Poster Presentation 25th Annual Lorne Proteomics Symposium 2020

A draft map of the Rice plant proteome (#106)

Yunqi Wu 1 2 , Karthik Kamath 1 3 , Matthew McKay 1 2 , Ardeshir Amirkhani 1 2 , David Cantor 1 2 , Gene Hart-Smith 1 2 , Dana Pascovici 1 2 , Mohsen Rahiminejad 4 , Armin Soleymaniniya 4 , Paul Haynes 2 , Ghasem Hosseini Salekdeh 4 , Mehdi Mirzaei 1 2
  1. Australian Proteome Analysis Facility, Sydney, NSW, Australia
  2. Faculty of Science and Engineering, Sydney, NSW, Australia
  3. Faculty of Science, Sydney, NSW, Australia
  4. Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran

Rice (Oryza sativa) is one of the most widely cultivated crops on the planet. It has the smallest genome and greatest biodiversity of all cereals and similarities in gene order (synteny), gene structure, gene sequence, and gene function, making it an ideal model cereal. The rice plant genome contains 35,678 predicted protein-encoding genes; however, over 89% of these genes lack confidently mapped protein level evidence. To address this gap and to expand on knowledge of the rice proteome, we performed high-resolution mass spectrometry based proteomics of rice plant. In-depth proteomic analysis of 30 distinct anatomical parts of the rice plant, including regenerative, reproductive and undifferentiated organs in different developmental stages, resulted in identification of 13,371 protein-coding genes (FDR 1%) with at least two unique peptides with the length of <30 & >9 amino acids (gold identifiable proteins referred to HPP guideline v.3). Error-tolerant sequence database searches, which search for all entries in the Unimod database in a systematic manner, revealed particularly widespread evidence for the identification of canonical proteins alongside sequence variants. These results extend the identified proteome coverage of rice to about 40% of the total annotated protein-coding genes in rice plants. This compendium of the rice proteome (to be available as an interactive web-based resource soon), as a community resource, can now drive disruptive innovation in rice cultivar improvement and propel rice research and application through improved understanding of rice biology.