Yam Breeding Research Articles

Exploring the Bush yam (Dioscorea praehensilis Benth) as a Source of Agronomic and Quality Trait Genes in White Guinea yam (Dioscorea rotundata Poir) Breeding

Yam (Dioscorea spp.) is an important food security crop in the tropics and subtropics. However, it is characterized by a narrow genetic base within cultivated and breeding lines for tuber yield, disease resistance, and postharvest traits, which hinders the yam breeding progress. Identification of new sources of desirable genes for these traits from primary and secondary gene pools is essential for this crop improvement. This study aimed at identifying potential sources of genes for yield and quality traits in a panel of 162 accessions of D. praehensilis, a semi-domesticated yam species, for improving the major yam species, D. rotundata. Significant differences were observed for assessed traits (p < 0.05), with D. praehensilis genotypes out-performing the best D. rotundata landraces for tuber yield (23.47 t ha−1), yam mosaic virus (YMV) resistance (AUDPC = 147.45), plant vigour (2.43) and tuber size (2.73). The study revealed significant genotypic (GCV) and phenotypic (PCV) coefficients of variance for tuber yield, YMV severity score, and tuber flesh oxidation. We had also a medium-to-high broad-sense heritability (H2b) for most of the traits except for the dry matter content and tuber flesh oxidation. This study identified some promising D. praehensilis genotypes for traits such as high yield potential (WNDpr76, CDpr28, CDPr7, EDpr14, and WNDpr63), resistance to YMV (WNDpr76, CDpr7, EDpr14, CDpr28, and EDpr13), high dry matter content (WNDpr76, CDpr28, and WNDpr24), low tuber flesh oxidation (WNDpr76, CDpr5, WNDpr31, CDpr40, and WNDpr94) and high number of tubers per plant (WNDpr76, CDpr7, CDpr68, CDpr29, and CDpr58). These genotypes could, therefore, be employed in breeding programmes to improve the white Guinea yam by broadening its genetic base.

Diversity of Water Yam (Dioscorea alata L.) Accessions from Côte d'Ivoire Based on SNP Markers and Agronomic Traits.

Dioscorea alata (L.), also referred to as water, winged, or greater yam, is one of the most economically important staple food crops in tropical and subtropical areas. In Côte d’Ivoire, it represents, along with other yam species, the largest food crop and significantly contributes to food security. However, studies focusing on better understanding the structure and extent of genetic diversity among D. alata accessions, using molecular and phenotypic traits, are limited. This study was, therefore, conducted to assess the pattern of genetic variability in a set of 188 D. alata accessions from the National Agronomic Research Centre (CNRA) genebank using 11,722 SNP markers (generated by the Diversity Arrays Technology) and nine agronomic traits. Phylogenetic analyses using hierarchical clustering, admixture, kinship, and Discriminant analysis of principal component (DAPC) all assigned the accessions into four main clusters. Genetic diversity assessment using molecular-based SNP markers showed a high proportion of polymorphic SNPs (87.81%). The analysis of molecular variance (AMOVA) showed low molecular variability within genetic groups. In addition, the agronomic traits evaluated for two years in field conditions showed a high heritability and high variability among D. alata accessions. This study provides insights into the genetic diversity among accessions in the CNRA genebank and opens an avenue for sustainable resource management and the identification of promising parental clones for water yam breeding programs in Côte d’Ivoire.

