Collaborative disease screening of the Andean Diversity Panel in South Africa (March 22-29, 2014)

Halo blight field and greenhouse trials

ARS collaborators in Potchefstroom at Halo blight field trial (left).  Dr. Deidre Fourie with halo blight trial in the greenhouse in Potchefstroom (right).

The 2014 ADP nursery, comprised of 410 entries and three replications, was planted under field conditions in Potchefstroom and Cedara, and in the greenhouse in Potchefstroom, by Dr. Deidre Fourie of the South African Agriculture Research Counil (ARC). The ADP nursery in Potchefstroom was inoculated with race 6 of the halo blight (HB) pathogen. HB is a serious disease of common bean in many countries of Eastern and Southern Africa. Race 6 is important because it overcomes all HB monogenic resistance ‘R’ genes. The HB disease in Potchefstroom in 2014 was consistently distributed throughout the entire field with many entries displaying high levels of HB severity (susceptibility) and some entries with resistance to HB. Thus, this was an excellent nursery for HB resistance screening. The most significant finding was the identification of 29 ADP entries with resistance to HB. Any ADP accession with resistance to HB at Potchefstroom is a potential new source of HB resistance to race 6.

These findings form a foundation of genotype response data that can be used for the development of Andean bean cultivars with resistance to HB in Africa and other locations worldwide. These findings also provide a base for additional studies of the HB disease. The ADP entries planted at Cedara exhibited a broad range of response to rust and angular leaf spot (ALS) diseases. Both diseases, that are widespread and economically important in Africa, occur naturally at Cedara. The reaction of known cultivars at Cedara indicated that 2014 was also an excellent year for rust and ALS resistance screening.

AFC Cold Storage and angular leaf spot ratings

Dr. Fourie showing ADP collection in AFC cold storage unit in Potchefstroom (left). Collaborators discussing angular leaf spot ratings in Cedara (right).

A total of 89 ADP entries were identified as resistant to ALS and 84 ADP entries as resistant to rust. Moreover, a total of 42 entries were resistant to both diseases. Equally important, of the 84 entries with resistance to rust at Cedara in 2014, 29 entries were also resistant to rust at Cedara in 2013. It was interesting and important that the six Mesoamerican ALS differential cultivars were highly resistant to rust and ALS at Cedara in 2014. Conversely, all six Andean ALS differential cultivars were either susceptible to rust and ALS in 2014 or had at least intermediate levels of severity to both diseases.

These results, as observed at Cedara in previous years, suggest that Andean cultivars in South Africa and other countries of Eastern Africa, are much more likely to be susceptible to ALS and rust, while the Mesoamerican cultivars are more likely to be resistant to both diseases. These results also suggest that the isolates of the ALS and rust pathogens present in the field at Cedara co-evolved with bean primarily of Andean origin since they generally infect Andean bean cultivars, but not Mesoamerican beans. Similar results are likely to be observed for rust, angular leaf spot, and anthracnose in other countries of Eastern and Southern Africa, where Andean beans predominate.

The ADP cultivars with resistance to rust and ALS are important candidates for further rust evaluation to determine if they harbor new Andean disease resistance genes that can be used to broaden the genetic base of common bean for resistance to highly variable pathogens. Finally, one of the most important discoveries of the evaluation in Potchefstroom and Cedara is the identification of 15 cultivars with resistance to the three diseases, HB, ALS, and rust.

Genetic Variability for Cooking Time in Dry Beans

Dry beans (Phaseolus vulgaris L) are a nutrient dense, low cost food and therefore are an excellent value for consumers (Drewnowski and Rehm, 2013).  In spite of this value, long cooking times limit bean consumption.  This is true in developing countries where cooking fuel is sometimes scarce and in developed countries where consumers don’t have time to invest in cooking (Brouwer. et al. 1989).  Understanding the genetic variability for cooking time in beans would help efficiently breed fast cooking bean varieties.  The objective of this study was to evaluate the cooking time of a panel of Andean bean lines from diverse market classes and seed types important in major bean growing and consuming regions of Africa and the Americas.

Modified Mattson-type cooker (left).  Technician measuring cooking times (right)

Modified Mattson-type cooker (left). Technician measuring cooking times (right)

Materials and Methods:  A subset of 250 bean lines of the Andean Diversity Panel (ADP) was grown in 2012 at the Montcalm Research Farm in Entrican, MI.  Two replications were planted per entry in a randomized complete block design.  The cooking time of each entry was then determined using a modified Mattson-type cooker (Mattson 1946) on 25 pre-soaked bean seeds in DI water for 12 hrs. Weight differences between raw and soaked seeds were measured to determine water uptake.  The optimum cooking time was recorded as the time it takes for 80% of the plungers to pierce the seeds (Wang, 2005).

