Team:SJTU-software/Integrated HP
Idea
Rice is one of the most important food crops for human beings. Nearly half of the world's population (more than 3 billion people) live on rice as their staple food. Therefore, how to effectively increase rice yield has become the key to solve global food problems. We have seen the 2019 iGEM team Purdue's significant work on rice blast prevention using genetic technology. This has inspired us to develop a software tool that can help synthetic biology researchers screen genes for various strains of rice, providing a reference for gene editing. Our program is preliminarily designed to use gene sequencing datasets to screen genes related to rice stress resistance traits, so as to provide a reference for using gene editing technology to cultivate high-yielding and stress-resistant rice lines.
Primary investigation
As a Chinese old saying goes, " Bread is the staff of life", food is a necessity for people’s lives. Agriculture is the foundation of the economy, and grain reserves are of great significance to maintaining the stability of the country. This year the Nobel Peace Prize was awarded to the United Nations World Food Program, which has made significant contributions to fighting hunger and improving living conditions. Farmers and scientists all over the world are working hard to increase food production. The best way is to increase the number of crops that can be grown per unit of land area and expand the plantings of high-yielding food crops globally.
So which crop has the potential to achieve high yield, high stress resistance and wide distribution?
Through communication with professor Dabing Zhang from the Department of Plant Development Sciences, School of Life Sciences and Technology, Shanghai Jiao Tong University, we were suggested to choose rice as our main research direction. Mr. Zhang, whose main research interests are the molecular regulation mechanism of rice reproductive development, introduced rice genome research and the importance of rice cultivation to global food issues in detailed.
Rice is widely grown around the world, and rice-based people account for more than half of the global population, especially in East Asia and Southeast Asia. China was the first country to grow rice, with a history dating back 7,000 years. Although China also grows wheat, corn, and other varieties, rice has always been a priority in Chinese food culture. More importantly, China has a relatively solid foundation for rice research. At the genomic level, thousands of rice lines have been fully sequenced. Moreover, the genetic control mechanism of rice traits such as plant height, ear length and pollen fertility has been fully studied. In addition, rice performs well in terms of yield and adaptability, and a rice-based diet is easier to be acceptable to the dietary habits of the majority of the world's population.
Improve
Because of the impact of COVID-19, we have focused our investigations and research domestically. In China, the eastern region has a suitable climate, sufficient agricultural development, and a high level of economic development. At the same time, traditionally, people in these areas often live on rice, which has relatively mature planting conditions and very advanced planting techniques. However, in the mid-western China, due to ecological and geographical constraints, agricultural development in many areas has been affected. For instance, Qinghai Province has a complex topography, straddling the Qinghai-Tibet Plateau, inland basins, and Loess Plateau, with large temperature differences and insufficient rainfall, making it unsuitable for growing food crops such as rice. With the impact of the COVID-19, it is not realistic to go abroad for field investigations. So we chose Qinghai Province as the main place for our human practice. Because we think the natural conditions, development history and religious background of Qinghai province are very representative.
Through the investigation and individual interviews of the local middle school students, we mainly learned about their dietary habits, nutritional structure and other basic information. Further more, we collected their views on new life science technologies and gene editing crops, and analyzed the market demand for the promotion of high-yield rice in the local market. At the same time, we bring our self-developed courses and virtual laboratory system to the local area to help students better understand our team and project and cooperate with our investigation. We created a questionnaire to investigate the local population's understanding of synthetic biology and their identification with the results of synthetic biology.
10% of the students thought that the video of the virtual experiment platform was not clear and vivid enough, and 3.45% of the students thought that the authenticity and restoration degree of the virtual experiment were not high enough. After receiving the feedback from the students, we improved animation on the operation details, optimized the experimental process and improved the user's experience. In addition, in order to increase the richness and operability of virtual simulation experiments, we will also cooperate with other teams to embed more software to realize other functions.
Human practices here have also refined our projects. We decided to discard some ancillary functions that were not relevant to the theme of "Rice gene screening" in the previous project design, and focus more intensively on the construction of a powerful database of rice gene analysis. In addition, the opinions of local residents on rice diet make us more clear "which rice traits are more important". Based on this, we improved the correlation gene screening algorithm and adjusted the corresponding weight parameters of different genes, so as to reflect the status of "important genes" and make them easier to be screened out.
Advice
After the activities in Qinghai Province, we took part in the 7th CCiC in August. During this online event, we had the opportunity to give a brief introduction to Riss and hear from other teams. This allows us to determine the relationships between our projects and those of other teams, so that we can better seek team cooperation and listen to other teams' advice.
Work sharing and discussion provide opportunities for collaboration. We got in touch with several other teams, had in-depth conversations and asked them what they thought of the project.
The judges discussed with us on some of the special needs of plant synthetic biologists and suggested that we expand our data sources so that our database can serve them better. They also suggested that we should investigate more literature to make sure the "genetic screening" algorithm is scientific, so that our project is more convincing.
We also discussed with Professor Wei Chaochun and Master Wei Yangzhen from the Department of Bioinformatics and Biostatistics at Shanghai Jiao Tong University in related fields. According to their advice, the key to solving our concern lies in using the rich heritage diversity of rice.
In their previous work, they have sequenced the entire genome of more than 3,000 rice lines and published important papers in Nature. Some of their research results can effectively improve the data volume of our project and further enrich the functions of the database. With their advice and help, we hope to assist the research on rice stress resistance, and have established a database that includes rice genes, RNA-seq, proteins, and other important information. They also advise us that we’d better perform clustering analysis and corresponding visualization of genomic data, which can help users better understand the data information we collect and the functions of the database, so that our project can better serve them. We will also help evaluate and mark undiscovered genes in order to recommend the most likely genes related to stress resistance to researchers
Feedback
After the project was formed, we invited teams from ZJUT, UESTC, and another great team from our university, SJTU-Bio-X-Shanghai, to experience and test our project, and invited them to provide suggestions and opinions for our further improvement in the future, as well as reference for iGEM participating teams interested in the field of our project.
The ZJUT team's project is also about building a database. Although the databases of the two teams are not related to each other subjectively, by testing the actual use of the databases, they also raised some valuable recommendations and made positive comments on the user interface and retrieval system of our databases.
The UESTC team did some interesting work at the protein level.So they raised some expectations for our project, such as being able to incorporate proteomic information from rice, showing downstream regulators of selected genes and ultimately encoded proteins.It is better to elucidate the molecular mechanism of stress tolerance in rice.They believe that synthetic biologists and botanists are eager to have highly integrated software tools that can help them establish close links between genomes, transcriptome and proteome, which will greatly facilitate their research.
