Advances in selection of improved lines from the Phaseolus Improvement Cooperative (PIC) populations in Tanzania

ARS scientists Phil Miklas, Karen Cichy, and Tim Porch participated in this trip focused on the evaluation of breeding lines in collaboration with Sokoine University researchers Dr. Susan Nchimbi. Significant progress was made in advancing breeding populations directed towards release of improved varieties in Tanzania. Thirty promising F4:7, 1st generation 2014 PIC (Phaseolus Improvement Cooperative) and ~100 F4:6, 2nd generation 2015 PIC breeding lines were selected. In addition, ~300 F4:5, 3rd generation 2016 PIC single plant selections were completed in Arusha and Mbeya (photos from Arusha below). These breeding lines, derived from 109 PIC populations specifically developed to combine abiotic and biotic stress tolerance, showed superior agronomic potential compared with checks and local landraces. The diversity, scale, and potential of the material in the PIC breeding pipeline is invaluable and requires continued support to ensure the release of varieties that promise to increase the productivity of common bean in the E. African region.

 Single plant selections (left) and selection of plant rows (right) from the PIC populations in Arusha, Tanzania.

Single plant selections (left) and selection of plant rows (right) from the PIC populations in Arusha, Tanzania.

Twelve superior lines from ADP evaluations during previous years were evaluated in on-station trials in Arusha, Mbeya, and Morogoro, and in on-farm trials in the Arusha and Mbeya areas (photos below). The first village near Arusha was Kikatiti (District of Arumeru) where bush beans were preferred (left photo below). The second village was Sakila (in Arumeru as well). This village was at a higher elevation with higher rainfall and fertile soils. A high incidence of white mold was found at this site. About 17 male and 2 female farmers participated in an evaluation of the material in the 12 entry ADP field trial with the local extension agent, indicating their most preferred and least preferred lines (middle photo below).

The first village near Mbeya was Ivuanga, in the District of Mbezi. The 4 male and 3 female farmers had selected individual plants to present the characteristics that they preferred. Several of the ADP were mentioned in this discussion as having good potential including ADP 395, ADP 468, and ADP 111 (right photo below). The two local checks in this area are Wanja and Kigoma. In the field, ADP 479, a red mottled, Calima type also looked promising. A second location in the village was also visited. This site had noticably lower soil fertility and reduced vigor. At this site, ADPs 395, 462, 468, and 479 again looked promising.  A second village was then visited in the vicinity, Nambala. An enthusiastic group of farmers composed of 13 men, 6 women, and 5 children showed us their plots, that had been irrigated by hand, that were at mid pod fill stage. It was too early to evaluate the material for yield performance, but they did indicate that palatability of the leaves was an important characteristic.

Family showing seed types in Kikatiti (left photo) and farmers evaluating APD lines in Sakila (middle photo) both near Arusha in the District of Arumeru. In the village of Ivuanga near Mbeya in the District of Mbezi, farmers evaluate ADP lines at maturity (right photo).

Family showing seed types in Kikatiti (left photo) and farmers evaluating APD lines in Sakila (middle photo) both near Arusha in the District of Arumeru. In the village of Ivuanga near Mbeya in the District of Mbezi, farmers evaluate ADP lines at maturity (right photo).

Selection of PIC breeding lines in Malawi and evaluation of high temperature trials in Vaalharts, South Africa

Dr. James Bokosi

Dr. James Bokosi with promising breeding line at the Bwumbe Station near Blantyre, Malawi.

At Bunda College, with Dr. James Bokosi, promising breeding lines were selected from 35 PIC (Phaseolus Improvement Cooperative) populations at a field site located at 14⁰11.249 S, 33⁰46.478 E and at an elevation of 1195 masl. Single plant selections from the F4 generation had been completed one year ago in Malawi, resulting in over 400 selections; followed by a generation advance in South Africa with Deidre Fourie (ARC). Dr. Bokosi then selected a subset of approximately 280 lines based on seed type and these were planted at the Bunda and Bwumbe Stations. At Bunda, a high frequency of mosaic and black root symptoms were identified, signaling the presence of bean common mosaic virus. Lines were selected based on yield, plant stand, and disease resistance. Approximately 10-20% of the lines were selected that will then be included in regional trials during the next season.

