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

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

doi:10.1186/s12870-019-2153-8

Table 2 Significant marker-trait associations for 378 individuals of the OxG population for morphological and yield-related traits using a mixed linear model approach

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

Category	Trait	SNP	Chromosome	Position (kb)	p-value	MAF	R²	FDR adjusted p-values	Nearby gene	SNP position relative to the candidate gene*	Candidate gene annotation
Morphological	LDW	S3_30,467,222	3	30,467,222	1.E-04	0.106	0.107	0.050	p5.00_sc00100_p0017	0	Mechanosensitive ion channel protein 10-like (MSL10)
	TD	S15_21,239,833	15	21,239,833	1.98E-05	0.493	0.097	0.010	p5.00_sc00036_p0097	+ 21.8 kb	Nucleic acid binding
	HT TD FA LA	S15_22,347,191	15	22,347,191	7.94E-05	0.496	0.098	0.084	p5.00_sc00036_p0145	+ 0.3 kb	Paired amphipathic helix protein (PAH)
		S15_22,553,489	15	22,553,489	7.94E-05	0.496	0.098	0.084	p5.00_sc00036_p0152	−0.6 kb	Serine threonine-protein kinase (STYK)
		S15_22,553,493	15	22,553,493	8.90E-05	0.495	0.098	0.084	p5.00_sc00036_p0152	−0.6 kb	Serine threonine-protein kinase (STYK)
		S15_23,645,020	15	23,645,020	7.94E-05	0.496	0.098	0.084	p5.00_sc00036_p0217	0	Class E vacuolar protein-sorting machinery protein (VPS)
	RL LXL	S13_20,856,724	13	20,856,724	3.22E-05	0.499	0.074	0.041	p5.00_sc00035_p0180	−12.0 kb	Guanine nucleotide-binding protein subunit gamma (AGC3)
		S13_23,674,227	13	23,674,227	3.22E-05	0.499	0.074	0.041	p5.00_sc00035_p0078	0	Extracellular ribonuclease (RNAse)
		S13_25,522,088	13	25,522,088	3.22E-05	0.499	0.074	0.041	p5.00_sc00128_p0001	0	lmbr1 domain-containing protein (IMBR1)
		S13_24,474,516	13	24,474,516	7.14E-05	0.497	0.070	0.067	p5.00_sc00035_p0043	0	Probable ran guanine nucleotide release factor-like (RANGRF)
Production	Yield BN	S5_41,396,842	5	41,396,842	1.E-04	0.132	0.059	0.410	p5.00_sc00003_p0367	+ 29 kb	Cation h(+) antiporter
Production	BW	S10_21,597,426	10	21,597,426	3.E-04	0.499	0.054	0.316	p5.00_sc00036_p0097	−8.0 kb	Zinc finger protein 8-like (ZFP)

^* SNP position relative to the closest candidate gene: upstream and downstream SNPs of candidate genes are specified with “–” and “+,” respectively. 0 indicates that SNPs are located within the candidate gene

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