Project Briefs

With approximately 11 million habitants, Guatemala is mostly a rural country, with 60 percent of the population living on farms and 50 percent of the population indigenous. Maize and beans are the main staple food in most households, with a per capita consumption of 9.4 kg per year. Since few other sources of protein are available, this amount is not sufficient to ensure an acceptable nutritional quality, especially within poor households.

The highlands of Guatemala are a unique bean producing region where intercropping (locally known as milpa) is still the main production system, mostly with a maize–bean association. The system uses climbing beans that grow around the corn stalks either concurrently or in a relay system. Unfortunately, on-farm productivity of these climbing beans is approximately one-third of their genetic yield potential, mostly due to the lack of improved cultivars able to withstand biotic and abiotic stresses. This low productivity significantly impacts food security and nutritional quality in the region, especially among women and children. Historically, climbing beans have received less attention and breeding efforts in comparison with the bush-type beans commonly grown in the lowlands, as shown by the significant yield gap between regions. The Feed the Future Innovation Lab for Legume Systems Research is starting a new project focused in the highlands of Guatemala with the goal of developing improved varieties of climbing beans that would increase productivity in the region. In addition, the Guatemalan climbing beans are a unique group of germplasm that has not been studied extensively and could offer new genetic variation for traits of economic importance.

Problem Statement and Justification

Dietary recommendations from the Guatemalan government suggest a 75:25 percent daily ratio of maize:bean for a good nutritional balance between carbohydrates and protein intake; however, collected information suggests that the actual daily maize:bean ratio in rural households is approximately 97:3 percent. As expected, the resultant lack of protein intake has reduced the nutritional quality in many households, significantly affecting children. Severe malnutrition cases and even deaths are reported in rural areas, mostly in the highlands.

Beans are grown on 31 percent of the agricultural land and mostly in the low- to mid-altitude regions (0–1500 masl [meters above sea level]) in a monoculture system. In contrast, intercropping (milpa) is the main production system in the highlands, where maize–bean is the most common crop association. The main bean producers are small landowners, largely in the highlands. These farmers plant 66 percent of the total area planted to beans in the country, yet the production is only 53 percent of the total national bean production. In contrast, large landowners (greater than 45 ha) in lowland areas produce 28 percent of the beans on only 18 percent of the area planted to beans.

On-farm productivity of these climbing beans is approximately one-third their genetic yield potential, mostly due to the lack of improved cultivars able to withstand biotic and abiotic stresses. Fungal and bacterial diseases and insect pests are the main cause for yield reductions. In addition, production is made with almost no inputs of fertilizers or other chemicals. Historically, climbing beans worldwide have received less attention and breeding efforts in comparison with the bush-type beans commonly grown in the lowlands, as shown by the significant yield gap between regions. There is an existing collection of approximately 600 accessions of climbing beans collected across all bean production regions in Guatemala. This collection is kept by ICTA and has been characterized morphologically and with few molecular markers (6 SSR primers). In addition, this is a group of germplasm that has not been intensively studied and, therefore, may be an untapped source for new genes for resistance/tolerance to biotic and abiotic stresses that could be useful for the entire breeding community.

Objectives

Development of germplasm with improved disease resistance and agronomic performance.
Characterization of the genetic diversity of this unique set of germplasm.
A better understanding of the current socioeconomic status and needs of bean production within the context of intercropping systems in the region.
Capacity building: training the next generation of plant breeders for Guatemala and establishing a long-term breeding plan to increase the productivity of climbing beans in the region.

Approaches and Methods

The bean breeding program at ICTA has selected a group of ten accessions from the germplasm collection that offer agronomic traits of interest, such as plant growth type, seed yield, disease resistance, earliness, and seed quality, among others. We will start field testing these ten accessions across ten to twenty locations. At the same time, genetic purification of selected lines will be done. After the first year of field testing, the best two lines will be selected for field testing in growers’ fields at three locations. Seed from promising lines will be multiplied and released to the public as a first generation of improved climbing beans while a more formal breeding program is being established. Given the uniqueness of this group of germplasm, it is necessary to ensure we are collecting all the genetic variability within this collection so it can be used in the future in breeding programs. To better understand the organization of the genetic diversity of this group, we will screen the core 300 accessions with the 6k BeanCAP chip and conduct a genetic diversity study of possible genetic relationships among the accessions. In addition, an assessment of variation within the ten selected lines will be made to account for the heterogeneity not only among but also within accessions and, possibly, to extrapolate that information to the rest of accessions. The collection will be also evaluated in the U.S. (greenhouse) for reaction to bean rust, anthracnose, Ascochyta leaf blight, bean common mosaic virus, and Mexican weevil. This core 300 collection could be used as a diversity panel that could be used for Genome Wide Association Studies (GWAS).

In addition, this project plans to do a small-scale socioeconomic study that will try to answer some of these questions. The results will help design future strategies to improve bean productivity and consumption in the region. A grower survey will be deployed in the main regions where climbing beans are produced. Results of this survey will be shared not only within the project but with other projects currently working in Guatemala (e.g., Másfrijol) and government agencies. A second phase of this study will evaluate the acceptability of new varieties by growers and in the last two years of the project, an assessment of adoption, dissemination, and impact will be made.

Anticipated Achievements and Outputs

The development and release of improved climbing beans with better agronomic performance (four years).
A better understanding of the organization of the genetic diversity within this unique set of germplasm (two years).
Identification of genomic regions associated with traits of agronomic/economic importance (four years).
An information database of the current market situation and production needs of climbing beans in the highlands of Guatemala (two years).
Training of the next generation of plant breeders (four years).
- Establishment of a long-term breeding approach (four years).