At Bwumbe Station near Blantyre, the same set of PIC lines were planted in three replications at the Bwumbe Station located at 15⁰55.555 S, 35⁰04.389 E and at 1138 masl. At Bwumbe, charcoal rot (caused by Macrophomina phaseolina) was the major constraint, resulting in reduced plant stands and reduced yield. In addition, wilt likely caused by Fusarium oxysporum, and Angular leaf spot were also found. We noted that distinct selections were completed in Bwumbe in comparison with Bunda, indicating the effectiveness of this approach of selection from a diverse set of populations in each target production environment. Separate trials of selections from the Durango diversity panel (DDP), and an advanced line trial and a national trial both from Malawi, were evaluated. In the process one line was identified from the national trial with impressive yield, architecture, disease resistance, and seed quality traits.

Selection of PIC lines at Bunda College

Selection of PIC lines at Bunda College

In Vaalharts, South Africa we evaluated high temperature trials with Deidre Fourie at the Jankempdorp ARC Station. The bean trial at the Vaalharts field site is located at 27⁰56.759 S, 24⁰50.548 E and at 1162 masl and covered over 2 hectares with 3 replications of the DDP and ADP and 72 PIC populations. The average temperatures indicate high temperature stress during the daytime, but an ideal night-time temperature regime, that resulted in typical high temperature stress effects, including reproductive organ abscission and pin bean formation. Visual ratings based on pod load (1-9) were completed on the ADP and DDP trials and selections were completed in 72 PIC populations.

Identifying typical effects of high temperature stress, including poor seed set and pin pods at ARC Station in Vaalharts, South Africa.

Identifying typical effects of high temperature stress, including poor seed set and pin pods at ARC Station in Vaalharts, South Africa.

Anthracnose Screening of ADP

Approximately 230 ADP lines of the ADP were screened with 8 races of anthracnose under controlled conditions at Michigan State University. Dr. James Kelly has provided this valuable dataset for sharing in light of the Open Data policy of the US government. This dataset represents the first comprehensive screening of the ADP with a broad set of races of a specific pathogen.

To download this file, click here.

Uganda participatory variety selection

Dennis Katuuramu (PhD student, Michigan State University) with a farmer group in Kamuli, Uganda evaluating a dry bean participatory trial.

Dennis Katuuramu (PhD student, Michigan State University) with a farmer group in Kamuli, Uganda evaluating a dry bean participatory trial.

A subset of the Andean Diversity Panel (ADP) comprised of 23 genotypes was screened on-farm across three districts in Uganda in 2015. The genotypes represent various market classes and were selected for faster cooking times and superior nutritional quality profiles. A participatory variety selection approach was used where the farmers belonging to nine farmer groups participated in the collection of both qualitative data (preference scores) and quantitative data (disease reactions, plant architecture, and seed yield). Farmers also rated seed quality preferences after harvest. In general, farmers preferred high yielding early maturing lines that exhibited tolerance to too little and/or too much water. A small seeded red mottled variety (Chijar) from Puerto Rico was consistently the most productive across all the agro-ecological zones used in the study.

Advancing dry bean germplasm and cultivar development for resource poor farmers in Malawi

Dr. James Bokosi performing single plant selections from PIC populations in Malawi

Dr. James Bokosi performing single plant selections from PIC populations in Malawi

Beans are an important crop in Malawi both nutritionally and for income generation, however, production does not meet the demand and with actual yields (400 kg ha-1) well below potential yield (2,000 kg ha-1). The major yield constraints range from poor agronomic practices, soil infertility, lack of improved cultivars, and drought. To this end, a program for common bean improvement was initiated for Malawi under the Feed-the-Future Grain Legumes program with Bunda College titled “Advancing dry bean germplasm and cultivar development for resource poor farmers in Malawi.” Bunda College is a campus of the Lilongwe University of Agriculture and Natural Resources (LUANAR) located 30 km from Lilongwe.

The project started in the 2014/2015 crop growing season through testing of Andean Diversity Panel (ADP) lines, Phaseolus Improvement Cooperative (PIC) breeding populations, and National Bean Yield Trials (NBYT). The ADP lines were grown at two sites, Bunda and Bvumbwe. The PIC populations were grown at three sites: Bunda, Bvumbwe, and Bembeke. The National Bean Yield Trial (NBYT) was grown at five sites: Bunda, Bembeke, Bvumbwe, Kasungu, and Champira and were composed of materials from the Bean/Cowpea CRSP project conducted from 2004 to 2007. These materials will be tested for their potential for release as new cultivars in Malawi. The seed types ranged from small- to large-seeded and from solid to mottled seed coat colors. The lines are a mix of Andean and Middle American lines and a variety of seed types including black, small red, carioca, brown, sugar cranberry, large red and red mottled.

