Abstract
Oil palm is the most important oil crop worldwide. Colombia is the fourth largest producer, primarily relying on production from interspecific hybrids, derived from crosses between Elaeis oleifera and Elaeis guineensis (OxG). However, conventional breeding can take up to 20 years to generate a new variety. Therefore, reducing the breeding cycle while improving the genetic gain for complex traits is desirable. Genomic selection (GS) is an approach with the potential to achieve this goal. In this study, we evaluated 431 F1 interspecific hybrids (OxG) and 444 backcrosses (BC1) for morphological and yield-related traits. Genomic predictions were performed with the G-BLUP model using three different population datasets for training the model: the same population (TRN1), the other population (TRN2), and both populations (TRN1+2). Higher multi-family prediction accuracies were obtained for foliar area (0.3 in OxG) and trunk height (0.47 in BC1) when the model was trained with TRN1. Single-family prediction accuracies were lower in the OxG compared to BC1 families for traits such as trunk diameter, trunk height, bunch number, and yield using TRN1. Conversely, lower prediction accuracies were obtained for most traits when the model was trained using TRN2 (< 0.1). Multi-trait models showed a substantial increase of the predictions for traits such as yield (0.22 for OxG and 0.44 for BC1), because of the genetic correlations between traits. The results herein highlighted the potential of GS for parental selection in OxG and BC1 populations, but further studies are required to improve the models to select individuals by their genetic value.
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Data availability
The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.
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Acknowledgements
The authors want to acknowledge William Tolosa for his support during sample collection and Paola Delgadillo for her support in the BC1 population DNA extraction. The access to the oil palm individuals complies with the genetic resource agreement for scientific research without commercial interest No. 74, signed between Agrosavia and Ministerio de Agricultura y Desarrollo Rural (MADR) of Colombia. The authors want to thank Shane Teachworth for his review of this document for English grammar and style.
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This research was funded by the Corporación Colombiana de Investigación Agropecuaria (Agrosavia), an entity under the Ministry of Agriculture and Rural Development (MADR) from Colombia, with funds obtained under law 1731 of 2014.
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GAGM processed the phenotypic and genotypic data, interpreted the results, and drafted the manuscript. JAOG processed the genotypic data and critically revised the manuscript. LPM conducted the field experiments, collected the data, discussed, reviewed, and revised the manuscript. SB designed the field experiments, reviewed, and revised the manuscript. LSB designed and supervised the genotypic work and critically revised the manuscript. MLC developed the genomic selection models and drafted and revised the manuscript. FEER designed and supervised the genotypic work and overall data analysis and critically revised the manuscript. All authors have read and approved the manuscript.
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Supplementary Fig. S1
Boxplots showing the average phenotypic distribution of morphological and yield-related traits, in OxG and BC1 oil palm. A. by population, B. by family. Significant differences are indicated by asterisks (p< 0.001) and by letters (p< 0.05). TD: Trunk Diameter, TH: Trunk Height, FA: Foliar Area, BW: Bunch, BN: Bunch number (PNG 827 kb)
Supplementary Fig. S2
Conventional vs. genomic selection-based breeding in oil palm. Traditional breeding relies on the generation of multiple crosses, for which progeny is evaluated and selected in the field for up to 20 years to finally generate one new oil palm variety. Genomic selection will reduce the breeding cycle by up to seven years, selecting superior lines, based on their genetic merit, using whole-genome regressions (PNG 548 kb)
Supplementary File S1
SNPs dataset identified in OxG and BC1 using the E. guineensis reference genome (TXT 15327 kb)
Supplementary Table S1
List of the OxG and BC1 oil palms used in this study (XLSX 39 kb)
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Garzón-Martínez, G.A., Osorio-Guarín, J.A., Moreno, L.P. et al. Genomic selection for morphological and yield-related traits using genome-wide SNPs in oil palm. Mol Breeding 42, 71 (2022). https://doi.org/10.1007/s11032-022-01341-5
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DOI: https://doi.org/10.1007/s11032-022-01341-5