Identification of quantitative trait nucleotides and candidate genes for tuber yield and mosaic virus tolerance in an elite population of white guinea yam (Dioscorea rotundata) using genome-wide association scan

BackgroundImprovement of tuber yield and tolerance to viruses are priority objectives in white Guinea yam breeding programs. However, phenotypic selection for these traits is quite challenging due to phenotypic plasticity and cumbersome screening of phenotypic-induced variations. This study assessed quantitative trait nucleotides (QTNs) and the underlying candidate genes related to tuber yield per plant (TYP) and yam mosaic virus (YMV) tolerance in a panel of 406 white Guinea yam (Dioscorea rotundata) breeding lines using a genome-wide association study (GWAS).ResultsPopulation structure analysis using 5,581 SNPs differentiated the 406 genotypes into seven distinct sub-groups based delta K. Marker-trait association (MTA) analysis using the multi-locus linear model (mrMLM) identified seventeen QTN regions significant for TYP and five for YMV with various effects. The seveteen QTNs were detected on nine chromosomes, while the five QTNs were identified on five chromosomes. We identified variants responsible for predicting higher yield and low virus severity scores in the breeding panel through the marker-effect prediction. Gene annotation for the significant SNP loci identified several essential putative genes associated with the growth and development of tuber yield and those that code for tolerance to mosaic virus.ConclusionApplication of different multi-locus models of GWAS identified 22 QTNs. Our results provide valuable insight for marker validation and deployment for tuber yield and mosaic virus tolerance in white yam breeding. The information on SNP variants and genes from the present study would fast-track the application of genomics-informed selection decisions in breeding white Guinea yam for rapid introgression of the targeted traits through markers validation.

Potential applications of the CRISPR/Cas technology for genetic improvement of yam (Dioscorea spp.)

AbstractYam (Dioscorea spp.) is an economically important crop grown in the tropical and subtropical regions, producing tuberous roots that serve as a staple food, an income source, and an excellent source of various pharmaceutical precursors. Yam production is constrained by disease and pest infestations and a range of abiotic stresses. Genetic improvement can significantly mitigate these challenges, improve productivity, expand the yam markets, and increase economic gains. However, several intrinsic attributes of the crop have curtailed progress in yam breeding. Advanced genetic engineering such as genome editing by sequence‐specific nucleases has emerged as complementary approaches to conventional breeding techniques. Mainly, the clustered regularly interspaced short palindromic repeats/CRISPR‐associated protein (CRISPR/Cas) system for genome editing has provided robust platforms for gene function analysis and crop improvement in the post‐genomic era. Despite its significance, research towards improving the yam species remains under‐represented compared to other staple tuber crops such as cassava and sweet potato. Thus, it is critical to explore avenues for increasing the genetic gains from this under‐exploited crop. The present review focuses on the progress and prospects for applying the CRISPR/Cas technology for yam improvement. The study elaborates on the currently available CRISPR/Cas tool for yam genome engineering and explores the potential applications of this toolkit in mitigating the various challenges encountered in yam production and consumption. Furthermore, we have delved into the challenges associated with this technology and the improvements made to minimize these challenges. The insights presented herein provide a guide for yam improvement to increase genetic gains from this under‐researched and under‐utilized resource.

Genome-Wide Association Studies for Sex Determination and Cross-Compatibility in Water Yam (Dioscorea alata L.).

Yam (Dioscorea spp.) species are predominantly dioecious, with male and female flowers borne on separate individuals. Cross-pollination is, therefore, essential for gene flow among and within yam species to achieve breeding objectives. Understanding genetic mechanisms underlying sex determination and cross-compatibility is crucial for planning a successful hybridization program. This study used the genome-wide association study (GWAS) approach for identifying genomic regions linked to sex and cross-compatibility in water yam (Dioscorea alata L.). We identified 54 markers linked to flower sex determination, among which 53 markers were on chromosome 6 and one on chromosome 11. Our result ascertained that D. alata is characterized by the male heterogametic sex determination system (XX/XY). The cross-compatibility indices, average crossability rate (ACR) and percentage high crossability (PHC), were controlled by loci on chromosomes 1, 6 and 17. Of the significant loci, SNPs located on chromosomes 1 and 17 were the most promising for ACR and PHC, respectively, and should be validated for use in D. alata hybridization activities to predict cross-compatibility success. A total of 61 putative gene/protein families with direct or indirect influence on plant reproduction were annotated in chromosomic regions controlling the target traits. This study provides valuable insights into the genetic control of D. alata sexual reproduction. It opens an avenue for developing genomic tools for predicting hybridization success in water yam breeding programs.