The 2014/2015 crop growing season was an unfavorable year for crop growth and production. It was characterized by heavy rains at the beginning leading to floods in some areas, followed by terminal drought to end the season. These conditions affected yields of many crops including beans. Bean yields were below average which made evaluation of materials challenging, however important phenotypic data were collected and selections made.

The performance of 38 ADP lines was evaluated at Bunda College with yields ranging from 139 to 935 kg ha-1 (ADP-0113=OPS-RS4) and at the Bvumbwe Research Station, where yields ranged from 95 kg ha-1to 479 kg ha-1 (ADP-0687=Pink Panther). Calima, a check variety, produced lower yields (289 kg ha-1) than the grand mean (386 kg ha-1).

A total of 480 single plant selections were obtained from 35 PIC populations. About 8 to 10 F4 plants were selected from each PIC population, planted in three replications, at the Bunda and Bvumbwe locations. Fewer selections were completed at the Bembeke location due to an unfavorable growing environment resulting from soil infertility, disease pressure and drought. The F5 plant rows from F4 plants were then planted in collaboration with Deidre Fourie at the ARC in South Africa. About 390 F5 progeny lines were selected from the generation advance in South Africa and sent to Malawi for evaluation during the 2016 field season.

The advanced breeding lines in the NBYT were ranked at each site based on yield. Entry F11 MDRB (B) 25 was ranked 1st at three sites: Bunda, Bvumbwe and Champhira, and ranked 2nd at Kaluluma; entry F3 MDRB (A) 8 was ranked 2nd at three sites: Champhira and Bembeke EPA; and entry F10 BC3 D/N 42 was ranked 1st, 2nd and 3rd at Bembeke EPA, Bunda and Bembeke sub-research stations, respectively. The check variety, Bwenzilaana, was ranked 1st, 2nd and 3rd at Kaluluma, Bembeke sub-research station, and Bembeke EPA, respectively.

Plans for the 2015/2016 growing season include continued evaluation of the ADP and continued selection from PIC populations. In addition, a new set of 35 PIC populations will be evaluated that will feed into the National breeding program. National yield trials on advanced lines will also be conducted that include the eight best lines from 2014/2015 combined with a new set of eight lines from preliminary yield trials. Overall this collaborative project is nearing the key objective of releasing germplasm or cultivars for bean production in Malawi.

ARS-Feed the Future Shared Data

This data sharing effort coincides with the Open Data policy of the US government. The data provided herein is an early draft version of the data that has been generated by the ARS Feed-the-Future Grain Legumes Project that is focused on common bean research. A zip file with the data described below can be downloaded by clicking on this link: http://arsftfbean.uprm.edu/uploads/ARS-FtF-Data-Sharing.zip.

Contents within the zip file: 

  1. ADP2
    This file contains a list of all the genotypes in the Andean Diversity Panel (ADP). The lines with a 1 in column H represent the 2nd generation ADP panel. This ADP-2 represents newly obtained genotypes and genotypes from the original ADP-1 selected to represent broad diversity based on the genotypic cluster analysis using the 6k SNP chip.
  2. PIC Populations
    This excel spreadsheet provides a list of the pedigrees of the first set of Phaseolus Improvement Cooperative (PIC) bulk breeding populations (F4 generation) available for general distribution.
  3. ADP 6k SNP chip data
    This is the original SNP data on a subset of the ADP based on the 6k BeanCAP SNP chip. This data is provided in a single excel spreadsheet.
  4. ADP GBS SNP data
    This genotyping-by-sequencing (GBS) dataset on the majority of the ADP, about 500 ADP genotypes, includes 31,194 SNPs. This ADPv1.0 SNP dataset includes SNP data that is the result of ApeKI restriction enzyme complexity reduction. A complete description of the files included in this folder is provided in the file “ADPv1.0-ApeKI-GBS_Summary.”

