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Open AccessArticle

Association Mapping between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids

NEIKER Tecnalia, Campus Agroalimentario de Arkaute, Apdo 46. 01080 Vitoria-Gasteiz, Spain
CIRAD, UMR AGAP, F-34398 Montpellier, France
AGAP, CIRAD, Univ Montpellier, INRA, Montpellier SupAgro, F-34398 Montpellier, France
South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, F-34398 Montpellier, France
La Fabril SA, km 5.5 via Manta–Montecristi, Avenida 113, 130902 Manta, Ecuador
Energy & Palma SA, Av. Atahualpa E3-49 y Juan Gonzales, Ed. Fundación Pérez Pallarez, Officina 4ª, Quito 170507, Ecuador
Department of Research & Development, PT Sampoerna Agro Tbk., Jl. Basuki Rahmat No. 788 Palembang 30127, Indonesia
Author to whom correspondence should be addressed.
Plants 2019, 8(10), 377;
Received: 19 June 2019 / Revised: 13 September 2019 / Accepted: 14 September 2019 / Published: 26 September 2019
(This article belongs to the Section Plant Genetics and Genomics)
Oil palm production is gaining importance in Central and South America. However, the main species Elaeis guineensis (Eg) is suffering severely from bud rod disease, restricting the potential cultivation areas. Therefore, breeding companies have started to work with interspecific Elaeis oleifera × Eg (Eo × Eg) hybrids which are tolerant to this disease. We performed association studies between candidate gene (CG) single nucleotide polymorphisms (SNP) and six production and 19 oil quality traits in 198 accessions of interspecific oil palm hybrids from five different origins. For this purpose, barcoded amplicons of initially 167 CG were produced from each genotype and sequenced with Ion Torrent. After sequence cleaning 115 SNP remained targeting 62 CG. The influence of the origins on the different traits was analyzed and a genetic diversity study was performed. Two generalized linear models (GLM) with principle component analysis (PCA) or structure (Q) matrixes as covariates and two mixed linear models (MLM) which included in addition a Kinship (K) matrix were applied for association mapping using GAPIT. False discovery rate (FDR) multiple testing corrections were applied in order to avoid Type I errors. However, with FDR adjusted p values no significant associations between SNP and traits were detected. If using unadjusted p values below 0.05, seven of the studied CG showed potential associations with production traits, while 23 CG may influence different quality traits. Under these conditions the current approach and the detected candidate genes could be exploited for selecting genotypes with superior CG alleles in Marker Assisted Selection systems. View Full-Text
Keywords: Elaeis guineensis; Elaeis oleifera; snakemake; lipids; tocols; carotene Elaeis guineensis; Elaeis oleifera; snakemake; lipids; tocols; carotene
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Astorkia, M.; Hernandez, M.; Bocs, S.; Lopez de Armentia, E.; Herran, A.; Ponce, K.; León, O.; Morales, S.; Quezada, N.; Orellana, F.; Wendra, F.; Sembiring, Z.; Asmono, D.; Ritter, E. Association Mapping between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids. Plants 2019, 8, 377.

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