Projected Developmental Outcomes

Improved germplasm/varieties of climbing beans are expected to be released after this four-year effort. Disease and pest resistance and greater tolerance to abiotic stress of improved cultivars should increase or produce more stable bean yields in the Guatemalan highlands. Collaboration with other projects will allow the dissemination of this genetic material to other regions, further increasing this project’s impact. This project will also produce a new information database of the current market situation and production needs of climbing beans in the highlands of Guatemala

Capacity Building of Partner Host Country Institutions

Two individuals from Guatemala will come to do graduate studies at NDSU (Plant Sciences), with the goal that those individuals will be incorporated into agricultural research back into Guatemala. We foresee research projects focused on the analyses of genetic diversity, genetic resistance to diseases, and production systems, among others. The graduate students will be provided a broad range of training in conventional and molecular plant breeding techniques so that they can assume roles of leadership in bean research programs in the target countries. In addition, an informal workshop will be made at NDSU for some members of the bean breeding program at ICTA during the third year. The goal of this training workshop will be to show the ICTA group how bean production is conducted in North Dakota (the largest bean producing state in the United States) and to provide training on molecular markers and other genomic tools that could help in the breeding process.

Improving Genetic Yield Potential of Andean Beans with Increased Resistances to Drought and Major Foliar Diseases and Enhanced Biological Nitrogen Fixation (BNF) (S01.A3)

Lead U.S. Principal Investigator

James D. Kelly, Michigan State University, USA

Collaborating Scientists

Wayne Loescher, Michigan State University, USA

James Steadman, University of Nebraska, USA

Carlos Urrea, University of Nebraska, USA

Karen Cichy, USDA-ARS, East Lansing, Michigan, USA

Eduardo Peralta, INIAP, Ecuador

Stanley Nkalubo, NaCCRI, Uganda

Kennedy Muimui, ZARI, Zambia

Abstract

Common bean (Phaseolus vulgaris L.) is the most important grain legume consumed in Ecuador, Uganda, and Zambia. Improved bean genotypes from Ecuador have a potentially significant spinoff in adaptability to upland farming systems in East Africa. Building on international bean germplasm, but particularly on the Ecuador germplasm, an opportunity exists to develop and to deploy improved bean varieties, using a combination of traditional and the latest molecular plant improvement techniques. An improved understanding of plant traits and genotypes with resistance to multiple stresses from abiotic (drought) and biotic (root rot and foliar pathogens) sources will provide unique genetic materials for enhanced plant breeding methods and sources to study plant tolerance mechanisms. Improvements in understanding the physiology of drought and evapotranspiration and the genetics of drought tolerance in common bean and the development of effective molecular and quantitative methods for the selection of drought tolerance are needed. The development of improved bean varieties and germplasm with high yield potential, healthy root systems, improved BNF with resistance to multiple diseases, and sustained or improved water use efficiency under limited soil water conditions are needed to increase profit margins and lower production costs. The project will use QTL (Quantitative trait loci) analysis and single-nucleotide polymorphism (SNP)-based genome-wide association mapping to uncover regions associated with drought tolerance, disease resistance, enhanced BNF, and shorter cooking time. Results of this project would contribute to improved yield, farm profitability, and human resources in the host countries and the United States.

Project Problem Statement and Justification

Beans are the second most important food legume crop in Zambia and a major source of income and cheap protein for many Zambians. Most of the bean crop (62 percent) is produced on 60,000 ha in the higher altitudes of northern Zambia. Andean beans are predominant and landraces are the most widely grown, although a few improved cultivars are also grown as sole crops or in association, mainly, with maize. Bean production is constrained by several abiotic and biotic stresses, including diseases, pests, low soil fertility, and drought. All the popular local landraces in Zambia are highly susceptible to pests and diseases that severely limit their productivity, reflected in the very low national yields ranging from 300 to 500 kg/ha that result in an annual deficit of 5,000MT. To avert future food shortages and feed the growing population of 13M, there is critical need for increasing the productivity of most food crops, including beans, since Zambia ranks 164 out of 184 countries on the Human Poverty Index. Ecuador has the only active Andean bean breeding program and past advances made in combining different disease resistances in bush beans need to be transferred to the climbing beans that play a vital role in the farming system and livelihood of small producers. Improvements in climbing beans can easily be transferred to many African countries that grow similar seed types.

Beans are an important crop in Uganda and are grown on more than 660,000 ha of land and consumed throughout the country. They are a major source of food and income for smallholder farmers, especially women and children. The majority of bean production in Uganda is dependent mainly on the use of inferior landrace varieties that are generally low yielding due to susceptibility to the major biotic and abiotic stresses, which gravely undermine the potential of beans as a food security crop, a source of income, and as a main source of dietary protein for the majority of Ugandans.

Drought affects 60 percent of global bean production; the severity of yield reduction depends on the timing, extent, and duration of the drought. The presence of other stresses, such as high temperature, root diseases, shallow infertile soils, and climate change all intensify the problem. Improvements in current understanding of the physiology of drought and evapotranspiration as well as the genetics of drought tolerance in common bean and the development of effective molecular and quantitative methods for the selection of drought tolerance are therefore needed. Targeting specific photosynthetic (Ps) traits using phenometric tools to identify and avoid drought sensitive components of the Ps process should lead to the identification of elite genotypes important for breeding improvement. The development of improved varieties and germplasm with high yield potential, healthy root systems, improved BNF with resistance to multiple diseases, and sustained or improved water use efficiency under limited soil water conditions are needed to increase profit margins and lower production costs. The project will use QTL analysis and SNP-based genome-wide association mapping to uncover regions associated with drought tolerance, disease resistance, enhanced BNF and faster cooking time.

