In the typical breeding of agricultural and horticultural crops, novel varieties have been created by selection of individuals which showed excellent traits. The data obtained in the breeding process were discarded after the selection of the best ones and were never used. However, the data obtained through breeding contain a wealth of information on the relationship between phenotypes and genes. Data-driven breeding (DDB) enables one to construct a system in which such data are automatically collected during the breeding process, to model the relationship between phenotype and marker genotypes based on the collected data, and to formulate optimal breeding strategies based on the models.
Next-generation sequencing technology has made it possible to create reference genome sequences in many types of crop species as well as develop a vast amount of DNA marker information at relatively low cost. In order to share the breeding process as common knowledge and to enable analysis as data, it is necessary to link the large amount of the genotype, phenotype and environmental data obtained in the breeding process, and to accumulate the data together with the selection results of breeders. Furthermore, in order to make models with the data and to enable the formulation of optimal breeding strategies based on the model, it is necessary to develop a high-quality, large-scale data accumulation system, and develop an application programming interface (API) that visualizes the data and supports breeding strategies.
Asian agriculture often produces divergent types of crops on relatively small fields compared to other regions in the world. Therefore, in breeding, it is necessary to breed varieties that are suited to the diversity in agriculture rather than monoculture. It is considered that information exchange between scientists and breeders in Thailand and neighboring countries, which are leading breeding in Southeast Asia, and Japanese scientists who are developing DDB APIs is important for development of DDB approaches that suit breeding for Asian agriculture. Therefore, we would like to hold a symposium to discuss the future development of DDB with scientists from both regions.
Breeding with genome-wide genotype information such as genomic selection is moving from the research to the practical phase. Data-driven Breeding project, funded SIP, Japan (2018-2022) has been developing tools to construct predictive models based on genome-wide genotype data.
Day 1: Monday the 20th of February 2023
Venue: Miracle Grand Convention Hotel
| TIME (GMT+7) |
AGENDA |
SPEAKERS |
| 08:30 - 09:00 |
Registration |
|
| 09.00 – 09.20 | Opening Ceremony |
|
| 09:20 - 09:30 |
Photo Session |
|
| Keynote Lectures | ||
| 09:30 - 10:00 | Genomics for data-driven breeding (On-Line) |
Prof. Rajeev K Varshney |
| 10:00 - 10:30 |
Rice Breeding Platform |
Dr. Theerayut Toojinda |
| 10:30 - 10:45 |
Coffee Break |
|
| Technical Sessions | ||
| 10:45 - 11:15 | The breeding strategies in crops that are important in Thailand |
Dr. Piya Kittipadakul |
| 11:15 - 11:45 |
Review of Data Driven Breeding |
Dr. Hiroyoshi Iwata |
| 11:45 - 12:15 |
The genomic breeding / genomic selection of mung beans |
Dr. Prakit Somta |
| 12:15 - 13:30 |
Lunch |
|
| 13:30 - 14:00 |
Improving quantitative traits in soybean using simulation-based selection |
Dr. Akito Kaga |
| 14:00 - 14:30 |
The genomic breeding/ genomic selection of animal |
Dr. Skorn Koonawootrittriron |
| 14:30 - 15:00 |
Sugarcane improvement through wild germplasm utilization in the collaboration of Japan and Thailand |
Dr. Yoshifumi Terajima |
| 15:00 - 15:15 |
Coffee Break |
|
| 15:15 - 15:45 |
Adaptation to climate change in Northern Vietnam by developing rapid-maturation rice varieties |
Prof. Seth Jon Davis |
| 15:45 - 16:15 |
Citrus Breeding 2.0: An integrative approach of genomics-assisted selection |
Dr. Tokurou Shimizu |
| 16:15 - 16:45 |
Panel Discussion: |
Moderator: |
Day 2: Tuesday the 21st of February 2023
Venue: Miracle Grand Convention Hotel
|
TIME (GMT+7) |
