Abstract
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.
Highlights
Genetic diversity and relatedness of accessions for coconut growing in Colombia was unknown until this study
This study aims to: (1) identify single nucleotide polymorphisms (SNPs) at the genome level, (2) investigate the genetic diversity and population structure, and (3) characterize the linkage disequilibrium (LD) in coconut growing in Colombia
Genotyping by Sequencing (GBS) analysis was performed in samples from 112 specimens of adventive and commercially cultivated coconut from the main coconut producing areas in both the Atlantic (Antioquia and Córdoba) and Pacific (Nariño, Cauca and Chocó) Colombian coasts
Summary
Genetic diversity and relatedness of accessions for coconut growing in Colombia was unknown until this study. 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. The “dwarf ” type palms are recognized for being self-pollinated, and displaying important domestication features such as short stems, high productivity in terms of fruit production, and low genetic variability[4] Both palm types gave rise to a vast number of coconut populations of pantropical distribution that are poorly characterized at the genomic level, and that are generally identified based on variable morphological and agronomic traits, which are not apparent in juvenile p hases[5,6,7]. The development of SNPs markers in coconut represents potential for application of molecular breeding techniques through marker-assisted selection (MAS) and association mapping
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have