16 trees were sampled by fogging with a biodegradable pyrethroid insecticide applied from 1m above the ground to the canopy. We found 641 individuals (45% identified to subfamily and 28% to genera) from seven superfamilies, 20 families and 118 morphospecies. Chalcidoidea was the most representative superfamily, Eulophidae the most diverse family and Braconidae the numerically dominant family. The sampling efficiency was 71% and 166 species are estimated to exist in the island. Approximately 71% of the estimated species were captured during this study. We report 12 genera new for the island. Rev. Biol. Trop. 62 (Suppl. 1): 307-315. Epub 2014 February 01.
SummaryIndependent origins of cultivated Coconut (Cocos nucifera L.) have been identified in the Old-World Tropics corresponding to the Pacific and Indo-Atlantic oceanic basins. We use unknown coconut cultivated varieties in northern South America to conduct genetic diversity and population structure analysis for the region using single nucleotide polymorphisms (SNPs) markers along the genome and phenotypic data.Analyses revealed two highly genetically differentiated subpopulations corresponding to Pacific and Atlantic oceanic basins. While, this pattern was initially revealed at a global scale, it has now been confirmed at a local scale using genomics in northern South America. We use genotypes identified here to estimate diversification times for main cultivated coconut varieties at a global scale: An early divergent Atlantic tall cultivar, splits from sisters Pacific Tall and Pacific Dwarf cultivars approximately 5400 years ago, while Pacific Tall and Pacific Dwarf cultivars split from a shared common ancestor approximately 1600 years ago.Five loci have been identified as candidate domestication targets, including genes related to vital functions such reproduction, respiration, and defense.These results propose a dated evolutionary hypothesis for the independent origins of cultivated coconut globally were diversification between coconut populations has happened very recently and within few generations.
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