Bean Disease Workshop (Complete Program and Presentations)

In this post you will find the complete program and relevant presentations from the Common Bean Disease Workshop on Angular Leaf Spot and Root Rot celebrated at the Protea Hotel Kruger Gate, Skukuza, South Africa.

Complete program in PDF Format (download)

Monday, July 20, 2015

  • M.A. Pastor-Corrales. A review of the angular leaf spot disease of common bean in Latin America and Africa and implications for improved disease management (download).
  • Ayana Hordofa Getachew. Importance and management of Angular leaf spot (Phaeoisariopsis griseola) in Ethiopia (download).
  • Elaine de Souza. Genetics and Breeding for ALS resistance in common bean (download).
  • Eric Nduwarugira Common Bean Disease Workshop on Angular Leaf Spot and Root Rots (download)
  • Kidane Tumsa Resistance breeding against major diseases of common bean in Ethiopia (download)
  • Maria Celeste Co-segregation Analysis of Genes Conferring Resistance to Angular Leaf Spot, Anthracnose, and Rust Pathogenes in Common Bean (download)
  • Paul Gepts PhaseolusGenes: from a marker database to a sequence database (download)
  • Rowland Chirwa Progress in identifying sources of resistance to angular leaf Spot (Phaeosariopsis griseola) in Malawi (download)
  • Thiago Livio P. O. Suoza Progress in Common Bean Breeding for Angular Leaf Spot Resistance (download)

Tuesday, July 21, 2015

  • Carlos Jara Root rots in beans: Generating knowledge and Resources for their control (download)
  • Carlos Urrea Identification of Root Rot Resistant Germplasm for Mozambique and Zambia (download)
  • Clare Mukankusi Breeding for root rot resistance in East and Central Africa (download)
  • Graciela Godoy-Lutz Diagnosis of Fungal Bean Root Rot Pathogens using Molecular and Culture Methods (download)
  • James Kelly Breeding for Root Rot Resistance Jim Kelly & Clare Mukankusi (download)
  • María del Mar Jiménez-Gasco Diversity, ecology and evolution of soilborne fungal plant pathogens (download)
  • Martin Chilvers Screening Andean dry bean germplasm for root rot resistance and phenotyping Pythium species for pathogenicity and virulence (download)
  • Robin Buruchara A review of the root rot diseases of common bean with emphasis in Latin America and Africa (download)

Thursday, July 24, 2015

  • Anthracnose James Kelly Anthracnose Update (download)
  • Phillip Miklas Breeding for resistance to BCMV and BCMNV (download)
  • Paul Kusolwa Breeding for Bruchid Resistance in Farmers’ Preferred Common Bean (P.vulgaris) varieties in Tanzania (download)
  • Phillip Miklas Breeding bean for resistance to common and halo bacterial blights (download)
  • M.A. Pastor-Corrales Major Genes Conditioning Resistance to Rust in Common Bean and a Protocol for Monitoring Local races of the Bean Rust Pathogne (download)

Common Bean Disease Workshop on Angular Leaf Spot and Root Rots

WkShp Attendees

Common Bean Disease Workshop on Angular Leaf Spot and Root Rots
Protea Hotel Kruger Gate, Skukuza, South Africa, July 20-23, 2015

The USDA-ARS Feed-the-Future Grain Legumes Project, in collaboration with ARC South Africa, hosted a consortium of 65 bean scientists from 14 countries, including: 35 participants from 10 African countries, 9 participants from 3 South American countries, and 21 participants from the U.S. including 4 USDA-ARS scientists that represent the ARS-FtF Grain Legumes Project.  Three ARS Administrators were also in attendance including Dr. Roy Scott, Dr. Eileen Herrera, and Dr. Chavonda Jacobs-Young who presented Certificates of Appreciation to three outstanding partners who had made significant contributions to the ARS-FtF Grain Legumes Project.

SEVEN ARS PARTICIPANTS - left to right Karen Cichy, Eileen Herrera, Phillip Miklas, Chavonda Jacobs-Young, Roy Scott, Talo Pastor Corrales and Timothy Porch.

SEVEN ARS PARTICIPANTS – left to right Karen Cichy, Eileen Herrera, Phillip Miklas, Chavonda Jacobs-Young, Roy Scott, Talo Pastor Corrales and Timothy Porch.

