Mutation Breeding in Coffee with Special Reference to Leaf Rust: Protocols

This open-access book provides a comprehensive overview of current methodologies for improving resistance to leaf rust in coffee, one of the world's most important cash crops and beverages. Coffea arabica L. (Arabica) accounts for about 60% of the world's coffee production. Coffee leaf rust (CLR), caused by the fungus Hemileia vastatrix is the major disease affecting Arabica coffee resulting in losses of over $1 billion annually. The geographical distribution of CLR is expanding due to climate change. Moreover, the genetic improvement of Arabica coffee is constrained due to its very narrow genetic base. This protocol book introduces essential concepts of mutation breeding as an efficient tool to increase the genetic diversity of Arabica coffee and presents practical methods on mutation induction and screening for resistance to CLR. Current breeding approaches, challenges and opportunities for Arabica coffee improvement are briefly reviewed and a survey of common coffee diseases with emphasis on CLR is presented. Practical protocols for mutation induction and screening for resistance to CLR are described, including novel methods for single-cell mutagenesis using in vitro cell and tissue culture techniques and for genome-wide screening of induced mutations using genomics tools. Each protocol chapter has an introduction and is supported by example results. Given the impact of recent CLR epidemics on Arabica coffee production in Latin America, the book is intended to serve as a timely reference and guide for students and researchers in the agricultural sciences, plant pathologists and breeders, as well as growers and end-users interested in producing novel coffee genotypes for genetic studies, breeding, and commercial applications.

Ivan L.W. Ingelbrecht is a Senior R&D Manager and Researcher in Plant Molecular Genetics and Breeding. He completed his PhD in Plant Molecular Biology at Ghent University, Belgium (1993). His career in international agricultural research began at the International Institute of Tropical Agriculture, Nigeria where he held successive positions as postdoc, Head of the Bioscience Laboratory and Coordinator of the Program on Biodiversity, Biotechnology and Breeding. He has worked as Intellectual Property Rights Liaison in the biotech company, CropDesign, Belgium. In 2016, he became Head of the Plant Breeding and Genetics Laboratory at the Joint FAO/IAEA Centre for Nuclear Applications in Food and Agriculture at the International Atomic Energy Agency, Austria. As a Team Lead, he established projects on the genetic improvement of coffee, banana, cocoa, and cassava with support from leading development investors and institutions from Africa, Latin America, the USA, and Europe. His recentresearch is focused on precision breeding of coffee and banana for resistance to Coffee Leaf Rust and banana Fusarium Wilt through integrated cell culture, genomics, and induced mutagenesis. He frequently supervises students, has published over 80 original research papers, and co-edited four books in the field of biotechnology, genetics, and plant breeding.

Maria do Céu Lavado da Silva is a Senior Researcher at the Coffee Rusts Research Center (CIFC), a Unit of Instituto Superior de Agronomia (ISA), School of Agriculture, University of Lisbon. She completed her Ph.D. degree in Agronomic Engineering (1996) at ISA. Her career began in 1984 at CIFC, developing activities on the cytology of plant-microbe interactions. She was awarded Calouste Gulbenkian Foundation Scholarships to the University of Toronto (1994) and Research Institute for Development in Montpellier (1995) and a Syngenta Award for Innovation in Agriculture in Portugal (2008). She hasled the CIFC research team since 2004. She has coordinated and participated in several projects with Institutions from Europe and Coffee Growing Countries. She has published over 90 original research papers. She is regularly involved in international training and supervision of graduate students. She is Vice-President of the Portuguese Society of Plant Pathology, an editorial board member of the journal Agronomy, and a board member of ASIC- Association for Science and Information on Coffee. Her main research focus is on the characterization of mechanisms underlying coffee resistance and susceptibility to the fungi that cause leaf rust and coffee berry disease.

Joanna Jankowicz-Cieslak is a plant molecular biologist and genome scientist with over 18 years' experience in the field of molecular biology, genomics and crop improvement with the use of mutation breeding techniques. She holds a PhD in biological sciences from the Jagiellonian University in Krakow, Poland. In 2019 she obtained a Habilitation degree in biology from the University of Silesia, Katowice, Poland for the work entitled "Techniques of induction and detection of genetic variability in functional genomics and breeding of plants of special importance in developing countries". Her research interests focus on the development and adaptation of new tools, protocols and guidelines for mutation induction and discovery in various crops such as coffee. She has extensive experience with induced mutagenesis, in vitro tissue culture, and the application of genomics tools for mutation-assisted breeding. She established the first reverse genetics approach for a vegetatively propagated crop, banana showing that mutations are stably induced and inherited over successive generations. She has (co-) authored over 60 original research papers, monographs and book chapters as well as co-edited four protocol books.