Optimized Protocol for In Vitro Pollen Germination in Yam (Dioscorea spp.).

Yam (Dioscorea spp.) plants are mostly dioecious and sometimes monoecious. Low, irregular, and asynchronous flowering of the genotypes are critical problems in yam breeding. Selecting suitable pollen parents and preserving yam pollen for future use are potential means of controlling these constraints and optimizing hybridization practice in yam breeding programs. However, implementing such procedures requires a robust protocol for pollen collection and viability testing to monitor pollen quality in the field and in storage. This study, therefore, aimed at optimizing the pollen germination assessment protocol for yam. The standard medium composition was stepwisely modified, the optimal growth condition was tested, and in vivo predictions were made. This study showed that the differences in yam pollen germination percentage are primarily linked to the genotype and growing conditions (i.e., medium viscosity, incubation temperature, and time to use) rather than the medium composition. The inclusion of polyethylene glycol (PEG) in the culture medium caused 67–75% inhibition of germination in D. alata. Although the in vivo fertilization was dependent on female parents, the in vitro germination test predicted the percentage fruit set at 25.2–79.7% and 26.4–59.7% accuracy for D. rotundata and D. alata genotypes, respectively. This study provides a reliable in vitro yam pollen germination protocol to support pollen management and preservation efforts in yam breeding.

Seed Viability, Seedling Growth and Yield in White Guinea Yam

The yam is an economic tuber crop utilized for food, feed, and various industrial applications. Botanical seed viability, seedling growth, and development are among factors that influence plant population dynamics, development, structure, and sustainability. However, little is known about seed viability, growth, and yield potential of seed-progenies developed using different mating designs. This study assessed seed germination, seedling growth, and yield traits in seed-progenies developed using North Carolina I (NC-1) and polycross mating designs. For this, seed germination and seedling nursery trials established using seed-progenies from different yam crosses were used. Results revealed that days to first seed germination (DAYFG), days to 50% germination (DAYSG), coefficient of velocity of germination, seed emergence speed (SES), germination index, final germination percent, and seedling vigor index significantly (p < 0.05) varied within and among NC-1 and PC-derived families. The mean days to first seed germination (DFSG) and DAYSG seed-progenies of NC-1 were significantly lower than the polycross progenies. Moreover, the seedling-progenies from the polycross produced a higher number of stems and more elongate tubers than those originated from the NC-1 mating. Progenies of family TDr1687 from a polycross mating were among the families that had the highest stem number (2.2), longest tuber (7.5 cm), and widest tuber (2.8 cm). The inter-family means of both NC-1 and polycross had a non-significant variation for mean tuber weight per plant. Our results suggest the relevance of seed germination and seedling attributes for selection of superior progenies at the early generation stage trials in yam breeding.

Genetic parameters, prediction, and selection in a white Guinea yam early-generation breeding population using pedigree information.

Better understanding of the genetic control of traits in breeding populations is crucial for the selection of superior varieties and parents. This study aimed to assess genetic parameters and breeding values for six essential traits in a white Guinea yam (Dioscorea rotundata Poir.) breeding population. For this, pedigree‐based best linear unbiased prediction (P‐BLUP) was used. The results revealed significant nonadditive genetic variances and medium to high (.45–.79) broad‐sense heritability estimates for the traits studied. The pattern of associations among the genetic values of the traits suggests that selection based on a multiple‐trait selection index has potential for identifying superior breeding lines. Parental breeding values predicted using progeny performance identified 13 clones with high genetic potential for simultaneous improvement of the measured traits in the yam breeding program. Subsets of progeny were identified for intermating or further variety testing based on additive genetic and total genetic values. Selection of the top 5% progenies based on the multi‐trait index revealed positive genetic gains for fresh tuber yield (t ha−1), tuber yield (kg plant−1), and average tuber weight (kg). However, genetic gain was negative for tuber dry matter content and Yam mosaic virus resistance in comparison with standard varieties. Our results show the relevance of P‐BLUP for the selection of superior parental clones and progenies with higher breeding values for interbreeding and higher genotypic value for variety development in yam.