AGENDA | SPEAKERS |
| 08:30 - 9:00 |
Registration |
|
| 09:00 - 09:45 |
Lecture on Basics on DDB |
Dr. Hiroyoshi Iwata |
| 09:45 - 10:30 |
Current Genotyping |
Dr. Sachiko Isobe |
| 10:30 - 10:45 |
Coffee Break |
|
| 10:45 - 12:15 |
Tutorial on DDB app |
Dr. Kiyoshi Honda Assisted by: |
| 12:15 - 13:30 |
Lunch |
|
| 13:30 - 15:00 |
Hands on: Breeding Game |
Mr. Julien Diot |
| 15:00 - 15:15 |
Coffee Break |
|
| 15:15 - 16:30 |
Hands on: Breeding Game (continue) |
Mr. Julien Diot |
Day 3: Wednesday the 22nd of February 2023
Venue: National Science and Technology Development Agency (NSTDA)
|
TIME (GMT+7) |
AGENDA |
| 08:30 - 09:00 |
Registration |
| 09:00 - 10:00 |
Transportation from Miracle Grand Hotel to NSTDA |
| 10:00 - 10:30 |
Plant Phenomics (BIOTEC Building) |
| 10:45 - 11:15 |
Plant Factory (INC2 Building) |
| 11:30 - 12:00 |
Thailand Bioresource Research Center (TBRC) (INC2 Building) |
| 12:00 - 13:00 |
Lunch |
| 13:00 - 14:00 |
Transportation from NSTDA to Miracle Grand Hotel |
Prof. Rajeev K Varshney
Director, State Agricultural Biotechnology Centre
Director of Centre for Crop & Food Innovation & International Chair in Agriculture & Food Security
Murdoch University, Australia
Prof. Rajeev Varshney is an agricultural research scientist specializing in genomics and molecular breeding with 20+ years of service in international agriculture while working in India, Germany, Australia, Mexico and several countries in Africa. He is serving Murdoch University as a Director, Centre for Crop & Food Innovation; Director, State Agricultural Biotechnology Centre; and International Chair in Agriculture & Food Security with the Food Futures Institute. Prof. Varshney is a globally recognized leader for his work on genome sequencing, cataloguing and utilizing genetic diversity, genomics-assisted breeding, seed system and capacity building in developing countries. He has made centrally important contributions towards improving food and nutrition security in India and several countries in Africa and Asia by assembling genomes, developing genomic resources and integrating genomic technologies in crop improvement programs in many tropical crops, and delivering several superior crop varieties to some of the world’s poorest farmers.
Prof. Varshney, a highly prolific author and Highly Cited Researcher for 9 consecutive years (2014-2022) in a row has published >500 papers in high impact factor journals including 20 papers in Nature journals. He has authored/edited >20 books published from international publishers like Springer, CRC Press, Wiley etc. Based on his publications, he has h-Index of >115 with >50,000 citations. He is the only agricultural/plant scientist in India, and the second plant biologist in Australia to achieve an h-index of >100 as per Google Scholar. He has been named as the Top Scientist in Agronomy & Crop Science category in the list of 250 Top Scientists in Australia by The Australian newspaper’s Research Magazine.
He is an elected fellow to about 10 science and agriculture academies/ societies in India, Germany, USA, etc. and recipient of several noted awards including the most coveted science award, Shanti Swarup Bhatnagar Prize, the most prestigious agricultural science award, Rafi Ahmed Kidwai Award from Government of India, and 2022 International Crop Science Award by the Crop Science Society of America. It is noteworthy that ICRISAT won the 2021- Africa Food Prize for the outputs and impact of Tropical Legume projects, led by Prof Varshney as Principal Investigator for 7 years.
Dr. Theerayut Toojinda
Deputy Executive Director|
Research and Development Bioscience and Biotechnology for Agriculture
National Science and Technology Development Agency (NSTDA)
Theerayut Toojinda completed his Ph.D. in Crop Science from the Oregon State University, USA in 1998. He has accumulated expertise in the field of plant breeding for almost 30 years. His expertise is in the field of genome mapping in plants, molecular breeding, gene identification and positional gene cloning.
