Key message This study generated the first high-density genetic map for D. alata based on genotyping-by-sequencing and provides new insight on sex determination in yam. Abstract Greater yam ( Dioscorea alata L.) is a major staple food in tropical and subtropical areas. This study aimed to produce the first reference genetic map of this dioecious species using genotyping-by-sequencing. In this high-density map combining information of two F1 outcrossed populations, 20 linkage groups were resolved as expected and 1579 polymorphic markers were ordered. The consensus map length was 2613.5 cM with an average SNP interval of 1.68 cM. An XX/XY sex determination system was identified on LG6 via the study of sex ratio, homology of parental linkage groups and the identification of a major QTL for sex determination. Homology with the sequenced D. rotundata is described, and the median physical distance between SNPs was estimated at 139.1 kb. The effects of segregation distortion and the presence of heteromorphic sex chromosomes are discussed. This D. alata linkage map associated with the available genomic resources will facilitate quantitative trait mapping, marker-assisted selection and evolutionary studies in the important yet scarcely studied yam species. Electronic supplementary material The online version of this article (10.1007/s00122-019-03311-6) contains supplementary material, which is available to authorized users.

Background: Greater yam, Dioscorea alata L., is a significant food security crop in tropical areas. However, low genetic diversity and various biological constraints, including susceptibility to viruses, ploidy, erratic and low flowering intensity, and asynchronous flowering hinder successful hybrid development and genetic gains in greater yam breeding programs. Therefore, pollen storage has gained much attention to facilitate genetic material exchanges, artificial pollinations and to increase the genetic gains in breeding programs. This 4-year study aimed at developing a practical long-term pollen storage technique for the successful development of yam hybrids. Fresh pollens were collected from two D. alata males, then lyophilized (two lyophilization treatments were applied), followed by storage at room temperature (24-25 oC) for 12 months. Moreover, the lyophilized and stored pollens were tested for viability by crossing with four female varieties. Results: Our results showed that lyophilization is effective for achieving viable pollens after 12 months of storage. Treatment 1 (48 h drying) showed higher pollen germination and fertility rates than Treatment 2 (72 h drying). Although we observed a reduction in viability of lyophilized pollens after 12 months of storage, we generated hybrid seedlings with success rates from 12 to 21% compared to 21-31% when using fresh pollens. Paternity testing based on molecular genotyping confirmed the hybrid status of the obtained seedlings, which grew well in a greenhouse. Conclusions: The results signify the importance of pollen lyophilization for yam breeding programs.

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