Objectives

Integrate traditional and marker-assisted selection (MAS) approaches to combine resistances to economically important foliar diseases, drought, and improved BNF and assess acceptability of fast cooking, high mineral content in a range of large-seeded, high-yielding red mottled, white, and yellow Andean bean germplasm for the Eastern Africa highlands (Zambia and Uganda), Ecuador, and the United States.
Characterize pathogenic and genetic variability of isolates of foliar pathogens collected in Uganda, Zambia, and Ecuador and identify sources of resistance to angular leaf spot (ALS), anthracnose (ANT), common bacterial blight (CBB), bean common mosaic virus (BCMV), and bean rust present in Andean germplasm.
Use SNP-based genome-wide association mapping to uncover regions associated with drought tolerance, disease resistance, cooking time, and BNF to identify QTLs for use in MAS to improve Andean germplasm.
Develop phenometric approaches to improving the efficiencies of breeding for abiotic stress tolerance, especially drought.
Institutional Capacity Building and Training for doctoral students from Zambia and Uganda, one doctoral and one MS student from the United States—all in Plant Breeding, Genetics and Biotechnology.

Approaches and Methods

We plan to conduct QTL mapping and develop molecular markers associated with drought and disease resistance and improved BNF in the Andean Diversity Panel. The pathogenic variability of isolates of foliar pathogens will be determined and identified sources of resistance to ALS, ANT, CBB, BCMV and bean rust will be identified in Andean germplasm. QTL for nitrogen fixation and related traits will be conducted using genome-wide association analysis in Andean bi-parental mapping populations. We will rely on new instrumentation and techniques now available at the Center for Advanced Algal and Plant Phenometrics at MSU to improve the efficiencies of breeding for stress tolerance, which will allow nondestructive and continuing measurements of photosynthetic properties (e.g., gas exchange and chlorophyll fluorescence), growth and plant architecture, and more detailed measurements of photosynthesis. These analyses will contribute to identifying new traits based on relationships between genotype and drought response. The acceptability of fast cooking, high mineral content will also be assessed using a pin drop (Mattson cooker) method in bean germplasm in Uganda, Zambia, and Ecuador; bi-parental mapping populations will be developed to identify QTL for cooking time. New discovered QTL will be used in breeding for all traits.

Anticipated Achievements and Outputs

Established and evaluated (mobile) nurseries for ALS, ANT, CBB, rust, and drought and identified source of resistance in Ecuador, Zambia, and Uganda.
Collected and characterized isolates of ANT, ALS, CBB, and Rust from different bean production regions of Zambia, Uganda, and Ecuador.
Initiated crossing of landraces with resistant sources of ALS, ANT, CBB, and Rust in Zambia, Uganda, and Ecuador and conducted progeny screening for different for resistances.
Identified Andean drought tolerant lines from a trial tested in Scottsbluff, Nebraska.
Assessed the acceptability of Andean lines with superior mineral bioavailability and short cooking times and initiated crossing for genetic improvement of Andean lines with superior mineral bioavailability, short cooking time, and disease resistance and developed high throughput/ nondestructive methods for determining cooking time.
Developed drought screening protocols (using both field and next generation phenometric-based techniques) and assembled a drought nursery to be tested in Africa and the United States.
Characterized biophysiological (gas exchange and chlorophyll fluorescence) characteristics associated with drought resistance.
Developed improved bush and climbing Andean beans with drought and multiple disease resistance.
Identified more robust markers for ANT and ALS and identified QTL for enhanced BNF and drought tolerance for use in MAS.

Projected Developmental Outcomes

New improved bean varieties with disease and drought resistance and shorter cooking times
Release of a new Andean cranberry bean variety with superior overall performance by MSU and two superior quality Mesoamerican navy and black bean varieties by MSU and UNL.
Release of two new Andean bean varieties by INIAP, Ecuador, and two varieties by ZARI, Zambia. These varieties would differ in seed types so the specific seed type is not yet identified.
Relevant pathogens, such as rust, characterized in Ecuador, Uganda, and Zambia.
The project will interface with scientists working for national programs in Ecuador, Uganda, and Zambia, who are heading up active bean breeding programs in each country. Broadening and strengthening these programs is vital to the long-term sustainability of the agricultural sector in all countries. Having the network to exchange germplasm when dealing with similar biotic and abiotic constraints promotes more rapid advancement and increases the opportunity of finding valuable genetic stocks that may result in future varieties with significant, future local impact.

Contributions to Institutional Capacity Building

Enhanced scientific capacity in Uganda and Zambia through graduate student training and short-term workshop: two PhD students for Africa, one MS student for Ecuador, and training for 16 staff (10 male, six female) in disease and pest identification in Uganda and Zambia. The project is planning to send participants to the other workshops being planned by the S01.A4 project.

Development and Implementation of Robust Molecular Markers and Genetic Improvement of Common and Tepary Beans to Increase Grain Legume Production in Central America and Haiti (S01.A4)

Lead U.S. and Host Country Principal Investigators, Institutions, and Countries

James Beaver and Consuelo Estévez de Jensen, University of Puerto Rico, Mayagüez, PR, USA

Timothy Porch, USDA/ARS/TARS, Mayaguez, PR, USA

Juan Osorno and Phil McClean – North Dakota State University (NDSU), Fargo, ND, USA

Juan Carlos Rosas, Escuela Agrícola Panamericana (Zamorano), Honduras

Julio Cesar Villatoro, Instituto de Ciencia y Tecnología Agrícola (ICTA), Guatemala

