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.

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.

This book is open access under a CC BY-NC 2.5 license. This book offers 19 detailed protocols on the use of induced mutations in crop breeding and functional genomics studies, which cover topics including chemical and physical mutagenesis, phenotypic screening methods, traditional TILLING and TILLING by sequencing, doubled haploidy, targeted genome editing, and low-cost methods for the molecular characterization of mutant plants that are suitable for laboratories in developing countries. The collection of protocols equips users with the techniques they need in order to start a program on mutation breeding or functional genomics using both forward and reverse-genetic approaches. Methods are provided for seed and vegetatively propagated crops (e.g. banana, barley, cassava, jatropha, rice) and can be adapted for use in other species.

This book offers low-cost and rapid molecular assays for the characterization of mutant plant germplasm. Detailed protocols are provided for the desiccation of plant tissues; the extraction of high-quality DNA for downstream applications; the extraction of single-strand-specific nucleases for single nucleotide polymorphism; and small insertion/deletion discovery using standard agarose gel electrophoresis. The methods described can be applied in any laboratory equipped for basic molecular biology and do away with the need for expensive freezers and toxic organic compounds. With the appropriate validation of sample quality and longevity, they can provide sufficient DNA for a variety of molecular applications, such as marker studies and TILLING, at approximately one tenth of the cost per sample when compared to commercial kits.

This book offers effective, low-cost and user-friendly protocols for the pre-field selection of salt-tolerant mutants in cereal crops. It presents simple methods for measuring soil salinity, including soil sampling and the analysis of water-soluble salts, and describes a detailed, but simple, screening test for salt tolerance in rice, wheat and barley seedlings, which uses hydroponics. The protocols are devised for use by plant breeders and can be easily accommodated into breeding practice.

Bananas are a staple food for over 500 million people and are also an important cash crop. Fusarium wilt, caused by the fungus Fusarium oxysporum f.sp. cubense, is one of the most destructive diseases of banana globally. Since the 1990s, an aggressive variant of this fungus, called Tropical Race 4 (TR4), severely affected banana plantations in Southeast Asia from where it spread to other continents, including Latin America, where the global banana export market is primarily centred. TR4 is a soil borne pathogen making the disease difficult to contain. The Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture implemented a Coordinated Research Project (CRP) 'Efficient Screening Techniques to Identify Mutants with Disease Resistance for Coffee and Banana" (2015-2020). This CRP brought together experts from Asia, Europe and Africa in addition to experts of the Joint FAO/IAEA Centre to develop resistance against TR4 through mutation-assisted breeding. Induced mutagenesis is particularly attractive in case of banana since most cultivated bananas are seedless, thus hampering conventional cross breeding. This Open Access book is a compilation of the protocols developed under the CRP specifically for TR4. The first part covers methods for mutation induction, including the integrated use of innovative single-cell culture with mutagenesis techniques. The book also describes up-to-date phenotypic screening methods for TR4 resistance in banana under field-, greenhouse- and laboratory conditions. Finally, molecular and bioinformatics tools for genome-wide mutation discovery following Next Generation Sequencing are also described. Given the imminent threat of Fusarium Wilt TR4 on banana production globally, it is our hope and intention that the book will serve as a timely reference and guide for banana breeders and pathologists worldwide who are committed to the genetic improvement of banana for Fusarium wilt resistance.

This book is open access under a CC BY-NC 2.5 license. This book offers 19 detailed protocols on the use of induced mutations in crop breeding and functional genomics studies, which cover topics including chemical and physical mutagenesis, phenotypic screening methods, traditional TILLING and TILLING by sequencing, doubled haploidy, targeted genome editing, and low-cost methods for the molecular characterization of mutant plants that are suitable for laboratories in developing countries. The collection of protocols equips users with the techniques they need in order to start a program on mutation breeding or functional genomics using both forward and reverse-genetic approaches. Methods are provided for seed and vegetatively propagated crops (e.g. banana, barley, cassava, jatropha, rice) and can be adapted for use in other species.