Citation
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
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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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).
Additional Metadata
Item Type: | Article |
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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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