Figure1:  Range in cooking time of 250 bean genotypes grouped by seed type.  Numbers in parentheses represent how many of genotypes in each market class.  The black line in each bar indicates the mean cooking time of the samples.

Figure1: Range in cooking time of 250 bean genotypes grouped by seed type. Numbers in parentheses represent how many of genotypes in each market class. The black line in each bar indicates the mean cooking time of the samples.

Results and Discussion:  Cooking data was collected on 250 bean genotypes representing diverse Andean germplasm from eight major market classes.  The cooking time ranged from 17 min to 90 min and the fastest and slowest cooking beans were both cranberry types (Figure 1).  As a group, the white beans were the fastest cooking and also had the least amount of diversity for range of cooking time.  This diversity analysis will be useful to identify parental materials, to understand the genetics control of cooking time, and to breed fast cooking beans in diverse Andean market classes.

References:  Brouwer I. et al. 1989. Nutritional impacts of an increasing fuelwood shortage in rural households in developing countries. Progress Food Nutr. Sci13:349-361.

Drewnowski A, Rehm C. 2013 Vegetable Cost Metrics Show That Potatoes and Beans Provide Most Nutrients Per Penny. PLoS One 8(5): e63277.

Mattson S. 1946. The cookability of yellow peas. Acta Agric Scand 2: 185-191.

Wang, N. and Daun, J. K. 2005. Determination of cooking times of pulses using an automated Mattson cooker apparatus. J. Sci. Food Agric., 85:1631–1635.

Root Phenotyping – Andean Diversity Panel

With global climate change, abiotic stresses are receiving considerable attention by plant breeders as there is an immediate need for improving drought and heat tolerance in crops throughout the world.  Dry bean is a major source of protein consumed by the poor and an important source of iron, folate, and other nutrients needed by the human body.  Though significant contributions of improved germplasm have been identified, highly productive and abiotic/biotic stress tolerant common bean varieties are needed in Africa in order to increase production and thereby improve nutrition.

Diversity panels can provide a broad range of germplasm and aid in the exploitation of genes underlying complex traits, such as drought. In this study, the Andean diversity panel (ADP) was evaluated at the Agricultural Research Institute of Mozambique (IIAM) Sussendenga, Mozambique Station in a collaborative research effort with Dr. Magalhaes Miguel (IIAM).

Processing of common bean plants for shovelomics root trait data collection in Sussendenga, Mozambique

Processing of common bean plants for shovelomics root trait data collection in Sussendenga, Mozambique

There is a high genotype by environment interaction for complex traits like drought tolerance and observing lines in different locations is of primary importance.  In Sussendenga, Mozambique, root traits were characterized, including: basal root angle, basal whorl number, basal root number, number of adventitious roots, stem diameter, tap root diameter, and nodule and disease ratings were collected on 287 lines in two replications by Jennifer Trapp (USDA-ARS), Karen Cichy (USDA-ARS), and Jimmy Burridge (Pennsylvania State University).  This data will be analyzed by association mapping using SNP data generated by Dr. Perry Cregan, USDA-ARS, using the BeanCAP SNP chip.

A subset from the 287 lines was grown in a field trial in Othello, WA to further characterize these lines under drought stress.  A total of 31 lines were grown in both locations and combined for root trait analysis.  Six of the 8 traits analyzed showed significant differences among lines and a correlation was computed between Sussendenga and Othello for those significant traits (Table 1).  The high correlation for tap diameter, basal root whorl number, and stem diameter indicate potentially heritable traits that could be useful for plant breeders given further evidence for their association with additional desirable traits.

Table 1. Correlation values for root traits between Sussendenga, Mozambique and Othello, WA.