Emmanuel Prophete, National Seed Service, Ministry of Agriculture, Haiti

Project Problem Statement and Justification

During the past 30 years, most of the growth in bean production in Central America and the Caribbean has occurred in the lowlands (< 1000 m), especially in the more humid regions. This project addresses several biotic and abiotic constraints often encountered in the tropical lowlands. The presence of BGYMV (Bean common mosaic necrosis virus) and BCMNV (Bean common mosaic necrosis virus) in the Caribbean, Central America, and southeastern Mexico make the selection for resistance to these viruses priority breeding objectives. Feed the Future Innovation Lab for Legume Systems Research plant breeders have developed and released black bean lines, such as DPC-40, XRAV-40-4, and MEN-2201-64ML that combine resistance to BCMNV and BGYMV. Small red bean breeding lines with the same combination of traits for disease resistance are currently being developed at Zamorano. Greater levels of common bacterial blight (CBB) and web blight (WB) resistance are needed for beans produced in warm and humid lowland regions, such as the Petén in Guatemala. Resistance to these diseases also permits increased production of beans in Central America during the first growing season, when rainfall is more abundant and reliable. This project’s plant breeders have developed Middle American and Andean bean breeding lines with different combinations of resistance to diseases (CBB, rust, angular leaf spot ALS, WB, and root rot), pests (bruchids, leafhoppers) and tolerance to edaphic constraints (low N soils, high temperature). This project will use these elite breeding lines as the base for the continued improvement of beans for our target countries.

There are regions and/or growing seasons in Central America and Haiti that are too hot and/or dry to produce common beans. The tepary bean (P. acutifolius) is a potential alternative grain legume for these stressful environments. Farmers on the Pacific coast of Central America and some countries of Africa already produce tepary beans on a limited scale. In addition to heat and drought tolerance, there are tepary beans with high levels of resistance to common bacterial blight, bruchids and other important traits. Resistance to BCMV and BGYMV as well as larger seed size and improved agronomic traits would increase the potential adoption of tepary beans. Interspecific crosses with common beans will be used to introgress these traits into tepary beans. This effort represents the first systematic attempt to genetically improve tepary beans.

Bean breeders were early adopters of marker-assisted selection (MAS) to identify lines with desired combinations of traits. This resulted in increased efficiency in the development of improved bean breeding lines. There are, however, molecular markers available for a limited number of traits. Others are only effective in a specific gene pool. Therefore, there is a need to develop new or more robust markers, particularly for traits of economic importance to bean breeding programs in the tropics. Recent advances by the BeanCAP project, led by North Dakota State University, in sequencing the bean genome and the development of an SNP array, will facilitate the mapping and development of molecular markers for traits of economic importance, while breeder friendly indel markers are a broadly applicable technology. The availability of phenotypic data in appropriate populations is a major factor limiting the development of these markers. This Feed the Future Innovation Lab for Legume Systems Research project will assist this effort through the development of the populations and information needed to identify the more robust markers. Dr. Phil McClean at NDSU will lead the collaborative effort to develop improved molecular markers.

There is an urgent need to strengthen the capacity of bean programs in Central America and the Caribbean to conduct research and to independently develop, release, and disseminate improved cultivars. This project will provide MS and PhD degree training in plant breeding and genetics and conduct informal workshops dealing with research techniques to enable national bean programs to contribute to the genetic improvement of beans for Central America and the Caribbean.

Objectives

Genetic improvement of common and tepary beans for Central America and Haiti
Develop and implement robust molecular markers for disease resistance genes
Strengthen the capacity of bean programs in Central America and the Caribbean to conduct research and to develop, release, and disseminate improved bean cultivars.

Research Approach and Methods

Conventional plant breeding techniques and marker-assisted selection are being used by project scientists to develop common bean cultivars and tepary bean breeding lines with enhanced levels of disease and pest resistance and greater tolerance to abiotic stresses. Regional performance trials are conducted in collaboration with national bean research programs and CIAT. Testing in different Central American and Caribbean countries provides additional information concerning the potential performance of breeding lines and expands the potential impact of the research supported by the Feed the Future Innovation Lab for Legume Systems Research. Interspecific populations will be developed to introgress BGYMV- and BCMNV-resistance from common bean to tepary bean.

The BeanCAP project developed a suite of approximately 3000 indel markers distributed across all common bean chromosomes that are codominant and designed to be functional with a single experimental condition (PCR protocol). The power of these markers is that they are simple to implement and thus completely portable in all laboratories and are amenable to multiplexing with suites of markers. Multiplexing reduces the cost of genotyping an individual line. The release of the common bean whole genome assembled sequence allows for precise localization of each of these markers. We will search the published literature and communicate with breeders, geneticists, and pathologists in other Feed the Future Innovation Lab for Legume Systems Research projects to identify genetic materials with contrasting phenotypes (e.g., resistance and susceptibility for the specific disease). Once the location of the marker is determined, it will then be compared to the indel database to discover 30 indel markers that straddle the physical location of the marker. Those indel markers will be used in PCR amplification to determine which one acts as a definitive marker that is unambiguous in its predictive power. NDSU and USDA/ARS scientists will collaborate to determine the potential use of P. vulgaris Indels for tepary genetic analysis and mapping

Anticipated Achievements and Outputs

Release and dissemination in the lowlands of Central America and the Caribbean of black and small red bean cultivars with BGYMV and BCMV (Bean common mosaic virus) resistance and greater tolerance to low soil fertility.
Release and dissemination in the lowlands of Central America and the Caribbean black, white, and Andean bean breeding lines with resistance to bruchids, BGYMV, BCMV, and BCMNV.
Release and dissemination of lowland black and white bean breeding lines with resistance to BGYMV, BCMV, BCMNV, and rust.
Release of yellow and red mottled bean lines with resistance to BGYMV, BCMNV, and BCMV.
New bioinformatic-based approach to facilitate marker development.
Release of tepary bean lines with virus resistance and improved agronomic traits.
Indel markers for traits of economic importance that will facilitate the selection of bean lines with the desired combination of traits.
Technical personnel in Central America and the Caribbean with greater capacity to produce reliable and repeatable results from field trials and to develop and release improved cultivars.
Graduate degree training in plant breeding of students from Central America and the Caribbean

Projected Developmental Outcomes

Several improved (black, small red, red mottled, and yellow) bean germplasm lines and cultivars are expected to be released in Central America and the Caribbean during the next five years. This Legume Innovation Laboratory project will continue, in collaboration with CIAT, to support bean research network activities in Central America and the Caribbean. Collaborative activities such as the regional performance nurseries will help to extend the impact of this project through the release of improved cultivars throughout the region. Disease and pest resistance and greater tolerance to abiotic stress of improved cultivars should increase or produce more stable bean yields in Central America and the Caribbean. The BCMNV resistant Andean bean lines and tepary bean breeding lines developed by this project will be shared with Legume Innovation Lab and Feed the Future projects working in Africa.

