Mapping the white Guinea yam to speed up breeding

David De Koeyer, IITA-Ibadan, Paterne Agre, IITA-Ibadan, Alex Edemodu, IITA-Ibadan

Yam—most valuable crop

Yam, a starchy tuber produced underground by several Dioscorea species, is one of the most valuable crops in West Africa. The region produces 93% of global yam. In Nigeria, yam production is valued at $13.7 billion, exceeding that of cassava, maize, sorghum, millet, and rice combined.

Pollen collection of male flowers for use in controlled pollinations: The first step to create new yam varieties. Photo by P. Agre, IITA.

 

However, despite its value and critical role in both food security and income generation for smallholder farmers, its cost of production is much higher than other crops in the region. It has high labor requirements—land preparation, planting, staking, weed control, and harvesting.  In addition, farmers must save up to one-third of their harvested crop as seed for planting in the next season. Yam is also highly vulnerable to a plethora of pests and diseases as well as population pressure and climate change; and its growing demand has driven cultivation of this crop onto less fertile land.

IITA yam research has developed solutions to these challenges including developing improved varieties.

Modernizing yam breeding

Yam breeding is a complicated and lengthy process that starts with approximately 10,000 distinct seedlings that progress through 6–7 years of selection then to on-farm evaluation and variety release trials across many locations. In the end, only 2–3 varieties with desired traits are released.

Because of this lengthy process, yam breeders need tools and procedures that efficiently and effectively evaluate performance and selection of the best parents for hybridization and the progenies with the highest probability of replacing or adding to the currently grown varieties or landraces. They also need to fully understand market requirements to ensure that the new varieties they develop are acceptable to farmers, processors, exporters, or consumers.

Cultivation and weed control in yam field using two-wheel tractor. Photo by A. Edemodu, IITA.

The IITA breeding team and partners, largely through the AfricaYam project (www.africayam. org) has made progress in modernizing and improving breeding efficiency of this poorly understood but vitally important crop.

Breakthrough in genome sequencing

A recent major development in these efforts was the development of a reference genome sequence for white Guinea yam ( D. rotundata) from IITA’s breeding population. This was a result of innovative collaboration between IITA, the Japan International Research Center for Agricultural Sciences (JIRCAS), the Iwate Biotechnology Research Center (IBRC/Japan), and the Earlham Institute (UK).

Bioinformatics and sequencing of RNA (RNAseq) identified 26,198 genes in the yam genome. A subset of these genes was used for phylogenetic analysis (studying the evolution of the yam species) which showed that the yam genes didn’t group with other representative monocots, including rice, palm, and banana.

The yam genome was found to have a unique set of genes encoding proteins with lectin domains known to be associated with protection against pathogens, nematodes, and insects. To illustrate the value of the yam reference genome, sequencing of separate pools of DNA from female and male plants
was conducted. The genome region controlling sex-determination was located on pseudomolecule 11 and DNA markers that are strongly linked to this trait were developed and evaluated.

Uses of reference genome

While the research team will continue to refine and improve the reference genome (Raising the profile of yam: Whole genome reference sequencing of a neglected orphan crop revealed, http://www.iita.org/news-item/raising-profileyam-whole-genome-sequencing-neglected-orphan-crop/ as improvements in sequencing technology and bioinformatics software develop, many studies have been initiated to use the reference genome for yam improvement.

DNA quality assessment: Loading of DNA sample on agarose gel to assess
quality of DNA. Photo by P. Agre, IITA.

Using genotyping by sequencing, a diverse collection of 941 yam landraces, breeding clones, and related wild/semi-wild species were genotyped to study genetic relationships and develop single nucleotide polymorphism (SNP) markers for quality control. Distinct clusters of germplasm based on species were identified and this information was used to identify a subset of germplasm for trait characterization and association analysis.

In total, 318 clones were selected and resequenced with IBRC and trait collection has been completed for one year. Over 14 million SNPs were identified after alignment of the sequences to the reference genome and analysis using a bioinformatics pipeline. Similarly, biparental intraspecific mapping populations have been developed for both D. rotundata and for D. alata , genotyped and characterized under field conditions. Genotyping of these populations is ongoing in collaboration with Centre de coopération internationale en recherche agronomique pour le développement (CIRAD).

Collectively, this data will be used to identify marker-trait associations for important agronomic, disease and pest resistance, and tuber quality traits. Sequenced-based DNA markers have been converted to markers suitable for high-throughput, lowcost genotyping platforms. Genome-wide and trait-associated markers will be tested using new breeding methods (markerassisted selection and genomic selection) to shorten the yam breeding cycle and qualitycontrol protocols using DNA markers will be established to reduce errors in the breeding program.

In combination with other technology improvements, genomics-based breeding can dramatically improve yam breeding in the next few years. IITA and its national partners in West Africa will be better positioned to develop yam varieties needed in the markets and deliver these to farmers faster.
The results were published in the Biomedical Journal https://bmcbiol.biomedcentral.com/ articles/10.1186/s12915-017-0419-x

Posted on October 27, 2018 in Improving Crops

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