Floral Biology and Pollination Efficiency in Yam (Dioscorea spp.)

Yam (Dioscorea spp.) is a monocotyledonous herbaceous vine cultivated for its starchy underground or aerial tubers in the tropics and subtropics. It is an allogamous and polyploid species that reproduces by both sexual and asexual mechanisms. However, many of the landrace cultivars, including most of the popular varieties, reproduce exclusively by vegetative propagation (planting the tubers). These varieties are either sterile or produce sparse and irregular flowering with high flower abortion rate, low fruit and seed set. Production of crossbreed seeds for genetic improvement and for maintaining genetic diversity in yams is, therefore, mainly achieved through natural or managed pollination. Flowering in yam is mostly dioecious and, in some instances, monoecious. Flowering asynchrony, sticky nature of the pollen grains, and cross incompatibility are among the challenges in making genetic progress in yam breeding. There are many limitations in basic and applied knowledge of yam flower biology and pollination. This paper, therefore, reviews the flowering biology, pollination, and methods of improving pollination efficiency in yam breeding programs.

Near-infrared spectroscopy applications for high-throughput phenotyping for cassava and yam: A review.

The review aimed to identify the different high-throughput phenotyping (HTP) techniques that used for quality evaluation in cassava and yam breeding programmes, and this has provided insights towards the development of metrics and their application in cassava and yam improvements. A systematic review of the published research articles involved the use of NIRS in analysing the quality traits of cassava and yam was carried out, and Scopus, Science Direct, Web of Sciences and Google Scholar were searched. The results of the review established that NIRS could be used in understanding the chemical constituents (carbohydrate, protein, vitamins, minerals, carotenoids, moisture, starch, etc.) for high-throughput phenotyping. This study provides preliminary evidence of the application of NIRS as an efficient and affordable procedure for HTP. However, the feasibility of using mid-infrared spectroscopy (MIRS) and hyperspectral imaging (HSI) in combination with the NIRS could be further studied for quality traits phenotyping.

Sample Preservation and Plant Sex Prediction in White Guinea yam (Dioscorea rotundata Poir.)

Introduction: Yam (Dioscorea spp.) is an economically important staple food in tropical regions, especially for people in West Africa. Understanding of the flowering behavior of the crop to determine potential manipulation available to accomplish crop improvement at early stage remain key challenge in the yam breeding. The methods that reliably yield quality DNA and distinguishing sex type at the early stage of growth have been a challenge in yam genetics and breeding studies. This study assessed the effect of sample preservation methods on DNA quantity and quality during extraction and potential of DNA marker to diagnose plant sex at the early seedling stage in white Guinea yam. Materials and Methods: Five sample preservation methods were assessed for quality DNA extraction during field leaf tissue collection, namely liquid nitrogen, dry ice, silica gel, 95% ethanol, and oven drying. The predicted sex at the seedling stage using the molecular marker was further validated with the visual score for the sex phenotype at the flowering stage. Results: According to the findings of the present study, the DNA extracted from leaf samples preserved in liquid nitrogen, silica gel, dry ice, and oven drying methods were higher in molecular weights 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 phenotypes) in the studied materials with 74% prediction accuracy. Conclusions: 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.

Paternity Assignment in White Guinea Yam (Dioscorea Rotundata) Half-Sib Progenies from Polycross Mating Design Using SNP Markers.