Theerayut is the best known rice breeder in the Greater Mekong Sub-region (GMS), particularly Thailand, Laos, Cambodia and Myanmar. His research is centered on the use of marker aided selection (MAS) to improve the effectiveness and precision of conventional rice breeding with the goal to improve tolerance to unfavorable environmental conditions and resistance to pests and diseases. He and his research team developed rice varieties which are flood-tolerant jasmine rice (Homcholasit), blast-resistant glutinous rice (Thanyasirin).
Dr. Piya Kittipadakul
Associate Professor
Plant Breeding and Plant Genetics
Departmrnt of Agronomy, Faculty of Agriculture
Kasetsart University, Thailand
Ph.D. in Plant Breeding and Plant Genetics from University of Wisconsin-Madison, U.S.A. Integrating quantitative genetics with molecular genetics in order to understand crop genetic architecture to increase the efficiency of selection in plant breeding program.
Research Programs: Cassava Breeding In charge of cassava breeding program of the Department of Agronomy to identify desirable traits from cassava germplasm and to develop new varieties with high yield and starch content including other good characteristics.
Dr. Hiroyoshi Iwata
Associate Professor
Laboratory Biometry and Bioinformatics
Department of Agricultural and Environmental Biology
University of Tokyo
Born in 1969, raised in Thailand and Indonesia during his childhood. Bachelor of Agriculture, The University of Tokyo (UT). Ph.D in Graduate School of Agricultural and Life Sciences, UT. After conducting researches in National Agriculture and Food Research Organization (NARO), Japan, under the theme of fusion between agriculture and information science, I have been Associate Professor of Laboratory of Biometry and Bioinformatics in UT since 2010. Now, I am focusing mainly on data sciences to accelerate plant breeding.
Dr. Prakit Somta
Associate Professor
Department of Agronomy (Faculty of Agriculture at Kamphaeng Saen)
Kasetsart University, Thailand
Ph.D. (Plant Breeding) 2005 Kasetsart University., Thailand, B.Sc. (Agriculture) (First class honor) 2000 Kasetsart University., Thailand
Experiences; Genetics, genetic resources, and breeding of legume crops, especially mungbean and soybean
Award; 2019 Outstanding Plant Breeder of the Plant Breeding and Multiplication Association of Thailand
Dr. Akito Kaga
Senior Scientist
Institute of Crop Science
National Agriculture and Food Research Organization (NARO), Japan
Dr. Kaga received his Ph.D. in Kobe University. He then worked at NARO in Tsukuba as Post-doctorate fellow, where he studied on cloning of bruchid resistance gene in mungbean. In 1999, he joined as permanent staff to genetic resource center at NARO, formerly Genebank, and has been working on exploring wild species of soybean, genus Vigna and studying mechanism of domestication of legumes from wild population. From 13 years ago, he concentrates his research activities on building genomic bases for Japanese soybean breeding and developed experimental resources; soybean core collection, chromosomal segmental lines, soybean mutant library. Recent research interests are; exploring responsible genes for important soybean traits using experimental resources, genomic prediction and selection for important traits and drone remote sensing for high-throughput field phenotyping.
Dr. Skorn Koonawootrittriron
Associate Professor (Animal Breeding)
Department of Animal Science, Faculty of Agriculture
Kasetsart University, Thailand
Dr. Skorn Koonawootrittriron research areas are aimed to improve genetic ability for economically important traits of livestock and aquatic animals under tropical conditions. Developing genetic and genomic-polygenic evaluations, selection and mating techniques, and strategies suitable for single-breed and multi-breed animal populations in the tropics are interested. Applying bioinformatics, molecular genetics, and genomics information to improve efficiency of livestock production in the tropics is also investigated. His expertise are in Animal Breeding and Genetic, Animal Science, Biostatistics andAnimal Husbandry.
Dr. Yoshifumi Terajima
Senior Scientist
Tropical Agriculture Research Front
Japan International Research Center for Agricultural Sciences (JIRCAS)
Dr. Yoshifumi Terajima is a sugarcane researcher having 22 years experiences of sugarcane breeding and produced more than 15 sugarcane varieties in Japan. He has been actively involved in developing breeding technologies for effectively utilizing wild germplasm to improve sugarcane and developed some high-yielding varieties using the germplasm. He received his Ph.D. degree from the University of Tsukuba, Japan, by summarizing these results. In addition, he has been conducting international collaborative research on sugarcane breeding with Khon Kaen Field Crops Research Center in Thailand and the Sugar Regulatory Administration in the Philippines.