Trait R2
Minimum Basal Root Angle 0.08
Adventitious Roots 0.06
Tertiary Branching 0.008
Stem Diameter 0.29
Tap Root Diameter 0.32
BRWN 0.32

Beans in Africa – Success Story – FTF Grain Legumes Project


Dry edible bean production provides a banquet for fungal pathogens to feast upon.  Small-holder subsistence farmers in poorer countries suffer the most from these uninvited guests, because they cannot afford fungicides or other technologies, such as disease resistance, to combat the pathogens. The major fungal diseases plaguing dry bean producers in Sub-Saharan Africa and worldwide are rust, angular leaf spot, anthracnose, and root rots. Our aim is to provide resource poor farmers with dry bean cultivars harboring resistance to one or more of the prevalent bean diseases that negatively affect their livelihoods.

One focus of our Feed the Future Grain Legumes Project has been to evaluate a large panel of accessions for resistance to the aforementioned diseases. The panel consists of old landraces and new cultivars representing the large seeded ‘Andean’ bean types produced around the world. Large-seeded beans are the preferred type in Africa. The greatest progress made thus far has been in the identification of broad spectrum resistance to rust in large seeded landrace cultivars that originate from Tanzania. These landraces, with confirmed resistance in field trials in Africa and the US, provide breeders with a valuable source of rust resistance for improving large-seeded African cultivars used by small-holder farmers. Another set of materials with broad spectrum resistance to rust was found within lines from the Ecuadorian National Program (INIAP), through work conducted in collaboration with the Feed the Future Legume Innovation Lab USAID project.

The identification of dry bean accessions with broad spectrum resistance to rust disease is an exciting discovery. Our project has already initiated crosses with these materials to transfer the resistance into other susceptible cultivars and dry bean market classes (yellow, red mottled, white, tan, etc.) for small-holder farmers in Sub-Saharan Africa.

Broad spectrum resistance to the devastating bean rust disease in Africa

Broad spectrum resistance to the devastating bean rust disease in Africa. Photograph A compares a Tanzanian landrace with broad spectrum resistance (left) to a susceptible accession (right). Notice the reduced biomass and vigor of the susceptible line. Photograph B shows typical rust symptoms, including necrotic leaf spots and fungal pustules, on susceptible dry bean leaves. Both images are from the Cedara Agricultural Research Station, Kwazulu Natal Province, South Africa. (Photo credits: Talo Pastor-Corrales, USDA-ARS Beltsville; 2013)


Report from Central America


Evaluation of Andean Diversity Panel in Honduras

The evaluation of bean golden yellow mosaic virus (BGYMV) in the ADP population was completed at the Escuela Agricola Panamericana (Zamorano) near Tegucigalpa, Honduras in August 2013. Participating were Juan Osorno (North Dakota State University), James Beaver (University of Puerto Rico), Karen Cichy (USDA-ARS), Tim Porch (USDA-ARS), and Juan Carlos Rosas (Zamorano).

BGYMV infection of ADP at Zamorano

BGYMV infection of ADP at Zamorano

The population was evaluated under severe BGYMV pressure. Several advanced lines from the U. of Puerto Rico, bred for BGYMV resistance, were the only genotypes showing resistance to this white fly transmitted virus. Although not a pathogen in Africa, BGYMV is common in Caribbean and Central American production areas and is an important breeding objective for Andean cultivars grown in the Caribbean. The visitors also toured the extensive breeding program of Dr. Rosas, regional common bean trials, and evaluated early generation breeding lines from Puerto Rico that are being advanced at Zamorano during the off-season in order to speed up the development of breeding lines for FtF countries in Africa.

Visit to common bean breeding programs in Guatemala

The ICTA breeding programs of Julio Cesar Villatoro and Fernando Aldana were then visited in Guatemala at the Chimaltenango and Quetzaltenango Research Stations.

Chimaltenango breeding program

Chimaltenango breeding program

The visitors met with Dr. Elias Raymundo, Director General of ICTA, regarding the progress with the different research projects and grants in the region. Dr. Raymundo then participated in the visits to the breeding programs. The program in Chimaltenango is working with breeding populations and there was a large seed increase of a new black bean cultivar ‘ICTA Super Chiva’.


The Quetzaltenango Station had plantings of bolonillo bean lines that are earlier in maturity and have a less aggressive climbing habit when intercropped with corn.

Diversity in intercrop system in Quetzaltenango

Diversity in intercrop system in Quetzaltenango

Drs. Osorno and Beaver are initiating Legume Innovation Lab projects (USAID) in Guatemala that take into account the diverse production systems of common bean that involve the intercropping of multiple species .

