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.

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 greater yam combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient lineage-specific genome duplication, followed by extensive genome-wide reorganization. Using our new genomic tools we find quantitative trait loci for susceptibility 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.

No abstract

Changes in sugar composition occur continuously in plant tissues at different developmental stages. Tuber dormancy induction, stability, and breaking are very critical developmental transitions in yam crop production. Prolonged tuber dormancy after physiological maturity has constituted a great challenge in yam genetic improvement and productivity. In the present study, biochemical profiling of non-structural sugar in yam tubers during dormancy was performed to determine the role of non-structural sugar in yam tuber dormancy regulation. Two genotypes of the white yam species, one local genotype (Obiaoturugo) and one improved genotype (TDr1100873), were used for this study. Tubers were sampled at 42, 56, 87, 101, 115, and 143 days after physiological maturity (DAPM). Obiaoturugo exhibited a short dormant phenotype and sprouted at 101-DAPM, whereas TDr1100873 exhibited a long dormant phenotype and sprouted at 143-DAPM. Significant metabolic changes were observed in non-structural sugar parameters, dry matter, and moisture content in Obiaoturugo from 56-DAPM, whereas in TDr1100873, significant metabolic changes were observed from 101-DAPM. It was observed that the onset of these metabolic changes occurred at a point when the tubers of both genotypes exhibited a dry matter content of 60%, indicating that a dry matter content of 60% might be a critical threshold for white yam tuber sprouting. Non-reducing sugars increased by 9–10-fold during sprouting in both genotypes, which indicates their key role in tuber dormancy regulation in white yam. This result implicates that some key sugar metabolites can be targeted for dormancy manipulation of the yam crop.

The persistent low yield and farmers' preference of their traditional yam varieties over the improved varieties necessitated this study to verify the adoption status of the released varieties in Nigeria. A total of 48 accessions of white yam (Dioscorea rotundata) were sampled from six states of Ebonyi, Enugu, Benue, Kogi, Nassarawa and Oyo within Nigeria yam-belt and were genotyped for relatedness to four released varieties from the National Root Crops Research Institute (NRCRI), Umudike yam breeding programme, while 14 accessions of water yam (D. alata) were sampled from four states of Benue, Kogi, Nassarawa and Oyo and were also genotyped for relatedness to three released varieties from International Institute for Tropical Agriculture (IITA), Ibadan. A total of 29 alleles were found in 5 sets of primers analyzed for 52 D. rotundata accessions and the number of alleles ranged from 5 (Dald08, SSR 51 and YM 34) to 8 (Dab2E07) with an average of 5.8 per locus. The observed heterozygosity ranged from 0.19 (YM34) to 0.77 (YM30). A total gene diversity of 0.63 according to Nei (1978) genetic distance coefficients was observed among the 52 D. rotundata accessions. Similarly, a total of 37 alleles were observed when 17 D. alata accessions were analysed with the 7 selected sets of primers. An average of 5.29 alleles was observed per locus. The observed heterozygosity varied from 0.47 (Dab2D06) to 0.82 (YM34). A total gene diversity of 0.58 was observed among 17 D. alata accessions according to Nei' genetic distance coefficients. Cluster analysis showed that the D. rotundata accessions were classified into 8 clusters. While, 17 accessions of D. alata were classified into 4 clusters. There were relationships between some released varieties and farmers accessions and also among the farmers' accessions from different locations, indicating that farmers might have given a preferred local name to the released varieties.

Yams are economic and medicinal crops with a long growth cycle, spanning between 9–11 months due to their 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. A total of 39 differentially accumulated metabolites (DAMs) were identified across the studied tuber dormancy stages in the two genotypes. A total of 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.

;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.

Changes in sugar composition occur continuously in plants tissues, at different develop-mental stages. Tuber dormancy induction, stability, and breaking are very critical developmental transitions in yam crop production. Prolonged tuber dormancy after physiological maturity has constituted a great challenge in yam genetic improvement and productivity. In the present study, biochemical profiling of non-structural sugar in yam tuber during dormancy was performed to determine the role of non-structural sugar in yam tuber dormancy regulation. Two genotypes of white yam specie; one local genotype (Obiaoturugo) and (TDr1100873) were used for this study. Tubers were sampled at (42, 56, 87, 101, 115, and 143) days after physiological maturity (DAPM). Obiaoturugo exhibited a short dormant phenotype and sprouted at 101DAPM, whereas TDr1100873 exhibited a long-dormant phenotype, and sprouted at 143DAPM. Significant metabolic changes were observed in non-structural sugar parameters, dry matter, and moisture content in Obiaoturugo from 56DAPM, whereas, in TDr1100873 significant metabolic changes were observed from 101DAPM. It was observed that the onset of these metabolic changes occurred at a point when the tubers of both genotypes exhibited dry matter content of 60%, indicating that dry matter content of 60% might be a critical threshold for white yam tuber sprouting. Nonreducing sugars increased by 9-10-fold during sprouting in both genotypes which indicates its key role in tuber dormancy regulation in white yam. This result implies that some key sugar metabolites can be targeted for dormancy manipulation of yam crop.