The development of robust indel markers for traits of economic importance should improve the efficiency of bean breeding programs. Multiplexing indel markers would permit simultaneous screening for multiple traits. Bean lines having desirable genotypes can be identified in earlier generations. Disease resistance genes can be combined without the need to screen lines with specific isolates or races of pathogens. These indel markers should have worldwide utility.

Contributions to Institutional Capacity Building

In-service training will be provided at NDSU for Legume Innovation Laboratory scientists to review recent advances in sequencing the bean genome and the utilization of SNP arrays to develop indel markers for traits of economic importance.
Workshops will be held at Zamorano to train technical personnel concerning bean research techniques with the goal of improving the quality of field research. Topics will include the development and management of field trials, breeding and selection methods, field evaluation techniques, research with Rhizobium, participatory plant breeding, production of basic seed stocks, and agroecological techniques.
Undergraduate students at Zamorano will be provided opportunities to participate in bean research activities related to Feed the Future Innovation Lab for Legume Systems Research project objectives.
M.S. degree training will be completed at the UPR by Ana Vargas (Nicaragua), Angela Miranda (Guatemala), and Diego Rodriguez (Ecuador).
Ph.D. degree training at NDSU of two bean researchers from Central America, the Caribbean, or Africa will be initiated. Both students will be trained in the use of conventional and molecular techniques.

Genetic Improvement of Cowpea to Overcome Biotic Stress and Drought Constraints to Grain Productivity (SO1.A5)

Lead U.S. Principal Investigator

Philip A. Roberts, University of California, Riverside, California, USA

Host Country (HC) and U.S. Co-PIs and Collaborators

Timothy J. Close, University of California, Riverside, USA

Bao-Lam Huynh, University of California, Riverside, USA

Issa Drabo and Jean-Baptiste Tignegre, Institut de l'Environment et des Recherches Agricole (INERA), Koudougou and Kamboinse, Burkina Faso

Ibrahim Atokple and Francis Kusi, Savanna Agricultural Research Institute (SARI), Tamale, Ghana

Ndiaga Cisse, Centre National Recherches Agronomie, Bambey, Institut Senegalais de Recherches Agricole (ISRA) and CERAAS, Thies, Senegal

Abstract
Cowpea is a highly nutritious grain legume crop vitally important to food security in sub-Saharan Africa, especially for women and children, where it complements cereals in the diet. However, in the Sudano–Sahel region of West Africa, typical smallholder farmer cowpea yields are only 10 to 20 percent of known yield potential. Biotic stresses caused by insect pests and diseases caused by pathogens, parasitic plants and nematodes, and abiotic stresses from drought and low-fertility soils are primary constraints to cowpea grain production.

This project focuses on cowpea breeding with emphasis on insect tolerance and resistance traits, combined where feasible with drought tolerance and disease resistance traits. More specifically, tolerance or resistance to aphids, flower thrips, and pod-sucking bugs is being pursued through trait discovery and molecular-driven breeding selection to generate improved cowpea varieties. Field and lab-based phenotyping in Burkina Faso, Ghana, and Senegal will be matched with SNP marker high-throughput genotyping to identify and select for target QTL in the cowpea genome. Advanced breeding lines are being tested regionally across the host countries to broaden their release potential. In addition, several near-release advanced lines will be performance tested for full release decisions in Burkina Faso and Senegal, capitalizing on previous USAID CRSP investment. In California, cowpea dry grain novel market classes of breeding lines will be advanced together with leveraged funding in support of the U.S. dry bean industry. Primary capacity building in each of the host countries will be achieved by graduate degree training in cowpea breeding and genetics coupled with short-term annual training of NARS scientists in molecular breeding.

Problem Statement/Justification
In the Sudano–Sahel region of West Africa, typical smallholder farmer cowpea yields are only 10 to 20 percent of known yield potential. Biotic stresses caused by insect pests and diseases caused by pathogens, parasitic plants, and nematodes and abiotic stresses from drought and low-fertility soils are primary constraints to cowpea grain production. By targeting insect tolerance and combining, where feasible, with drought tolerance associated traits, we have a realistic opportunity to increase cowpea productivity. To be widely adopted, new cowpea varieties must have features desired by consumers as well as farmers, including grain appearance, cooking qualities, and processing characteristics. Breeding targets include large white grains with rough seed-coat, preferred throughout West Africa and amenable to direct dry milling; they can be marketed over a wide area, buffering supply and pricing in the region. Cowpea varieties with large white grain and resistance to pests would increase marketing opportunities in both West Africa and the United States. Large rough brown seed type is also in high demand, especially in large urban centers in Nigeria. Current, premium rough-brown cultivars like Ife Brown are susceptible to pests and diseases and require genetic improvement. Our project targets West Africa cowpea production in FTF focus countries Ghana and Senegal, and also Burkina Faso, which offers regional importance from an agroecological perspective for cowpea yield gain.

