Genome-wide association study (GWAS) for morphological and yield-related traits in an oil palm hybrid (Elaeis oleifera x Elaeis guineensis) population

Jaime A Osorio-Guarín,Paola Delgadillo-Duran,Luz Stella Barrero,Silvio Bastidas,Leidy P Moreno,Gina A Garzón-Martínez,Felix E Enciso-Rodríguez,Omar E Cornejo

doi:10.1186/s12870-019-2153-8

Jaime A Osorio-Guarín, Paola Delgadillo-Duran + Show 6 more

Open Access

https://doi.org/10.1186/s12870-019-2153-8

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Abstract

BackgroundThe genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production.ResultsUsing genotyping-by-sequencing (GBS), we identified a total of 3776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes.ConclusionsWe provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding.

Highlights

The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa
Most importantly, increasing the number and weight of fruits means a higher productivity per palm and a higher income for farmers. For this reason, leveraging Quantitative Trait Loci (QTL) or genes related to these traits could contribute to the development of plant breeding strategies, such as marker-assisted selection that help with the selection of promising accessions in earlier stages and reduce the breeding cycle
There is need for further work that focuses on the biological functions of the set of potential candidate genes found in our research since the correlations we have identified in our association study cannot, as yet, be dubbed as causations

Summary

Introduction

The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. Within the Arecaceae family, the African oil palm (Elaeis guineensis), native to West Africa, is the primary source of most of the vegetable oil found worldwide [3]. Dense genetic maps were subsequently constructed using simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers, which have been used for QTL identification. Using this approach, Jeennor and Volkaert [14] identified a QTL associated with bunch weight using a mapping population of 69 accessions and generated a genetic map with 89 SSRs and 101 SNPs. Further, Billotte et al [15] used a multi-parent linkage map elaborated with 251 SSRs and reported QTLs associated with bunch traits. Similar approaches have enabled the identification of 164 QTLs associated with 21 oil yield components using SSR, AFLP, and RFLP markers [16]

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