Breeding for drought tolerance by integrative design: the case of common bean (Phaseolus vulgaris L.) in Ethiopia Asrat Asfaw Thesis committee Thesis supervisor Prof. dr. ir. P. C. Struik Professor of Crop Physiology Wageningen University Thesis co-supervisors Dr. ir. C.J.M. Almekinders Assistant Professor, Technology and Agrarian Development Group Wageningen University Dr. M. W. Blair Crop breeder and geneticist Department of Plant Breeding, Cornell University, Ithaca, USA Other members Prof. dr. ir. E. Jacobsen, Wageningen University Prof. dr. K.E. Giller, Wageningen University Dr. ir. L. Visser, Centre for Genetic Resources, Wageningen Prof. dr. A. Tsegaye, Addis Ababa University, Ethiopia This research was conducted under the auspices of the Graduate School Production Ecology and Resource Conservation (PE & RC) and Wageningen School of Social Sciences (WASS). Breeding for drought tolerance by integrative design: the case of common bean (Phaseolus vulgaris L.) in Ethiopia Asrat Asfaw Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M. J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Tuesday 6 September 2011 at 4 p.m. in the Aula. Asrat Asfaw Breeding for drought tolerance by integrative design: the case of common bean (Phaseolus vulgaris L.) in Ethiopia 188 pages Thesis Wageningen University, Wageningen, NL (2011) ISBN: 978-90-8585-977-2 Abstract Asfaw, A (2011) Breeding for drought tolerance by integrative design: the case of common bean (Phaseolus vulgaris L.) in Ethiopia. PhD thesis, Wageningen University, The Netherlands, 187pp. Drought stress is the most important limitation facing crops now and in the future. This makes improving adaptation to drought stress a major objective of crop breeding. Breeding efforts in common bean developed drought tolerant genotypes but the genetics and preferences of farmers for drought tolerance are largely un-studied. This study assessed genetic, physiological and social aspects of drought tolerance in common bean breeding. More specifically the study was envisioned as developing common bean varieties with increased levels of drought tolerance in farmers’ preferred grain types for southern Ethiopia. Multiple approaches that combine laboratory, greenhouse and field level analysis with participatory experimentation deploying tools in the biological and social science arenas were used. The findings demonstrate that farmer use and management of common bean seed and varieties in southern Ethiopia are characterized by varying conditions, varying practices and the dynamics of a changing climate and market. Farmers recognize that climate is changing but only half of them have adapted some of the cropping practices. Marginality of production ecology related with climate change, market dynamics, cropping system and culinary preferences make common bean farming at farmer level a series of moving targets that are problematic for a drought breeding program to hit simultaneously. Moreover, exposure to new variety types influence farmers’ preferences. In addition to this diversity in production environments and variation in farmers’ preferences, the plant’s response to drought stress is complex and diverse. Targeting specific plant responses to target areas is a difficult challenge for common bean breeders as shown by the quantitative trait loci (QTL) analysis. But, this study has generated information for specific qualitative and quantitative targets in the breeding design. These include: 1) farmers’ preferences are not static nor are they consistent across gender, location, individual and co-evolve with exposure; 2) original differences in introduced germplasm from the primary centers of domestication were the base for East African common bean diversity and there are distinct germplasms at national or regional level; 3) the relevance of continued photosynthate accumulation as a trait for common bean drought tolerance; 4) root based QTL can be identified but may not be compatible with yield related traits although their selection can benefit from tightly linked markers; 5) only a few major QTLs with high QTL×E interaction were detected whereas a large proportion of genetic variance remained unexplained by the QTLs for traits related to drought avoidance, photosynthate accumulation and (re)mobilization, highlighting the difficulty in detecting QTL in drought studies in common bean; and 6) exposing farmers to new drought-tolerant variety types makes them aware of drought selection traits and creates new market niches for new products. Hence, more drought-tolerant common bean genotypes for a range of farmer conditions, markets and preferences can only be developed on the basis of an integrated understanding