The project aims to 1. discover insect tolerance and resistance QTL for cowpea breeding application; 2. increase the productivity of African and US cowpea producers through the development of improved varieties that possess resistance or tolerance to the major insect stresses combined with drought tolerance or disease resistance impacting cowpea production; 3. expand farmer marketing opportunities by breeding improved cowpea varieties with desirable grain characteristics; and 4. provide training and capacity building in modern cowpea breeding to African researchers.

The project employs genomics and modern breeding methods to improve cowpea for yield-limiting constraints, emphasizing insect tolerance and resistance. Significant gain can be made by targeting the major insect threats that occur at early (aphids), mid-flowering and pod-set (flower thrips), and later pod-filling (pod-sucking bugs) stages of the cowpea season. Some promising leads on resistance and tolerance donors and initial QTL identity have been made to provide good starting points in the project. High throughput SNP genotyping platforms, high density consensus cowpea genetic maps, plus numerous discovered QTL for important biotic stress resistance and abiotic drought and heat tolerance traits are now available. Several early generation populations carrying various target traits provide a valuable starting point for breeding advancement. We have been working closely with the CGIAR–GCP Integrated Breeding Platform program development using our cowpea data as a test user case; these technological advances are being applied to the project work.

Objectives

Discover QTL for insect resistance and apply in molecular breeding for target regions in West Africa and the United States.
Complete release and validation of advanced cowpea lines developed under the Pulse CRSP in Burkina Faso, Senegal, and United States.
Increase capacity of NARS in Burkina Faso, Ghana, and Senegal to serve the cowpea sector.

Research Approach and Methods

We have developed the necessary tools to exploit molecular breeding for cowpea, including genetic SNP markers; high density SNP-based genetic maps, including consensus maps; a high-throughput SNP genotyping platform for cowpea; QTL for many major biotic and abiotic stress resistance and tolerance traits; and accompanying software programs. These tools enable selection of multiple traits simultaneously across the genome. Under three subobjectives on aphid, flower thrips, and pod-sucking bug resistance, the approach is to discover and validate QTL underlying the target insect tolerance/ resistance traits, then apply the QTL knowledge to breeding population development and advancement. The KASP SNP platform has 1,022 mapped SNPs providing excellent coverage across the cowpea genome. Breeding parents and progenies (individuals or bulked families) will be phenotyped and genotyped for QTL discovery or trait selection. Genotyping data will be used for both foreground (trait) and background selection. Three backcrossing populations per partner will be developed to combine insect tolerance and drought plus other traits carried by the chosen parents. Intercrossing of advanced backcross line will provide further opportunity to combine additional traits. Molecular profiling of insect populations in the target countries will be made to index biotype variation.

We are capitalizing on the previous Pulse CRSP breeding effort by completing the release requirements of advanced lines now in the final stages of performance testing. In Senegal, three prerelease large white grain type cowpeas and in Burkina Faso, 20 prerelease CRSP advanced lines require final on-farm multilocation performance testing. They will also offer the opportunity for tracking along the impact pathway as new releases entering the seed multiplication and distribution process in each country. Gender considerations have been incorporated into the trait selection process regarding grain types preferred by women farmers, processors of value-added products, and consumers. A second component of this objective is to use our SNP marker genotyping capability to advance the backcrossing of the BT gene insertion for Maruca-resistance into preferred varieties using breeding populations in Burkina Faso and Ghana. The genome-wide SNP data will be used to measure the percent recovery of the recurrent parent background to expedite the backcrossing selection process.

Anticipated Achievements and Outputs

Biotype definition of aphid populations in response to aphid resistance genes in cowpea will produce new knowledge important to insect resistance breeding. Similar approaches will be made for flower thrips and pod bug insect populations.
QTL governing cowpea tolerance and resistance to aphids, flower thrips, and pod-sucking bugs will be discovered and validated, providing new breeder resources (mapped QTL tagged with SNP markers and new understanding for their successful application).
Improved cowpea varieties and advanced breeding populations of consumer preferred market types with resistance to biotic stresses and drought tolerance will be produced by recurrent backcrossing to introgress specific traits into preferred varieties, and recurrent selection to develop next generation varieties.
Variety releases will be made from existing CRSP-developed cowpea advanced lines in Burkina Faso and Senegal.

Projected Developmental Outcomes
Higher yielding cowpea varieties will increase the nutritional status of diets for women and children in sub-Saharan Africa. Higher yielding, market-preferred cowpea varieties will generate additional family income to support improved living conditions and child educational opportunities. New knowledge of insect tolerance and resistance traits in cowpea will benefit grain legume breeding programs beyond the project host countries. Short- and long-term training will increase the likelihood of next generation cowpea breeders applying modern breeding in sub-Saharan Africa.

Contributions to Institutional Capacity Building
A combination of short-term and long-term training activities is being conducted to develop capacity in modern cowpea breeding in the NARS of Burkina Faso (INERA), Ghana (SARI), and Senegal (ISRA). The QTL discovery and molecular breeding activities provide an excellent training framework for both new and senior breeders in cutting-edge molecular breeding approaches. Training includes both short-term visits by HC breeders to UC Riverside, breeding workshops coupled to LIL and related project annual meetings, and long-term degree training to develop a new generation of cowpea breeders. Graduate students (two already enrolled) are being trained directly at UC Riverside in cowpea genetics, pathology, and molecular breeding, and also by mentoring those working on cowpea breeding dissertation projects at WACCI, Ghana, and other African Universities.