White Guinea yam is mostly a dioecious outcrossing crop with male and female flowers produced on distinct plants. Fertile parents produce high fruit set in an open pollination polycross block, which is a cost-effective and convenient way of generating variability in yam breeding. However, the pollen parent of progeny from polycross mating is usually unknown. This study aimed to determine paternity in white Guinea yam half-sib progenies from polycross mating design. A total of 394 half-sib progenies from random open pollination involving nine female and three male parents was genotyped with 6602 SNP markers from DArTSeq platform to recover full pedigree. A higher proportion of expected heterozygosity, allelic richness, and evenness were observed in the half-sib progenies. A complete pedigree was established for all progenies from two families (TDr1685 and TDr1688) with 100% accuracy, while in the remaining families, paternity was assigned successfully only for 56 to 98% of the progenies. Our results indicated unequal paternal contribution under natural open pollination in yam, suggesting unequal pollen migrations or gene flow among the crossing parents. A total of 3.8% of progenies lacking paternal identity due to foreign pollen contamination outside the polycross block was observed. This study established the efficient determination of parental reconstruction and allelic contributions in the white Guinea yam half-sib progenies generated from open pollination polycross using SNP markers. Findings are useful for parental reconstruction, accurate dissection of the genetic effects, and selection in white Guinea yam breeding program utilizing polycross mating design.

Nodal vine cutting technique for assessing nematode resistance in yams

Identifying resistance to plant-parasitic nematodes in yams is a major challenge in yam breeding programmes due partly to insufficient planting material (tubers) for evaluation. Susceptible yam cultivar, TDr 93-31 was inoculated with 0 (control), 200, 500, 1000 and 2000 eggs/individuals each of Meloidogyne incognita, Scutellonema bradys and Pratylenchus brachyurus. Vine cuttings of two cultivars each of Dioscorea rotundata, D. alata and D. dumetorum were compared to conventional minisett method in a second experiment. Planted vines and minisetts were inoculated with 500 and 5000 eggs/individuals respectively. Data were collected on percentage vine survival, fresh root and tuber weight, number of tubers and nematode population and damage. Vine survival was not significantly different between control and inoculated vines. Maximum damage rating (>60%) was observed with initial inoculum of 1000 eggs of M. incognita and 200 individuals of S. bradys and P. brachyurus. The two cultivars of D. alata and D. rotundata developed visible symptoms and supported nematode reproduction while the D. dumetorum cultivars did not. The reaction of yam cultivars planted as vines was consistent with results from conventional minisett method. The lowest inoculum of 200 egg/juveniles was sufficient to elicit a reaction from vines in the vertical sack system.

Analysis of seed yam varieties, sources and quantity demanded by farmers in major yam producing districts in Ghana

The study analysed the varieties, sources and quantities of seed yam demanded by farmers for cultivation in order to inform policies aimed at ensuring adequate supply of quality seed yam of desirable varieties at an affordable price to boost yam productivity for improved income and livelihoods. A structured questionnaire was administered to 380 randomly selected yam farmers in three major yam producing districts in Ghana in 2015. The data analysis was done using STATA statistical software. The study identified Pona/Punjo, Lariboko, Asana, Afebetuye, Dente, Olondo and Kparinjo as the yam varieties mainly cultivated by farmers in a reducing order with high market demands by consumers. Own production remains the major source of seed yam for farmers. The estimated monetary value of quantity of seed yam used by farmers for cultivation in 2014 farming season was GH¢ 198, 552,841.0 (USD 51,706,469.0) in the study locations. About GH¢ 5,679,979.0 (USD 1,479,161.2) worth of quantities of seed yam was obtained from the market and other sources. The results demonstrate the existence of market potential for commercial seed yam production and supply in Ghana. Commercial seed yam certification system and yam breeding activities should target the identified yam varieties.

Review of empirical and emerging breeding methods and tools for yam (Dioscorea spp.) improvement: Status and prospects

AbstractYam (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.

Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling.

