BackgroundRoot and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop.ResultsTo accelerate marker-assisted breeding of yam, we performed genome analysis of white Guinea yam (Dioscorea rotundata) and assembled a 594-Mb genome, 76.4% of which was distributed among 21 linkage groups. In total, we predicted 26,198 genes. Phylogenetic analyses with 2381 conserved genes revealed that Dioscorea is a unique lineage of monocotyledons distinct from the Poales (rice), Arecales (palm), and Zingiberales (banana). The entire Dioscorea genus is characterized by the occurrence of separate male and female plants (dioecy), a feature that has limited efficient yam breeding. To infer the genetics of sex determination, we performed whole-genome resequencing of bulked segregants (quantitative trait locus sequencing [QTL-seq]) in F1 progeny segregating for male and female plants and identified a genomic region associated with female heterogametic (male = ZZ, female = ZW) sex determination. We further delineated the W locus and used it to develop a molecular marker for sex identification of Guinea yam plants at the seedling stage.ConclusionsGuinea yam belongs to a unique and highly differentiated clade of monocotyledons. The genome analyses and sex-linked marker development performed in this study should greatly accelerate marker-assisted breeding of Guinea yam. In addition, our QTL-seq approach can be utilized in genetic studies of other outcrossing crops and organisms with highly heterozygous genomes. Genomic analysis of orphan crops such as yam promotes efforts to improve food security and the sustainability of tropical agriculture.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-017-0419-x) contains supplementary material, which is available to authorized users.

Yam (Dioscorea spp.) is an important tuber crop with tremendous potential as a functional food in the tropics and subtropics. However, the crop has not shown progressive productivity gain over decades due to various production constraints. This paper reviews the progress achieved in empirical breeding endeavours and the development, status and application of emerging breeding tools and technologies to translate genetic gains in yam improvement. Significant progress has been made in yam genetic improvement over the years which has led to the identification and development of several improved clones and sources of variability for various economically important traits. Substantial efforts have also been made to develop diverse molecular markers, transcriptome and metabolome profiles of crucial traits, trait mapping and generate reference genome sequences of the key species. However, there seems to be a slow translation of research improvements into widespread applications. These advances and the integration of empirical and emerging methods and technologies into the breeding process will enhance yam breeding efforts and ensure the quick delivery of improved varieties that possess superior agronomic and quality traits.

Yam (Dioscorea sp.) is a major source of food for millions of people in tropical and sub-tropical regions, especially in West and Central Africa where at least 60 million people depend on it. It is also a major source of income and an integral part of socio-cultural life. In addition to their food uses, some Dioscorea species are exploited for pharmaceutical products. Yam cultivation is undergoing intensification in many production zones leading to challenges in the management of soil fertility and structure, increasing pressure of diseases and pests (including weeds), and requirements for new varieties better suited to the changing biophysical and socio-economic circumstances. Greater attention also needs to be paid to raising labor productivity and improving access of producers to affordable and higher quality planting materials. These challenges, and the opportunities associated with the biology of the crop, need to be addressed more systematically and earnestly through collaborative research and development, and effective dissemination of the results to relevant stakeholders. The increasing capacity for, and international collaboration in, research and development on yam augur well for the future of the crop and the millions of people who depend on it.

Yam (Dioscorea spp.) is a nutritional and medicinal staple tuber crop grown in the tropics and sub-tropics. Among the food yam species, water yam (Dioscorea alata L.) is the most widely distributed and cultivated species worldwide. Tuber dry matter content (DMC) and oxidative browning (OxB) are important quality attributes that determine cultivar acceptability in water yam. This study used a single nucleotide polymorphism (SNP) assay from a diversity arrays technology (DArT) platform for a genome-wide association study (GWAS) of the two quality traits in a panel of 100 water yam clones grown in three environments. The marker–trait association analysis identified significant SNPs associated with tuber DMC on chromosomes 6 and 19 and with OxB on chromosome 5. The significant SNPs cumulatively explained 45.87 and 12.74% of the total phenotypic variation for the tuber DMC and OxB, respectively. Gene annotation for the significant SNP loci identified important genes associated in the process of the proteolytic modification of carbohydrates in the dry matter accumulation pathway as well as fatty acid β-oxidation in peroxisome for enzymatic oxidation. Additional putative genes were also identified in the peak SNP sites for both tuber dry matter and enzymatic oxidation with unknown functions. The results of this study provide valuable insight for further dissection of the genetic architecture of tuber dry matter and enzymatic oxidation in water yam. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving food quality traits in water yam.

A genetic linkage map of the tetraploid water yam ( Dioscorea alata L.) genome was constructed based on 469 co-dominantly scored amplified fragment length polymorphism (AFLP) markers segregating in an intraspecific F(1) cross. The F(1) was obtained by crossing two improved breeding lines, TDa 95/00328 as female parent and TDa 87/01091 as male parent. Since the mapping population was an F(1) cross between presumed heterozygous parents, marker segregation data from both parents were initially split into maternal and paternal data sets, and separate genetic linkage maps were constructed. Later, data analysis showed that this was not necessary and thus the combined markers from both parents were used to construct a genetic linkage map. The 469 markers were mapped on 20 linkage groups with a total map length of 1,233 cM and a mean marker spacing of 2.62 cM. The markers segregated like a diploid cross-pollinator population suggesting that the water yam genome is allo-tetraploid (2n = 4 x = 40). QTL mapping revealed one AFLP marker E-14/M52-307 located on linkage group 2 that was associated with anthracnose resistance, explaining 10% of the total phenotypic variance. This map covers 65% of the yam genome and is the first linkage map reported for D. alata. The map provides a tool for further genetic analysis of traits of agronomic importance and for using marker-assisted selection in D. alata breeding programmes. QTL mapping opens new avenues for accumulating anthracnose resistance genes in preferred D. alata cultivars.