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Identification and characterization of differential gene expression in the mesocarp and kernel of oil palm nuts using suppression subtractive hybridization

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Abstract

Suppression subtracted hybridization (SSH) and dot blotting were used to identify differential gene expression in the mesocarp and kernel of oil palm nuts. The different types of nut tissue show differences in fatty acid anabolism and the synthesis of other important compounds. In total, 302 clones from forward SSH libraries and 238 clones from reverse SSH libraries were identified following differential screening, respectively. Among these, 120 clones from the forward SSH library and 81 clones from the reverse SSH library, showed tenfold or more differential expression levels, and were sequenced. Sequence analysis revealed that 76 clones (28 from the forward SSH library and 48 from the reverse SSH library) represent non-redundant cDNA inserts. The differential expression of 39 subset genes in the two different tissues was further confirmed by RT-PCR analysis. Functionally annotated blasting against the GenBank non-redundant protein database classified all 76 candidate genes into six categories, according to their putative functions. Interestingly, our results show that a group of significantly differentially expressed genes are involved in processes associated with oil palm nut maturation, such as the synthesis of medium-chain saturated fatty acids and phytic acid, nut development, and stress/defense responses. This study describes some relationships between gene expression and metabolic pathways in mature oil palm nuts, and contributes to our understanding of oil palm nut ESTs.

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Abbreviations

BBIs:

Bowman–Birk serine proteinase inhibitors

EST:

Expressed sequence tag

KAS:

β-ketoacyl-ACP synthases

MADS:

MCM1-AGAMOUS-DEFICIENS-SRF

MIPs:

Myo-inositol 1-phosphate synthase

RT-PCR:

Real-time polymerase chain reaction

SSH:

Suppression subtracted hybridization

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Acknowledgments

This research was supported by the National Natural Science Foundation of China (NSFC) (No: 30560092 and 31060259) and National Nonprofit Institute Research Grant of CATAS-ITBB.

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Authors and Affiliations

  1. Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences and Key Laboratory of Tropical Crops Germplasm Resources Utilization of Ministry of Agriculture, Hainan, Danzhou, 571737, China

    Li Xu

  2. Key Laboratory of Tropic Biological Resources of Ministry of Education, Hainan University, Hainan, 570228, China

    Yijun Yuan, Lin Zhang, Li Wan, Yusheng Zheng & Dongdong Li

  3. Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology and Analysis & testing center, Chinese Academy of Tropical Agricultural Sciences (CATAS), Hainan, China

    Peng Zhou

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  1. Li Xu
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  2. Yijun Yuan
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  3. Lin Zhang
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  4. Li Wan
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  5. Yusheng Zheng
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  6. Peng Zhou
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Correspondence to Peng Zhou or Dongdong Li.

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Communicated by J. Dean

Li Xu and Yijun Yuan contributed equally to the work.

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Xu, L., Yuan, Y., Zhang, L. et al. Identification and characterization of differential gene expression in the mesocarp and kernel of oil palm nuts using suppression subtractive hybridization. Tree Genetics & Genomes 7, 999–1010 (2011). https://doi.org/10.1007/s11295-011-0390-6

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  • DOI: https://doi.org/10.1007/s11295-011-0390-6

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