Genome-wide diversity analysis to infer population structure and linkage disequilibrium among Colombian coconut germplasm

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.

High density linkage to physical mapping in a unique Tall x Dwarf Coconut (Cocos nuciferaL.) outbred F2uncovers a major QTL for flowering time colocalized with theFLOWERING LOCUS T (FT)

“…The parental F 1 plants composed a commercial production plantation with seeds resulting from controlled pollination between a pollen mix of several Tall coconut parents on female flowers of several Dwarf plants. In the particular case of coconut, we took advantage of the fact that the Dwarf variety is essentially a fixed inbred line with very little if any residual heterozygosity, while the Tall parents are allogamous, heterozygous and genetically diverse (Santos et al, 2020; Wang et al, 2021; Muñoz-Pérez et al, 2022). The F 1 plants SNP genotypes would potentially differ only in what was inherited from the Tall parents, but SNP markers fixed in the Tall variety and polymorphic in relation to the Dwarf would segregate in a 1:2:1 ratio in the F 2 , irrespective of what Tall parent generated each different F 1 plant which in turn were intercrossed to produce the F 2 population.…”

“…Only recently has this scenario begun to change with studies employing single nucleotide polymorphism (SNP) markers for diversity studies [14], linkage mapping to support genome assembly [15], and whole genome sequencing for genome-wide studies (GWAS) [6]. Understanding the genetic basis of morphological traits that determine precocity with a particular interest in early flowering, would represent an important step towards breeding advancement of coconut.…”

“…Furthermore, genetic mapping in the cited studies has been carried out either with low portability AFLP markers or a limited set of microsatellites, which do not provide adequate sequence-level information for deeper investigation of putative genes underlying mapped QTLs. Only recently has this scenario begun to change with studies employing single nucleotide polymorphism (SNP) markers for diversity studies (Muñoz-Pérez et al, 2022), linkage mapping to support genome assembly (Yang et al, 2021), and whole genome sequencing for genome-wide studies (GWAS) (Wang et al, 2021). Understanding the genetic basis of morphological traits that determine precocity with a particular interest in early flowering, would represent an important step towards breeding advancement of coconut.…”

High-density linkage to physical mapping in a unique Tall × Dwarf coconut (Cocos nucifera L.) outbred F2 uncovers a major QTL for flowering time colocalized with the FLOWERING LOCUS T (FT)

“…Furthermore, genetic mapping in the cited studies has been carried out with either low portability amplified fragment length polymorphism (AFLP) markers or a limited set of microsatellites, which do not provide adequate sequence-level information for deeper investigation of putative genes underlying mapped QTLs. Only recently has this scenario begun to change with studies employing single-nucleotide polymorphism (SNP) markers for diversity studies ( Muñoz-Pérez et al., 2022 ), linkage mapping to support genome assembly ( Yang et al., 2021 ), and whole-genome sequencing for genome-wide studies (GWASs) ( Wang et al., 2021 ). Understanding the genetic basis of morphological traits that determine precocity with a particular interest in early flowering would represent an important step toward breeding advancement of coconut.…”

Mining and validating novel SSR markers based on coconut (Cocos nucifera L.) whole genome and their use for phylogenetic analysis

“…Milestones for the use of molecular markers in coconut include RAPD (Rajesh et al 2014), AFLP (Nartvaranant 2019), SNP (Muñoz-Pérez et al 2022), and SSR (Caro et al 2022). However, SSR (Simple Sequence Repeat) markers are the most recommended because they are highly polymorphic and co-dominant markers (Hao et al 2020).…”