Orthologous Revelation between Elaeis guineensis, Arabidopsis thaliana and Solanum lycopersicum

Year 2020, Volume: 3 Issue: 2, 164 - 179, 15.08.2020

Nurul Hidayah Samsulrizal , Muhammad Hazuki Nur Sabrina Ahmad Azmi Zatty Syamimi Mat Said Nurnıwalıs Abdul Wahab Zubaidah Ramlı

https://doi.org/10.38001/ijlsb.717846

Abstract

Oil palms are important commodity crop in Malaysia as major contributor to agriculture sector. Thus, the need for better yield production is urgent to accommodate rising local and global demand while reducing the land expansion for oil palm plantation. This can be achieved by identifying the agronomical important traits in oil palm using comparative genomic approach. In this study, gene related to plant height, fruit development and fruit ripening in oil palm were predicted by comparing Elaeis guineensis genome sequence with Arabidopsis thaliana and Solanum lycopersicum genome sequence. The model plant chosen are based on its special attribute such as completely sequenced and fleshy fruit model. The analysis begun with orthology analysis using InParanoid, and SonicParanoid. There are 9,624 orthologous genes identified common among species selected. The reformatted orthologous genes were then annotated with Gene Ontology (GO) using Blast2GO program. The process of annotation include blast with local database (DIAMOND), mapping, annotation and project statistical analysis. 100% of the orthologous gene blasted has sequence of significant similarity but only 61.79% of the sequence has GO assignment. By using the annotated orthologous genes generated, only small amount of gene associated with trait of interest was predicted i.e. gibberellins (GAs) 10 genes, bassinosteroids (BRs) 14 genes, auxin (9 genes), fruit development (8 genes) and fruit ripeing (4 genes). These agronomical important genes could be utilized in genetic engineering and molecular breeding to improve the production of palm oils.

Keywords

comparative genomic, ortholog, SonicParanoid

Project Number

International Islamic University Malaysia (IIUM) Research Initiative Grant Scheme (RIGS17-022-0597)

Thanks

We sincerely thank the staff and administration of International Islamic University Malaysia and The Malaysian Palm Oil Board for their assistance and support in this study.

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