IPM-omics: Scalable and Sustainable Biological Solutions for Pest Management of Insect Pests of Cowpea in Africa (S01.B1)

Lead U.S. Principal Investigator

Barry Robert Pittendrigh, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801 USA

Host Country Pis and U.S. Co-PIs

Manuele Tamò, IITA, Benin,

Clémentine Dabiré-Binso, INERA, Burkina Faso

Ibrahim Baoua, INRAN, Niger

Stephen Asante, SARI, Ghana

Haruna Braimah, CRI, Ghana

Julia Bello-Bravo, UIUC Co-PI

Leonard Hinnou, INRAB-Benin

Abstract

Cowpea is an important protein source for tens of millions of West Africans living on less than $2 a day. The major biotic constraint on cowpea crops in West Africa is an insect pest complex. Pesticides and/or transgenics will not provide the long-term solutions needed to bring these pest populations below the economic thresholds needed by cowpea farmers. The only remaining logical strategy: Integrated Pest Management (IPM) involving a pipeline of diverse pest control solutions. Our program is focused on the development and deployment of scalable pest control solutions involving a combination of traditional pest control and deployment strategies and cutting-edge technologies, including genomics and GIS to help direct the most effective deployment of these approaches. Testing and deploying cutting-edge information communication and technology (ICT) tools is also a part of the scaling of these solutions.

Our program, IPM-omics, involves defining the pest problems, bringing forward appropriate solutions through a biocontrol/biopesticide pipeline, and scaling these solutions through multipronged strategies that will include farmer field flora, ICT approaches, women’s cooperatives, and partnerships with small-scale industries. We have and will continue to develop online interfaces that make our outcomes easily available to other groups that can benefit from the materials; we will continue to develop approaches so that we can share solutions with outsides groups that can help in the scaling and sustainability of these solutions. We will develop, deploy, and test training/technology packages/programs that will be passed-off to groups (e.g., NGOs, national/international agencies), and we will determine the potential for impact of this approach.

Problem Statement and Justification

Insect pests of cowpeas dramatically reduce yields for cowpea farmers in West Africa, many of whom live on less than $2 per day. Arguably, the greatest biotic constraints on cowpea (Vigna uguiculata [L.] Walp.) production are insect pests. The major pests of cowpea in the field in northern Nigeria, Niger, and Burkina Faso include the legume pod borer (Maruca vitrata Fabricius); the coreid pod-bugs (Clavigralla tomentosicollis Stal and Anoplocnemis curvipes [F.]); the groundnut aphid (Aphis craccivora Koch); and thrips (Megalurothrips sjostedti Trybom). Foundational work has been initiated to understand these insect pests in the areas where we propose to work to develop and deploy solutions. This foundational work has positioned us well to have a better understanding of pest biology and population structure (due to molecular tools), which will help direct current and future pest control strategies.

Although biocontrol agents, transgenic plants, and traditional plant breeding for insect-resistant varieties are all potentially effective methods for controlling pests of cowpeas, a continued refinement of our understanding of pest populations is needed to integrate these—and other—pest control options into an overall integrative pest management plan to maximize cowpea production in the field. IPM refers to a pest control strategy in which a variety of complementary approaches are used to minimize the negative effects of pests on a given crop or cropping system. As we develop, refine, and deploy IPM strategies, we must understand the important life-history parameters of these pest insects in relationship to their environment.

Scalable IPM solutions are going to be highly necessary to increase yields, which are dramatically affected by pest populations. From the last cycle of the CRSP program, we observed that a logical set of combined IPM strategies could increase yield of cowpeas by more than 100 percent (e.g., neem plus M. vitrata-specific virus spray controls). We also have developed and released biocontrol agents that can be released across more areas of West African and establish themselves in the field to suppress insect populations over the long-term; this approach is highly cost-effective, sustainable, farm-sized, and gender neutral. Over the next four years, we will research, develop, implement, and determine the impacts of an IPM-omics program for cowpea in West Africa. We will continue to research and develop scalable solutions, with the potential for larger-scale impact with donor community buy-in.

Objectives

Define the pest problems on cowpea in Ghana, Burkina Faso, Niger, and Benin
Discover, document, and set the stage for scaling of appropriate IPM solutions
Scaling of solutions
Capacity Building Research Approach and Methods

Research Approach and Methods

Objective 1. We have and will continue to use a mixture of field studies and molecular tools to define the pest population on cowpea across multiple ecological zones in Ghana, Burkina Faso, Niger, and Benin.

Objective 2. We have and will continue to bring forward ecologically sound and highly cost-effective pest control strategies for the pests of cowpea. This will involve the continued development of appropriate solutions through host plant resistance traits, a biocontrol/biopesticide pipeline, and other IPM solutions that involve local educational programs.

Objective 3. We will research and deploy tangible outputs for the scaling of our IPM solutions. This includes, but is not limited to, releasing of biocontrol agents that can establish in the environment (and control the pest populations), testing the potential for cottage industries for biopesticide production, and, finally, creating scalable educational tools for IPM.

Objective 4. We will continue to capacity build through diverse educational programs that range from graduate student and technician training to ICT technologies that help local institutions increase their impact.

Anticipated Achievements and Outputs

In the past phase of this program our approach of combining field and molecular data gave us important insights into the movement patterns of M. vitrata; the results from this work are now driving recommendations for pest management strategies for this species. In the next phase of this project, we expect to develop similar insights and recommendations for other pest species that attack cowpea in the field.
Our program has both developed novel pest control strategies for the control of the pests of cowpeas (e.g., neem plus a virus that kills M. vitrata larvae) and emerging new biocontrol agents that will be highly useful in minimizing pest populations on cowpeas.
We expect to develop, based on our research outputs, the most cost-effective strategies for biocontrol agent release. Additionally, we also expect to determine the potential for local biopesticide production through women’s cooperatives, from both a technical and market prospective.
We will train new MS and PhD students with a focus on IPM for cowpeas and the population genomics of the pests of cowpeas, cross-train technicians and scientists in our network, and develop scalable ICT solutions for the educational component of our IPM program.

Projected Developmental Outcomes

We expect to have a greater understanding of the pest problems of cowpeas to facilitate the cost-effective development and deployment of IPM solutions for cowpea farmers in Ghana, Burkina Faso, Niger, and Benin. It is expected that many of these strategies will have the potential to double the yield of cowpea crops in the field.