Dr. Tokurou Shimizu
Former Senior Scientist, Genomics, Citrus Research Division
NARO Institute of Fruit Tree and Tea Science
Tokurou Shimizu obtained his Ph.D for biochemistry in Saitama University and started his carrier at the National Institute of Fruit Tree Science (NIFTS) in 1992. He started genome research of citrus in 1994 and participated in the launch of the International Citrus Genome Consortium in 2003. Dr. Shimizu worked on genome analysis of citrus in collaboration with citrus breeding programs in NIFTS and domestic institutes. His study covers DNA marker development, gene isolation and expression analysis, marker-assisted selection, bioinformatics, genotyping analysis for variety identification and phylogenetic analysis. He revealed pedigrees of more than 60 varieties in 2016 and also released the first Satsuma draft genome sequence in 2017. Based on these studies, he proposed a new breeding approach, Citrus Breeding 2.0, to achieve fast breeding in a minimum duration. After he retired from NIFST in 2022, he continues working to support breeding from the genomic point of view.
Dr. Sachiko Isobe
Head, Lab of Plant Genetics and Genomics
Kazusa DNA Research Institute
Sachiko Isobe started her career as a conventional red clover breeder in 1997. She gained PhD from the United Graduates School of Agricultural Sciences, Kagoshima University in 2006, and has worked for plant molecular genetics and genomics in Kazusa DNA Research Institute since 2007. Currently she is a lab head of Plant Genomics and Genetics performing de novo whole genome sequencing, molecular genetics, DB construction and digital phenotyping for plants. She is also a leader of Lab of Plant DNA Analysis, which provides contract-based services such as genome analysis of cultivated plants and related microorganisms, and development of practical technology for their analysis.
Dr. Kiyoshi Honda
Professor - Dept. of Astronautics and Aeronautics, Chubu University
Advisor and Chief Scientist - ListenField
Professor Kiyoshi Honda has over 30 years of research experience in satellite remote sensing, field sensor networks and crop modeling applications. He earned his Doctor of Engineering degree from the Faculty of Agriculture, Tokyo University. Professor Honda also pioneered an interoperable API platform for Japanese agriculture, which was included in Japan’s agricultural reform policies. He now heads the development and operation of an API-based plant breeding platform aimed at supporting the breeding workflows of Japanese institutions.
Mr. Julien Diot
PhD Student at University of Tokyo
Data Scientist at Listen Field
Julien Diot started his training in agriculture at Montpellier SupAgro, France. Among the various subjects studied, he focused his interest on statistics and computer science and graduated with a major in “Data-Science for Agriculture”. During this time, he developed a "serious role playing game" to teach breeding to graduate level students. The concept is to place the students in a breeder's seat and let them make their own breeding campaign thanks to simulations while competing to each-others.Julien is now a Ph.D student at the University of Tokyo in the laboratory of Biometry and Bio-informatics. His research, supported by the Cross-ministerial Strategic Innovation Promotion Program (SIP), focuses on the use of Bayesian approaches for the optimisation of breeding schemes. In addition to his Ph.D, he is a data-scientist for a Japanese startup, ListenField, where he helps developing a Data-Driven breeding platform.
Prof. Seth Jon Davis
Chair and Professor
University of York, Department of Biology
Wentworth Way, York, United Kingdom
Set J. Davis is currently Chair of Plant Biology and Professor; University of York, York, UK. His cuurent research ionterests are Using Arabidopsis, rice and barley, we unravel the mechanistic interconnections within the circadian-clock clock. In this there is use of systems modeling, metabolite profiling, cell biology, quantitative genetics and molecular genetics to show how allelic variation in clock genes are associated to developmental and metabolic traits associated to crop yield, particularly in response to climate change.