Other organizations participating in and/or sponsoring the event included CIAT, PABRA (Pan Africa Bean Research Alliance), USAID- Legume Innovation Lab, and the Kirkhouse Trust (African Bean Consortium). Event sponsors included Dry Bean Producers Organization (DPO), Pannar Seed, and Syngenta South Africa.

AWARDEES - receiving Certificates of Appreciation from Dr. Jacobs-Young for contributions to the ARS-FtF, Grain Legumes Project included L-R Dr. Deidre Fourie, Plant Pathologist, ARC, South Africa, Dr. Susan Nchimbi-Msolla, Plant Breeder and Geneticist, Sokoine University of Agriculture, Tanzania, and Dr. Consuelo Estevez de Jensen, Plant Pathologist, University of Puerto Rico.

AWARDEES – receiving Certificates of Appreciation from Dr. Jacobs-Young for contributions to the ARS-FtF, Grain Legumes Project included L-R Dr. Deidre Fourie, Plant Pathologist, ARC, South Africa, Dr. Susan Nchimbi-Msolla, Plant Breeder and Geneticist, Sokoine University of Agriculture, Tanzania, and Dr. Consuelo Estevez de Jensen, Plant Pathologist, University of Puerto Rico.

The workshop addressed two common bean diseases of global significance, angular leaf spot which is the most critical disease problem of beans grown in Africa and South America, and root rots which are endemic worldwide. The first two days of the workshop consisted of presentations by keynote speakers and participants concerning the past, present, and future research needs for combating these major disease problems. During the third day participants were split into four working groups: angular leaf spot pathology, angular leaf spot breeding, root rot pathology, and root rot breeding, with each group responsible for presenting future research needs. The fourth day was used for presentations by experts to update the participants on breeding for resistance to bruchid seed weevils and important bean diseases caused by bacterial (common blight, halo blight), fungal (anthracnose, rust) and viral (bean common mosaic virus, bean common mosaic necrosis virus) pathogens. Significant impacts are expected from the global research strategies and collaborations developed by the consortium of scientists to better understand the pathogens, improve pathogen characterization and host screening protocols and tools, and facilitate resistance gene discovery and deployment into improved common bean cultivars for enhanced control of angular leaf spot and root rot diseases worldwide.

Group of women scientists in attendance at the workshop

Group of women scientists in attendance at the workshop

 

Tanzanian PIC population selection and trial evaluation

In collaboration with Drs. Susan Nchimbi and Paul Kusolwa, Sokoine University, single plant selections were completed from 35 PIC populations and a number of trials were evaluated in Arusha and Mbeya, Tanzania from 6/07 to 6/13/2015.

Single plant selections from 35 PIC populations were completed at Selian (Arusha; left photo) and at Uyole (Mbeya; right photo) Stations.

Single plant selections from 35 PIC populations were completed at Selian (Arusha; left photo) and at Uyole (Mbeya; right photo) Stations.

Evaluation of the ADP

A subset of 47 lines from the ADP population, that performed well in 2014, were evaluated at the Selian Station in Arusha for white mold; and in Mbeya for rust, angular leaf spot and vigor. This ADP subset was replicated three times. The average score for ALS was 5.7, and for rust and vigor were 3.9 and 3.0, respectively, in Mbeya. Tanzanian breeding lines were identified with potential for release.

Evaluation of the Durango Diversity Panel

Two hundred pinto, pink, small/medium red, and great northern lines and cultivars were evaluated in Arusha and Mbeya, for reaction to rust, white mold, angular leaf spot and adaptation. The full range of response was seen for each disease, from very susceptible to resistant, and good production potential was noted for some genotypes at both sites. Much of the germplasm in this panel was well adapted to both environments. Openness to seed types in Tanzania may create an opportunity for pinto and great northern market classes, while the small red class is already an acceptable market class.

 Single Plant Selection from PIC populations

Single plant selections from 35 PIC populations were completed at Selian (Arusha; left photo) and at Uyole (Mbeya; right photo) Stations. About 600 selections were completed. Plant rows of selections from 2014 from the PIC-005 population, Canada (ADP-0010) x CAL 143, and from the PIC-003 population, Kilombero (ADP-0004) x AND 277 population, showed no disease in Arusha and were evaluated for rust and angular leaf spot in Mbeya. These lines show promise for future release.