The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

Water yam (Dioscorea alata L.) is one of the most important food yams with wide geographical distribution in the tropics. One of the major constraints to water yam production is anthracnose disease caused by a fungus, Colletotrichum gloeosporioides (Penz.). There are no economically feasible solutions as chemical sprays or cultural practices, such as crop rotation are seldom convenient for smallholder farmers for sustainable control of the disease. Breeding for development of durable genetic resistant varieties is known to offer lasting solution to control endemic disease threats to crop production. However, breeding for resistance to anthracnose has been slow considering the biological constraints related to the heterozygous and vegetative propagation of the crop. The development of saturated linkage maps with high marker density, such as SSRs, followed by identification of QTLs can accelerate the speed and precision of resistance breeding in water yam. In a previous study, a total of 1,152 EST-SSRs were developed from >40,000 EST-sequences generated from two D. alata genotypes. A set of 380 EST-SSRs were validated as polymorphic when tested on two diverse parents targeted for anthracnose disease and were used to generate a saturated linkage map. Majority of the SSRs (60.2%) showed Mendelian segregation pattern and had no effect on the construction of linkage map. All 380 EST-SSRs were mapped into 20 linkage groups, and covered a total length of 3229.5 cM. Majority of the markers were mapped on linkage group 1 (LG 1) comprising of 97 EST-SSRs. This is the first genetic linkage map of water yam constructed using EST-SSRs. QTL localization was based on phenotypic data collected over a 3-year period of inoculating the mapping population with the most virulent strain of C. gloeosporioides from West Africa. Based on threshold LOD scores, one QTL was consistently observed on LG 14 in all the three years and average score data. This QTL was found at position interval of 71.1–84.8 cM explaining 68.5% of the total phenotypic variation in the average score data. The high marker density allowed identification of QTLs and association for anthracnose disease, which could be validated in other mapping populations and used in marker-assisted breeding in D. alata improvement programmes.

Anthracnose, caused by Colletotrichum gloeosporioides, is one of the major constraints limiting water yam (Dioscorea alata) production in the tropics. In this region, yam anthracnose control is mostly achieved by the deployment of moderately resistant yam genotypes. Therefore, screening for new sources of anthracnose resistance is an important aspect of yam research in the tropics. The reliability and applicability of different yam anthracnose rating parameters has not been fully examined. Disease severity on detached leaves in the laboratory and leaf severity, lesion size, and spore production on whole plants in the greenhouse were used to screen an F1 yam population and correlate screening results with field evaluations. Anthracnose lesion size had the smallest predicted residual means but whole-plant severity and detached-leaf severity had the best variance homogeneity and relatively small predicted residual means. The concordance correlation coefficient (rc) and κ statistic were used to determine the agreement between anthracnose rating parameters and field evaluations. Detached-leaf (rc = 0.95, κ = 0.81) and whole-plant (rc = 0.96, κ = 0.86) evaluations had high positive agreement with field evaluation but spore production (κ = 0.69) and lesion size (κ = 0.57) had moderate positive agreement. These results suggest that all the evaluated rating parameters can be used to successfully screen yam germplasm for anthracnose resistance but lesion size and spore production data may need to be transformed.