Success Story – FTF Research Team

Photo showing dry bean diversity

Photo showing dry bean diversity

Landraces represent cultivated crop germplasm that has been grown for centuries by subsistence farmers.  These farmer selected cultivars can be uniform for seed shape and color, or represent mixtures of different seed types. Similarly, agronomic traits can be uniform or mixtures of plant types.  Many landraces are locally adapted but can be distributed regionally. Landraces, because of their natural selection under low input production systems and often in less than ideal environments, are great reservoirs of genetic diversity for many different traits including adaptation to low fertility soils, drought, and other abiotic and biotic stresses. With this in mind, the FtF ARS Bean Team, obtained all the dry bean landraces accessions that had been collected from East Africa and housed by the USDA-ARS, National Plant Germplasm Repository, in Pullman, WA (250 accessions).  A subset of 95 landrace accessions originally collected from Tanzania, and representative of the large seeded market classes currently grown there, were first increased for seed in Prosser, WA, and then evaluated in a replicated field trial at Sokoine University of Agriculture in Morogoro, Tanzania. The trial, coordinated by Professor Susan Nchimbi and Eninka Mndolwa (Research Associate), sought to test the accessions for general adaptation under low soil fertility. Yields ranged from 640 to 1650 kg/ha, and some accessions possessed more nodules for biological nitrogen fixation than others (ranging from 4 to 38 nodules).    The positive and significant correlation 47% between grain yield and nodule number observed in this trial, supports that accessions with more nodules have potential to yield more in low fertility soils.  These data, and observations for disease reaction against fungal (angular leaf spot, rust) and viral (bean common mosaic) pathogens provides a rich baseline dataset to guide future utilization of these landrace accessions in breeding of improved dry bean cultivars for East Africa.

Visit to the National Programs in Mozambique, Malawi, CIAT and Bunda College

Miklas and Porch visited the National Program in Mozambique and the National Program, Bunda College, CIAT, and Africa Rising project in Malawi and investigated possible collaborations to increase dry edible bean productivity in the region. In the Northern highlands of Mozambique, the FtF team will collaboratively develop highly productive dry beans with ashy stem blight and terminal drought resistance for selection by the National Program, and in Malawi highly productive dry beans with heat, drought and ashy stem blight resistance. Most dry beans in both countries are produced without inputs thus suffer from low soil fertility, drought, and disease. The ARS-FtF dry bean project is geared toward increasing dry bean productivity for low input agriculture systems in FtF countries.


A large population of dry bean lines (Andean Diversity Panel) composed of large-seeded types that are preferred across Africa was planted in MZ and seed was provided to Bunda College in Malawi for planting next season. These trials will provide information on the major diseases and abiotic stresses present, and will allow for the study of the genetics of the major constraints in the region. A headquarters for operations in Malawi with a post-doc level coordinator of activities would facilitate the work of FtF ARS bean dry bean researchers in the region.

Evaluation of ADP in South Africa

Pastor-Corrales traveled to South Africa to evaluate the Andean Diversity Panel (ADP), a common

In Cedara, South Africa I front of a bean susceptible to rust.

In Cedara, South Africa, Dr. Pastor-Corrales in front of a bean susceptible to rust.

bean nursery comprised of some 350 Andean common bean cultivars. The large-seeded Andean beans are the preferred dry bean type planted and consumed in Eastern and Southern African countries. Diseases, including rust, are a significant limitation to dry bean production in this area and rust is recurrent and widespread.

The ADP was planted in Cedara Agricultural Research Station, KwaZulu-Natal Province. The rust disease was quite severe throughout the field in all susceptible check cultivars, indicating that 2013 was an excellent year and Cedara an excellent site for the rust evaluation of the ADP. About 75 of the 350 ADP entries were resistant to rust; 99 entries were susceptible and the other entries were intermediate in their reaction to rust.

In Chilanga, Zambia, evaluating the ADP for root rot with local collaborators.

In Chilanga, Zambia, evaluating the ADP for root rot with local collaborators.

The resistant cultivars are candidates for further rust evaluation under greenhouse conditions in Beltsville, Maryland. Some of these cultivars with rust resistance in future evaluations will be used as parents to improve the rust resistance in common bean cultivars planted by farmers in Easter and Southern African countries. Pastor-Corrales also traveled to Zambia to evaluate the ADP for reaction to soil borne pathogens that cause root rot of beans. Based on the emergence of young pants evaluated, two root diseases were found and about 100 ADP entries had excellent germination suggesting that they may be resistant to root rots. Additional evaluations are needed to identify those with genetic resistance to root rots.