Dioecy (distinct male and female individuals) and scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are largely unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata), generating 20,236 unique tags. Of these, 13,901 were represented by a minimum of 10 tags. A total 88 tags were significantly differentially expressed in male, female and monoecious plants, of which 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of three candidate genes.We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two consecutive years. Over 85% of accessions were either male or non-flowering, less than 15% were female, while monoecious plants were rare. Intensity of flowering varied between male and female plants, with the former flowering more abundantly than the latter. Candidate genes identified in this study can be targeted for further validation and to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve efficiency of yam breeding.

Spatial Multivariate Cluster Analysis for Defining Target Population of Environments in West Africa for Yam Breeding

Yam (Dioscorea spp.) is a major staple crop with high agricultural and cultural significance for over 300 million people in West Africa. Despite its importance, productivity is miserably low. A better understanding of the environmental context in the region is essential to unlock the crop's potential for food security and wealth creation. The article aims to characterize the production environments into homologous mega-environments, having operational significance for breeding research. Principal component analysis (PCA) was performed separately on environmental data related to climate, soil, topography, and vegetation. Significant PCA layers were used in spatial multivariate cluster analysis. Seven clusters were identified for West Africa; four were country-specific; the rest were region-wide in extent. Clustering results are valuable inputs to optimize yam varietal selection and testing within and across the countries in West Africa. The impact of breeding research on poverty reduction and problems of market accessibility in yam production zones were highlighted.

Carotenoid profiling of yams: Clarity, comparisons and diversity

Screening carotenoids of elite accessions of yam (Dioscorea spp.) used in the global yam breeding program has been conducted to quantitatively determine the carotenoid composition of the crop. Comparisons to previous data reporting cerotenoid levels in yam has been made, in order to deduce greater perspectives across multiple studies. Characterisation of complex species and accession -specific profiles have shown a rich base of diversity that can inform breeding strategies. Key findings include; (i) the identification of accessions rich in β-carotene which can aid provitamin A biofortification, (ii) Data disputing the commonly held belief that yellow Guinea yam (D. cayennensis) has higher β-carotene content than that of white Guinea yam (D. rotundata), and (iii) the tentative identification of C25-epoxy-apocarotenoid persicaxanthin with potential implications for tuber dormancy.

Metabolite profiling of yam (Dioscorea spp.) accessions for use in crop improvement programmes

IntroductionNinety-seven percent of yam (Dioscorea spp.) production takes place in low income food deficit countries (LIFDCs) and the crop provides 200 calories a day to approximately 300 million people. Therefore, yams are vital for food security. Yams have high-yield potential and high market value potential yet current breeding of yam is hindered by a lack of genomic information and genetic resources. New tools are needed to modernise breeding strategies and unlock the potential of yam to improve livelihood in LIFDCs.ObjectivesMetabolomic screening has been undertaken on a diverse panel of Dioscorea accessions to assess the utility of the approach for advancing breeding strategies in this understudied crop.MethodsPolar and lipophilic extracts from tubers of accessions from the global yam breeding program have been comprehensively profiled via gas chromatography-mass spectrometry.ResultsA visual pathway representation of the measured yam tuber metabolome has been delivered as a resource for biochemical evaluation of yam germplasm. Over 200 compounds were routinely measured in tubers, providing a major advance for the chemo-typing of this crop. Core biochemical redundancy concealed trends that were only elucidated following detailed mining of global metabolomics data. Combined analysis on leaf and tuber material identified a subset of metabolites which allow accurate species classification and highlighted the potential of predicting tuber composition from leaf profiles. Metabolic variation was accession-specific and often localised to compound classes, which will aid trait-targeting for metabolite markers.ConclusionsMetabolomics provides a standalone platform with potential to deliver near-future crop gains for yam. The approach compliments the genetic advancements currently underway and integration with other ‘–omics’ studies will deliver a significant advancement to yam breeding strategies.

Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination

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.