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Yams are economic and medicinal crops with a long growth cycle, spanning between 9-11 months due to the prolonged tuber dormancy. Tuber dormancy has constituted a major constraint in yam production and genetic improvement. In this study, we performed non-targeted comparative metabolomic profiling of tubers of two white yam genotypes, (Obiaoturugo and TDr1100873), to identify metabolites and associated pathways that regulate yam tuber dormancy using gas chromatography-mass spectrometry (GC-MS). Yam tubers were sampled between 42 days after physiological maturity (DAPM) till tuber sprouting. The sampling points include 42-DAPM, 56-DAPM, 87DAPM, 101-DAPM, 115-DAPM, and 143-DAPM. A total of 949 metabolites were annotated, 559 in TDr1100873 and 390 in Obiaoturugo. 39 differentially accumulated metabolites (DAMs) were identified across the studied tuber dormancy stages in the two genotypes. 27 DAMs were conserved between the two genotypes, whereas, 5 DAMs were unique in the tubers of TDr1100873 and 7 DAMs were in the tubers of Obiaoturugo. The differentially accumulated metabolites (DAMs) spread across 14 major functional chemical groups. Amines and biogenic polyamines, amino acids and derivatives, Alcohols, flavonoids, alkaloids, phenols, esters, coumarins and phytohormone positively regulated yam tuber dormancy induction and maintenance, whereas, fatty acids, lipids, nucleotides, carboxylic acids, sugars, terpenoids, benzoquinones, and benzene derivatives positively regulated dormancy breaking and sprouting in tubers of both yam genotypes. Metabolite set enrichment analysis (MSEA) revealed that 12 metabolisms were significantly enriched during yam tuber dormancy stages. Metabolic pathway topology analysis further revealed that six metabolic pathways (linoleic acid metabolic pathway, phenylalanine metabolic pathway, galactose metabolic pathway, starch and sucrose metabolic pathway, alanine-aspartate-glutamine metabolic pathways and purine metabolic pathway) exerted significant impact on yam tuber dormancy regulation. This result provides vital insights into molecular mechanisms regulating yam tuber dormancy.

The overall agronomic and food quality assessment revealed that the elite yam clones advanced to on-farm testing namely TDa1100374, TDr1401220 and TDr1400158 are suitable for official release. The water yam candidate TDa1100374, produced higher yields and performed better than the checks and showed stability across diverse agro ecologies in Nigeria. It also showed highly resistant reaction to yam diseases with an appealing creamy white tuber flesh colour, with slow rate of oxidation. The TDa1100374 showed low peel loss during processing, higher tuber dry matter content and exhibited an excellent boiled and pounding qualities. On the other hand, the white yam candidate, TDr1401220 showed remarkable yield potential and adaptation across locations while TDr1400158 expressed higher yield but showed a specific adaptation to northern Guinea savannah and the rain forest savannah transition zones. Combined with their high yields and high resistance to yam diseases (virus and anthracnose), both candidates reported excellent industrial and nutritional attributes including high flour yields, dry matter and low peel loss. Their tubers exhibited appealing qualities including a creamy white tuber flesh with slow rate of oxidation. Among the 461 farmers participated in the evaluation the candidate yam varieties in comparison to the standard and local check cultivars for the agronomic and food quality attributes, majority preferred TDr1400158 for excellent pounding qualities while TDr1401220 for good boiled yam quality. Incidentally, more of the consumers/farmers preferred the boiled (53%) and pounded yam (62%) from their local varieties more that the products from TDa1100374. However reverse trend was observed for the tuber yield (63%), tuber appearance (61%) and tuber shape (60%) where they preferred the test genotype over their local varieties.

Methods for high-quality DNA extraction and knowledge of sex expression and flowering time are essential for applying genomic-assisted breeding and improve the success with hybridization in Guinea yam. A dioecious or monoecious pattern of flowering and sometimes non-flowering is a common phenomenon within and between the Dioscorea species. The flowering in yam plants raised from botanical seeds often takes an extended period, mostly till the first clonal generation after propagation from the tubers. The prolonged process of testing required to identify plant sex and flowering intensity in yam breeding often poses a challenge to realize reduced breeding cycle and apply genomic selection. This study assessed sample preservation methods for DNA quality during extraction and potential of DNA marker to diagnose plant sex at the early seedling stage in white Guinea yam. The predicted sex at the seedling stage was further validated with the visual score for the sex phenotype at the flowering stage. DNA extracted from leaf samples preserved in liquid nitrogen, silica gel, dry ice, and oven drying methods was similar in quality with a high molecular weight than samples stored in ethanol solution. Yam plant sex diagnosis with the DNA marker (sp16) identified a higher proportion of ZW genotypes (female or monoecious phenotypes) than the ZZ genotypes (male phenotype) in the studied materials with 74% prediction accuracy. The results from this study provided valuable insights on suitable sample preservation methods for quality DNA extraction and the potential of DNA marker sp16 to predict sex in white Guinea yam.

