Association of SNP markers with height increment in MPOB-Angolan natural oil palm populations

Ooi L. C. L., . and Low E. T. L., . and Singh R., . and Abdullah N. A. P., . and Rajanaidu N., . and Maizura I., . and Ong P. W., . and Marhalil M., . and Rafii M. Y., . Association of SNP markers with height increment in MPOB-Angolan natural oil palm populations. pp. 61-70. ISSN 1511-2780

Low height increment is one of the desired traits in oil palm breeding and improvement programmes as dwarf palms facilitate fruit harvesting and extend the economic life of the crop. In this study 346 natural oil palms collected from Angola and maintained by the Malaysian Palm Oil Board (MPOB) were used. Analysis of variance (ANOVA) for height increment showed a significant difference (P 0.001) among families in populations indicating substantial genetic variation for marker-trait association study. We applied nine carefully selected single nucleotide polymorphism (SNP) markers to genotype the oil palms via cleaved amplified polymorphic sequence (CAPS) method. Population structure analysis involving 18 SNP alleles divided the palms into two sub-populations with no obvious relative kinship (values 0.3). For association analysis between the SNP markers and height increment three models were tested. The incorporation of population structure (Q) and relative kinship (K) as correction factors in the model had helped reduce false positive associations. Generally the mixed linear model (MLM) with Q K exhibited a more stringent model with less spurious associations detected. Based on this model one significant marker SNPG00006_FatI corresponding to indole-3-acetic acid (IAA)-amido synthetase gene was identified to be associated with height increment (P 0.05). The marker although potentially specific to MPOB-Angolan germplasm can assist in introgressing the dwarf phenotype into advanced breeding materials through marker-assisted selection (MAS).

Full text available from: Official URL: http://jopr.mpob.gov.my/association-of-snp-markers...

Abstract

Low height increment is one of the desired traits in oil palm breeding and improvement programmes as dwarf palms facilitate fruit harvesting and extend the economic life of the crop. In this study 346 natural oil palms collected from Angola and maintained by the Malaysian Palm Oil Board (MPOB) were used. Analysis of variance (ANOVA) for height increment showed a significant difference (P 0.001) among families in populations indicating substantial genetic variation for marker-trait association study. We applied nine carefully selected single nucleotide polymorphism (SNP) markers to genotype the oil palms via cleaved amplified polymorphic sequence (CAPS) method. Population structure analysis involving 18 SNP alleles divided the palms into two sub-populations with no obvious relative kinship (values 0.3). For association analysis between the SNP markers and height increment three models were tested. The incorporation of population structure (Q) and relative kinship (K) as correction factors in the model had helped reduce false positive associations. Generally the mixed linear model (MLM) with Q K exhibited a more stringent model with less spurious associations detected. Based on this model one significant marker SNPG00006_FatI corresponding to indole-3-acetic acid (IAA)-amido synthetase gene was identified to be associated with height increment (P 0.05). The marker although potentially specific to MPOB-Angolan germplasm can assist in introgressing the dwarf phenotype into advanced breeding materials through marker-assisted selection (MAS).

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Item Type:	Article
AGROVOC Term:	Oil palm
AGROVOC Term:	Elaeis guineensis
AGROVOC Term:	Genetic markers
AGROVOC Term:	Genes
AGROVOC Term:	Genetic variation
AGROVOC Term:	Genetic variability
AGROVOC Term:	Genotypes
AGROVOC Term:	Germplasm
AGROVOC Term:	Nucleotide sequence
AGROVOC Term:	Planting
Depositing User:	Ms. Suzila Mohamad Kasim
Last Modified:	24 Apr 2025 06:28
URI:	http://webagris.upm.edu.my/id/eprint/24116

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