Improving crops

Enhancing yam breeding for increased productivity and improved quality in West Africa

  • October 16, 2020

An IITA-led project called AfricaYam involves a network of research organizations in the four leading producer countries of the West Africa yam belt: the National Root Crops Research Institute (NRCRI) and the Ebonyi State University (EBSU) in Nigeria; two research institutes under the Council for Scientific and Industrial Research (CSIR) in Ghana (the Crops Research Institute and the Savanna Agricultural Research Institute; le Centre National de Recherche Agronomique (CNRA), Côte d’Ivoire; and l’ Université d’Abomey-Calavi (UAC), Dassa Center, Benin.

Yam breeders

Patrick Adebola, AfricaYam Project Leader (right) with Emmanuel Chamba of CSIR-SARI, (left) in a yam crossing block in Tamale, Ghana.

Key research organizations outside the region also play significant roles in the project. These are the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Guadeloupe, France; Iwate Biotechnology Research Center (IBRC), Japan; James Hutton Institute (JHI), UK; Japan International Research Center for Agricultural Sciences (JIRCAS); and Boyce Thompson Institute (BTI), Cornell, USA. The main project goal is to increase yam productivity while reducing production costs and environmental impact by developing and deploying end-user preferred varieties with a higher yield, excellent resistance to pests and diseases, and improved food quality.

Achievements

The project has made significant and steady progress during its duration.

Improved infrastructure and capacity development for active am breeding in West Africa

Before AfricaYam, many of the yam research programs in West Africa lacked the critical equipment and infrastructure to run effective yam breeding programs. The project made significant improvements in needed infrastructure and equipment at IITA and the national research systems in Benin, Côte d’Ivoire, Ghana, and Nigeria. National programs received new vehicles, screen houses, yam barns, and other small equipment. Yam breeders and technicians in each partner country got several specialized training, such as automated data collection, management, and analysis, disease phenotyping, and breeding techniques, including controlled pollinations and trial management to ensure the collection of quality data. The project facilitated several exchange visits among national partners and advanced institutions, which provided learning opportunities in new breeding techniques and tools. The exchange visits also improved communication among the programs leading to a better understanding of breeding schemes and variety identification systems used by IITA and the programs in the four participating countries. At the end of phase I, the project had engaged a total of 37 students (10 Ph.D., 12 MSc, and 15 BSc). These have equipped the yam breeding programs of national institutes with additional human capacity.

 

Strong and active yam breeding community of practice

A Yam Breeding Community of Practice (CoP) was established (www.africayam.org) and currently has 283 registered members. The CoP creates and maintains close links among yam breeding programs in West Africa and allows sharing of experiences and information on breeding methods, crossing techniques, best field practices, screening protocols, propagation methods, sharing of data and procedure updates on safe germplasm exchange between IITA and project partners.

AfricaYam and IITA yam

AfricaYam and IITA yam breeder Asrat Amele with May-Guri Saethre, IITA Deputy Director General Research for Development

Dr Robert Asiedu Inspecting rice field

inspecting field trials in Ibadan and with Robert Asiedu, R4D Director for West Africa, at the Abuja Station

Development of genomic resources

The project developed ample genomic resources and established several populations for genetic studies. The biparental mapping population and diversity panels of Dioscorea rotundata and D. alata were genotyped and phenotyped for crucial traits. Genotyping platforms, including genotyping-by-sequencing (GBS), Diversity Array Technology (DarT), and whole-genome resequencing (WGRS), were successfully applied and generated millions of single nucleotide polymorphism (SNP) markers. Iwate Biotechnology Research Center (IBRC) completed the first version (TDr96F1-PCv1), and the second version (TDr96_F1_PCv2) of the reference genome of Guinea yam accession TDr96_F1. The recently released Version 2 is more accurate than the first version.

Africa Yam Participants group photograph

Participants at the AfricaYam 2018 annual progress review and work planning meeting, Abidjan, Cote d’Ivoire.

Population genomics, linkage as well as GWAS analysis were carried out to understand the genetic variation that is responsible for phenotypic variability in yam for key traits. Quantitative trait loci were identified for flower sex, tuber dry matter, tuber oxidative browning, and flowering intensity. The DNA marker linked to plant sex expression was validated and is being applied in D. rotundata breeding. Medium to high through-put phenotyping technologies for anthracnose and yam mosaic virus (YMV) have been developed and validated. These include cost-effective and high-throughput phenotyping tools for YMV (mechanical inoculation under screen house conditions and field phenotyping) and YAD (DLA and field phenotyping). Detached leaf assay (DLA), the ‘Leaf Doctor’, and ‘ESTIMATE’ applications were standardized and optimized. A Near Infrared Spectroscopy (NIRS) calibration model for the prediction of moisture, ash, protein, crude fiber, and tannin contents in dry tuber samples (flour) of diverse D. rotundata breeding lines was also developed.

Establishment of yam database (YamBase)

YamBase and associated statistical tools were developed through a partnership with the Boyce Thompson Institute (BTI) and made available to the yam breeding and research community. The database has enabled breeders to maintain and access their data, breed, and generate new knowledge about the genetic basis of important breeding traits through the use of embedded analysis tools and pipelines. Yam trait ontology (TDv.5.0) composed of 182 variables was finalized and published in a crop ontology and YamBase in February 2017 (http://www.cropontology.org/ontology/CO_343/Yam). The database contains a yam genome browser, yam ontology tools, phenotyping tools, and social networking features. The database has been updated and currently counts over 57,000 accessions with over 1500 genotypes, seven breeding programs, 214 assayed traits, about 614,000 phenotype scores, and over 500 trials. The database has contributed to harmonizing data and standardizing procedures across breeding programs. It has also enhanced collaboration across partners and supports the yam breeding community of practice. These interactions with partner projects and other programs already have a positive impact.

Yam population and varietal development

Yam target environments were redefined for varietal testing, selection, and breeding (characterized by soil type, land use for yam, weather, prevalent diseases, farmers’ livelihood, and market linkages). Project members now have access to a map (based on GPS-derived coordinates) showing breeding sites and representative testing and selection sites for the target environments. A significant number of improved D. alata and D. rotundata genotypes were developed and shared among the national partners for further testing and commercial deployment. Also, heterotic groups were defined, new breeding populations were developed, and the existing populations were advanced to the next breeding stages. Six D. alata varieties (four in Ghana and two in Nigeria) and two D. rotundata varieties in Benin were released from the product of previous crosses and selections from local collections. Several new varieties have also been nominated and are in the pipeline for release. The products from crosses made by the project are currently in Cycle-1 under the population improvement pipeline, and those with varietal potential are in advanced performance testing (first multi-environment testing) under the clonal development pipeline. The first varietal release from AfricaYam crosses is anticipated in 2024.

 

Authors: Patrick Adebola, IITA-Abuja; Asrat Amele, IITA-Abuja; Agre Partene, IITA-Ibadan; Lava Kumar, IITA-Ibadan; Busie Maziya-Dixon, IITA-Ibadan; Michael Abberton, IITA-Ibadan; and Robert Asiedu, IITA-Ibadan.

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