Contributions to Institutional Capacity Building

Our program will continue to train the next generation of scientists in Ghana, Burkina Faso, Niger, and Benin who will focus on issues associated with pest problems in cowpea through the training of undergraduate, master’s, and PhD students. We will also promote the cross-training of scientists and technicians across the four host-country programs and with U.S. scientists to build a network capable of understanding pest problems on cowpea in West Africa and to develop the sharing of solutions. We will continue to develop, to test, and to deploy novel ICT programs in local languages, alongside and in conjunction with farmer field flora, in order to take our pest control innovations into the hands of cowpea farmers. Finally, our ICT infrastructure will allow us the capacity to share these pest control approaches directly with other government and nongovernment organizations as well as international organizations involved in the dissemination of pest control solutions.

Farmer Decision Making Strategies for Improved Soil Fertility Management in Maize–Bean Production Systems (S02.1)

Lead U.S. Principal Investigator

Robert Mazur, Iowa State University, Des Moines, Iowa, USA

Host Country Pis and U.S. Co-PIs

Eric Abbott, Iowa State University, USA

Andrew Lenssen, Iowa State University, USA

Ebby Luvaga, Iowa State University, USA

Russell Yost, University of Hawai'i at Manoa, USA

Julia Bello-Bravo, University of Illinois at Urbana– Champaign, USA

Barry Pittendrigh, University of Illinois at Urbana–Champaign, USA

Moses Tenywa, Makerere University, Uganda

Haroon Sseguya, Makerere University, Uganda

Onesmus Semalulu, National Agricultural Research Laboratories, Uganda

Ricardo Maria, Institute of Agriculture Research of Mozambique, Mozambique

Cassamo Sumila, Institute of Agriculture Research of Mozambique, Mozambique

Abstract

Poor and declining soil fertility is the primary constraint to common bean productivity among smallholder farmers in Africa, affecting cropping systems, food security, nutrition, incomes, and livelihoods. Adoption of improved crop management practices, particularly regarding soil fertility, has been modest. Our central premise is that addressing soil-related constraints requires understanding farmers’ current practices and enhancing their capabilities in diagnosing and finding solutions to yield constraints.

Problem Statement/Justification

Smallholder farmers in Africa—women and men—manage complex, multifunctional maize–bean cropping systems in diverse landscapes and agroecosystems. Common beans serve multiple important roles in their cropping systems, food security, nutrition, incomes, and livelihood resilience. They register low yields and experience pervasive poverty and food insecurity. Low productivity is due to poor soil fertility, limited access to improved seed varieties, excess water during plant growth, insects, and diseases. Typical yields of 200 to 500 kg ha^-1 are significantly less than the 2000 kg ha^-1 often obtained in researcher-managed fields. Poor and declining soil fertility is considered the primary constraint to common bean productivity, responsible for 30 percent of the yield gap. Grain legume research programs identify and develop improved technologies and management practices that can substantially increase yields. However, adoption of improved crop management practices, particularly for soil fertility, has been modest for beans.

This research project is based on two premises: 1. sustainable intensification of agriculture production requires improved soil fertility management in which legumes are an integral part of cropping systems and 2. addressing soil-related constraints requires not simply increasing access to fertilizers or use of other soil amendments, but—fundamentally—enhancing smallholder farmers’ capabilities in diagnosing and finding solutions to important yield constraints.

Project activities are taking place in key bean production regions in two important Feed the Future (FTF) focus countries: Uganda, where maize and beans are promoted through FTF projects in 62 districts, and Mozambique, where Feed the Future priority provinces are Nampula and Zambézia; beans are a priority crop). Increasing bean productivity can help reduce poverty and improve nutrition. In Uganda, beans are the most important legume crop, and fifth crop overall. In Mozambique, beans are a cash crop for 35 percent of producing households; the country is the largest informal exporter of maize and beans in southern Africa (50 percent share of regional exports in both). Poor soil fertility has been identified as a major factor in reduced bean yields, and both countries have weak extension systems and rural institutions, so that access to crop technologies, inputs, and credit is limited primarily to informal systems.

Objectives

Characterize farmers’ motivations, current knowledge and practices, problem diagnoses and solutions, and livelihood and risk management strategies.
Develop and refine models about farmers’ decision making.
Develop and validate appropriate diagnostic and decision support aids.
Develop and assess the effectiveness of innovative approaches for dissemination of information and decision support aids, training, and follow-up technical support.
Enhance institutional research capacity relative to grain legumes.

Research Approach and Methods

This project seeks to develop tools (methods and procedures) that will enable smallholder farmers with varying levels of education to better diagnose soil-related production constraints and make improved site-specific crop system management decisions that contribute to higher productivity (including grain legumes) in the short-term as well as improvements in soil fertility in the long-term. It will also assess the effectiveness of innovative communication approaches and technologies to engage farmers with diverse characteristics and other key stakeholders in widespread dissemination and adoption of diagnostic and decision support aids in different agroecological contexts. Core research activities are:

Participatory rural appraisal and baseline surveys for activity planning, taking into account critical social, economic, and cultural factors that impact decision making and the adoption of new strategies and technologies, and for monitoring changes over time
Farmer innovator and scientific analyses of soil-related constraints
Participatory, on-farm studies using identified possible solutions
Participatory, gender equitable development and validation of diagnostic and decision support aids
Development and pilot-testing of innovative sociotechnical approaches for communication, dissemination, and scaling up

Anticipated Achievements and Outputs

Characterization of smallholder bean farmers’ agricultural motivations, current knowledge and practices, problem diagnoses, and livelihood and risk management strategies (by 2015)
Models of farmer decision-making strategies that reflect influences of social, cultural, ec