Yam, a tuber crop, was domesticated alongside some African cereals and defines a cradle of domestication in West Africa., While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River was a major cradle of African agriculture.

The main tropical root, tuber and banana crops addressed within RTBfoods project are: cassava (Manihot esculenta), yam (Dioscorea spp.), sweetpotato (Ipomoea batatas), potato (Solanum tuberosum) and the East African Highland banana (Musa AAA group): Matooke. These crops share common biological traits: they are vegetatively propagated, flowering of varieties is erratic, ploidy levels are variable, they are allogamous and highly heterozygous. Breeding starts with the selection of parents based on their individual value. Hybrids are evaluated for a few traits and undesirable genotypes are discarded as soon as possible (Lebot, 2013). The national programs and CGIAR have been conducting RTB breeding programs for more than 30 years. A lot of progress has been made in the characterization of genetic resources, development of phenotyping tools, optimization of breeding schemes and lastly the integration of genomic tools in breeding programs. Genome Wide Association Studies and/or Genomic Selection are applied to all the crops concerned. Implementing of genetic and molecular approaches is contributing actively to the acceleration of the rate of genetic gains in the different on-going breeding projects. These efforts allowed the release of high yielding varieties and abiotic and/or biotic resistant ones. The quality is a trait, which is addressed from the beginning of the process or at the end when the breeding for the targeted traits was reached (Friedmann et al. 2018). Breeders use basic quality parameters associated with consumer preference (high dry matter, color, oxidation, and various attributes of the roots, tubers, or fruit) as selection criteria. The heritability of roots, tubers and banana quality traits valued by processors and end-users is little known or completely lacking for certain crops. Indeed, the means and subsequently the research investment on each crop, for quality and breeding, are not equal. We reviewed the statistics on the papers published on each crop by the international scientific community, recorded in the Web of Science. We applied the filter on the quality alone and in combination with the breeding filter. We found that research on quality in potatoes is far ahead with 3805 references recorded when the quality filter is applied alone and 273 when the quality and breeding filters are applied together. Cassava comes in second place (578, 57) followed by sweetpotato (154, 38) and yam (115, 10). For Matooke only 11 references were found without filter application. Although these statistics can be discussed and most likely are not as accurate, they reflect the scarcity of data and studies on breeding for the quality for these crops. Although, the work on RTB breeding for quality is not exhaustive and did not encompass all the quality traits, it can be very instructive. Within an institute, due to the turn-over, different researchers might have worked on this field. Data are stored but not shared or mined for the targeted traits. In universities and institutes, students have produced theses. The results have not been published in peer-reviewed papers but they are still of interest and could be used. In this document, each institute has gathered the information they have access to, to report the state of knowledge on the targeted crop. The objective of this review is to make an inventory of the previous activities on RTB breeding for quality, based on the papers published by the scientific community and on the activities conducted by research centers partners of the project. This review focuses on the breeding for product quality and is not intended to cover all breeding activities conducted within the different on-going projects. This review is a starting point, which will allow us to identify the gap analysis for each crop. Subsequently, within the RTBfoods projects, using the high throughput phenotyping (HTPP) methods developed, the breeding activities can be conducted in a way to fill up these gaps.

Yam (Dioscorea sp.) produces a starchy tuber cultivated for human consumption. It is a backbone for food security in tropical countries, especially in West Africa. The most cultivated species, D. rotundata, originated from Africa. However, due to the lack of archaeological data and genetic tools, very little is known about yam domestication. Currently, the wild progenitor of yam is unclear and the geographical origin of yam cultivation has not been elucidated. Here, we took advantage of the recent sequencing of the D. rotundata genome and the development of new powerful analyses to get new insights into the domestication process of African yam. We analyzed a large sampling of cultivated yam and its two closest wild relatives, the savannah species D. abyssinica and the forest species D. praehensilis, collected in West Africa and Cameroon. Whole genome resequencing produced more than 3 million good quality SNPs and revealed a strong genetic structure between the three species, as well as between Cameroon and West African countries. Using coalescent models, we showed that cultivated yam was domesticated from the forest species D. praehensilis. Spatially explicit models inferred an origin of yam culture expansion in the Niger River basin, in a region located in north Benin.