Differential Expression Analysis in High-yielding and Low-yielding Philippine Coconut through Transcriptome Sequencing
Ma. Regina Punzalan1,2, Gamaliel Lysander Cabria1,2, Ma. Anita Bautista1,2,
Ernesto Emmanuel3, Ramon Rivera3, Susan Rivera3, and Cynthia Saloma1,2*
1Philippine Genome Center (PGC), University of the Philippines,
Diliman, Quezon City 1101 Philippines
2National Institute of Molecular Biology and Biotechnology, University of the Philippines,
Diliman, Quezon City 1101 Philippines
3Philippine Coconut Authority – Zamboanga Research Center (PCA-ZRC),
San Ramon, Zamboanga City 7000 Philippines
The demand for coconut oil (CNO) continues to rise in the global market. This puts pressure for coconut-producing countries such as the Philippines to increase CNO and copra production. Baybay Tall (BAYT) is known to have the highest copra yield among the tall coconut varieties in the Philippines. However, traditional breeding techniques that rely on the use of morphological markers are very limited, laborious, and time-consuming. In order to improve breeding strategies for increased copra production, differential gene expression analysis was performed on coconut shell and kernel of high-yielding and low-yielding palms. High-quality RNA was isolated from the endosperm (ES or kernel) and endocarp (EC or shell) of nut tissues followed by transcriptome sequencing using Illumina HiSeq2000. De novo transcriptome assembly was performed using Trinity. Read abundance was estimated using Corset and differentially expressed genes were identified using edgeR. In total, 1,945 genes were found to be differentially expressed (FDR < 0.05) from the nut tissues. Annotation of the transcripts revealed that only 82 of the differentially expressed genes have significant annotation. Potential gene-targeted markers (GTMs) were designed for 64 candidate genes, which can be further validated for possible use in the marker-assisted selection of high-yielding palms. Microsatellite (SSR) sequences were identified in 19,147 unigenes in the EC and 17,394 in the ES. However, only two SSRs were found among differentially expressed genes in the EC and only one in the ES. Functional analysis revealed that high nut yield could arise from concerted actions of several transcription activators and regulatory proteins leading to increased cell division, secondary cell wall formation, enhanced energy metabolism, and activated stress response. Taken together, these processes contribute to increased kernel volume and thus increase in copra yield. Identified genes in this study can be used as potential targets in improving productivity in the Philippine coconut.
Copra, or dried coconut kernel, is a highly resourced commodity in the tropics. CNO is extracted from copra and the residue from extraction can be used as feeds for livestock. The use of CNO is favored over other vegetable oils due to its lower long chain fatty acid and higher medium chain saturated fatty acids content, higher burning point, and its perceived medical advantages (Young 1983, Dyer et al. 2008, DebMandal and Mandal 2011). . . . read more
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