of farmers’ production conditions, existing seed system practices and different physiological processes that regulate drought tolerance in the plant. In general, the results from the present work contribute to integrative breeding strategies that incorporate participatory, physiology and marker-aided selection to breed new varieties of drought-tolerant common bean that combine a range of mechanisms in farmers’ preferred grain types. Keywords: Decentralized breeding, drought stress, farmer preference, genetic diversity, participatory variety selection, population structure, quantitative trait loci Acknowledgements Bringing thesis writing to an end is a historic moment and a great achievement in one’s carrier. Various individuals and institutions supported the process. First of all, it gives me an immense pleasure to express my sincere and great thanks to my supervision team: Prof. dr. ir. Paul C. Struik (Centre for Crop Systems Analysis, Wageningen University), Dr. ir. Conny J.M. Almekinders (Technology and Agrarian Development Group, Wageningen University) and Dr. Matthew W. Blair (Cornell University) for their learned guidance, sustained help, constructive criticism and constant encouragement during proposal development, field research and thesis writing. I met Dr. Conny and Prof. Paul for the first time in May 2004 during an IAC course at Wageningen and talked especially with Conny about my PhD study plan here in Wageningen. Since then I was in touch with Conny and finally this study was on board in 2007 by the financial support from the Netherlands Organization for International Co-operation in Higher Education (NUFFIC). Dr. Conny has travelled to my field research sites in Ethiopia and provided enormous learning opportunities in basic scientific writing and other aspects which were instrumental for the success of the study. Your supervision and guidance were invaluable and highly appreciated. I am grateful to Dr. Matthew for his encouragement especially in combining molecular aspects with social aspects. He provided me space in his laboratory at CIAT (International Centre for Tropical Agriculture) for the molecular work and the technical inputs he gave me in this respect are highly acknowledged. I also owe a debt of gratitude to Prof. Paul for his willing help, keen interest in my study, weekly discussions during the writing phase and making the trajectory to the Aula real. I am also sincerely obliged and indebted to Prof. P. Richards for the inestimable helps during the initial phase of my study. I would like to thank all my revered members of the supervision team for their academic support and hospitality during the whole period of the study. I extend my heartfelt thanks to fellow students and colleagues in the Technology and Agrarian Development Group (TAD) for their valuable helps, advice, discussion and encouragement throughout. I would like to mention some of the PhD students of the group whose company and friendly attitude I enjoyed during the course of my study, F. Okry, A. Mokuwa, A. Barraza, Chen R., Sabarmattee, B. Teeken and Jacintha. I also thank my colleagues and friends, Tsedeke Kocho, Teshale W. Hababo, Birhane Kidane, Etetu Sewangizawu, Bethel Belachew, Bereket and his family, Yosef and his family, Ashenafi and Areaya for social and emotional support during my stay at Wageningen. I owe to record my grateful acknowledgment to Inge Ruisch for unlimited administrative support that made my stay at Wageningen possible and enjoyable. Inge, your sympathetic help in those hard times in August 2010 is always fresh in my memory. Muchas gracias! I am sincerely obliged and indebted to many farmers in the research sites of Awassa, Boricha, Amaro, Konso, Loma, Gofa and Inseno for their participation in the study and for sharing their knowledge on the different aspects of variety and seed management. I owe much gratitude to the field research assistants who helped interview farmers and facilitated translation during group discussion. My especial thanks go to Tadesse Haile, Wondimagegn, Bereket D., Tamirate C., Demeke T., Fistum A., Moshe K., Samuel B., Fekadu G., Gashahun W., Daniel A., Lema T., Tegene A., Jose P., Daysi Bravo, Paula L. Hurtado, Cesar A.O. Nieto, Abebe W., Abebe G., Tadesse L., Gadewu G., Tesema H., and Ageze A. who helped me during the on-station research and data processing. I extend my heartfelt thanks to breeders, extension agents and farmers who participated in preference elicitation and in-field selection. I also wish to acknowledge useful discussions with Dr. S. Beebe, Dr. I.M. Rao and other staff of CIAT and thank Dr. Beebe for reading some of the manuscripts and giving valuable suggestions. I am