Enhancing yam improvement for West Africa

Hiroko Takagi

EDITS Project: JIRCAS International Collaborative Research for West African crops

In the past, most agricultural investments and international agricultural research in Africa were focused on developing major cereals and crops for export. Recently, however, the focus has shifted to approaches to diversify agricultural innovations in defined locations to contribute to productivity and profitability increase and achieving sustainable food security to overcome poverty and malnutrition. In addition to so-called “major global crops”, attention has also been placed on many more crops that are regionally or locally important for nutrition and income and that are often underresearched but are nutritious, valued culturally, adapted to local environments, and contribute to diversifying regional agriculture systems.

The Japan International Research Center for Agricultural Sciences (JIRCAS), together with several Japanese research institutions and IITA, initiated in 2011 a 5-year collaborative research project called “Evaluation and Utilization of Diverse Genetic Materials in Tropical Field Crops (EDITS)”. The project focuses on yam (EDITS-Yam) and cowpea (EDITS-Cowpea), and aims to generate a solid understanding of the available wide genetic resources in these West African traditional crops, and develop efficient evaluation techniques for effective crop improvement. The outputs from these collaborative efforts are expected to contribute to breeding programs in West Africa.

JIRCAS is playing a key role by linking the Japanese scientific capacities to African communities through IITA, which is the entry point for many overseas research institutions to overcome the various constraints in African agriculture. The knowledge and techniques gained from the collaborative research project is expected to enhance the development of improved yam and cowpea varieties that can help promote rural livelihoods in West Africa.

EDITS-Yam

Yam is a traditional staple crop of significant economic and sociocultural importance in West Africa. The demand for yam is projected to increase, mostly due to population growth in the region. However, little improvement of farm yields has been registered in this crop in the last few decades, indicating an urgent need for more investment in yam research and development. To increase its productivity and enhance the income generation capacity of small-holder farmers, research-for-development should focus on increasing productivity through improved varieties and production technologies to meet the regional needs.

The last couple of years saw a breakthrough in genome sequencing technologies, and in the application genomic information to plant breeding. Genome analysis and improved molecular techniques would tremendously facilitate germplasm characterization, genetic mapping and tagging, and functional genomics of yam. These new tools, if incorporated into the breeding program, will pave the road for effective genetic improvement of yam. Since April 2011, JIRCAS together with the Iwate Biotechnology Research Center (IBRC) and IITA, has been implementing EDITS-Yam to develop and use advanced genomic and molecular tools to enhance germplasm evaluation and improvement for D. rotundata in West Africa.

EDITS-Yam is designed to strengthen genotyping using molecular tools and develop phenotyping protocols to facilitate yam breeding. The project aims to (1) generate the first reference genome of D. rotundata (Guinea yam), (2) develop and apply genomic information and molecular tools in yam breeding, (3) provide improved tools for biodiversity analysis and identification of potentially useful germplasm, and (4) develop phenotyping protocols for important agronomic traits. The outputs from this collaborative research are expected to contribute to the enhancement of yam breeding activities in the region. Consequently, new improved varieties will provide better food security and income for the small-holder farmers in West Africa and beyond.

Progress in 2011-2013

Sequencing of Guinea yam genome

To enhance Guinea yam breeding by fully exploiting modern genomics tools, generating a reliable reference sequence is a prerequisite. To this end, we have been gathering efforts to obtain the first whole genome sequence (WGS) of D. rotundata. The de novo assembly is currently in its final stage. The reference of genome will be completed soon, and the finding will be shared with the global yam community (Fig. 1).

Whole-genome sequencing-based analysis of diversity in Guinea yam

Next generation sequencing (NGS) allows large-scale genome-wide discovery of genetic markers that are important for genomic and genetic applications such as construction of genetic and physical maps, and analysis of genetic diversity. As a component of the on-going effort to construct the first draft sequence of D. rotundata and accelerate the breeding program, WGS-based genetic diversity analysis of D. rotundata accessions is under way. So far, 10 D. rotundata breeding materials, including five landraces and five breeding lines, have been resequenced. These materials are diverse with respect to traits such as maturity time, yield, tuber quality, and resistance to nematode and Yam mosaic virus (YMV), and have been extensively used as parental lines in the IITA yam breeding program.

Aligning the Illumina paired-end short reads obtained from resequencing of the breeding materials to D. rotundata scaffold sequence allowed genome-wide extraction of single nucleotide polymorphism (SNP) and insertion/deletion (indel) markers, which are being used to estimate the genetic relatedness among the lines/accessions studied and reveal the genetic diversity available to breeders. Findings of this study will have huge implications for genetic and genomic studies in yams, including among others, the application of SNPs, the most abundant genetic markers in genomes, for the development of high throughput genotyping platforms and for marker-assisted breeding. More accessions will be considered for resequencing in the future to mine the diversity in D. rotundata in detail.

Diversity Research Set (DRS) as a tool for diversity evaluation of D. rotundata germplasm

The availability of genotypic and phenotypic tools is critical to understand the diversity present in germplasm collections and enhance the active use of genetic resources. IITA currently holds over 2,000 accessions of D. rotundata. Of these, we selected a subset of experimental materials called Diversity Research Set to develop genotyping and phenotyping tools and protocols for germplasm evaluation.

In principle, DRS should be small in size for ease of handling and to allow a detailed analysis of diversity, but retain most of the diversity present in the original collection both at molecular and morphological levels. Accordingly, 106 accessions have been selected as the DRS-EDITS based on 21 key morphological traits, ploidy level, and SSR polymorphisms. The materials are currently being used for (1) detailed genotyping using DNA markers generated from the ongoing WGS, (2) morphological characterization and identification of key descriptors for regional D. rotundata collection, and (3) detailed phenotyping of economically important traits (Fig. 2)

Developing phenotyping protocols

In yam, as well as other root and tuber crops, phenotyping remains the major bottleneck to fully use genotyping information in germplasm evaluation and breeding. EDITS-Yam is also aiming to develop phenotyping protocols on key traits such as tuber yield, earliness of tuber growth and maturation, starch content and properties in collaboration with agronomists and food science specialists. These protocols, once developed, will be used for large-scale phenotyping applied to genetic and diversity studies (Fig. 3).

The information generated and tools developed in the framework of the EDITS-Yam project are expected to contribute immensely to broadening the knowledge base in yam, thereby facilitating the management of available genetic resources and aiding efficient use of yam germplasm for future improvement of the crop. This project and the collaboration it forged are expected to contribute to raising the profile of yam, and trigger the initiation of more and concerted international approaches to yam research for development. The preliminary outputs from the EDITS-Yam project suggest that there is a need for complementary studies to effectively use genetic and genomic tools being generated for yam improvement. To this effect, possibilities for additional resources are being explored.