Microsatellite segregation analysis and cytogenetic evidence for tetrasomic inheritance in the American yam Dioscorea trifida and a new basic chromosome number in the Dioscoreae

Genome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea

A rhizomatous Dioscorea crop 'Edo-dokoro' was described in old records of Japan, but its botanical identity has not been characterized. We found that Edo-dokoro is still produced by four farmers in Tohoku-machi of the Aomori prefecture, Japan. The rhizomes of Edo-dokoro are a delicacy to the local people and are sold in the markets. Morphological characters of Edo-dokoro suggest its hybrid origin between the two species, Dioscorea tokoro and Dioscorea tenuipes. Genome analysis revealed that Edo-dokoro likely originated by hybridization of a male D. tokoro to a female D. tenuipes, followed by a backcross with a male plant of D. tokoro. Edo-dokoro is a typical minor crop possibly maintained for more than 300 years but now almost forgotten by the public. We hypothesize that there are many such uncharacterized genetic heritages passed over generations by small-scale farmers that await serious scientific investigation for future use and improvement by using modern genomics information.

Preferential Homologous Chromosome Pairing in a Tetraploid Intergeneric Somatic Hybrid (Citrus reticulata + Poncirus trifoliata) Revealed by Molecular Marker Inheritance

The creation of intergeneric somatic hybrids between Citrus and Poncirus is an efficient approach for citrus rootstock breeding, offering the possibility of combining beneficial traits from both genera into novel rootstock lineages. These somatic hybrids are also used as parents for further tetraploid sexual breeding. In order to optimize these latter breeding schemes, it is essential to develop knowledge on the mode of inheritance in the intergeneric tetraploid hybrids. We assessed the meiotic behavior of an intergeneric tetraploid somatic hybrid resulting from symmetric protoplast fusion of diploid Citrus reticulata and diploid Poncirus trifoliata. The analysis was based on the segregation patterns of 16 SSR markers and 9 newly developed centromeric/pericentromeric SNP markers, representing all nine linkage groups of the Citrus genetic map. We found strong but incomplete preferential pairing between homologues of the same ancestral genome. The proportion of gametes that can be explained by random meiotic chromosome associations (τ) varied significantly between chromosomes, from 0.09 ± 0.02 to 0.47 ± 0.09, respectively, in chromosome 2 and 1. This intermediate inheritance between strict disomy and tetrasomy, with global preferential disomic tendency, resulted in a high level of intergeneric heterozygosity of the diploid gametes. Although limited, intergeneric recombinations occurred, whose observed rates, ranging from 0.09 to 0.29, respectively, in chromosome 2 and 1, were significantly correlated with τ. Such inheritance is of particular interest for rootstock breeding because a large part of the multi-trait value selected at the teraploid parent level is transmitted to the progeny, while the potential for some intergeneric recombination offers opportunities for generating plants with novel allelic combinations that can be targeted by selection.

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

INTRODUCTION

Ninety-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.

OBJECTIVES

Metabolomic 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.

METHODS

Polar and lipophilic extracts from tubers of accessions from the global yam breeding program have been comprehensively profiled via gas chromatography-mass spectrometry.

RESULTS

A 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.

CONCLUSIONS

Metabolomics 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.

Evidence of Genomic Exchanges between Homeologous Chromosomes in a Cross of Peanut with Newly Synthetized Allotetraploid Hybrids

Cultivated peanut and synthetics are allotetraploids (2n = 4x = 40) with two homeologous sets of chromosomes. Meiosis in allotetraploid peanut is generally thought to show diploid-like behavior. However, a recent study pointed out the occurrence of recombination between homeologous chromosomes, especially when synthetic allotetraploids are used, challenging the view of disomic inheritance in peanut. In this study, we investigated the meiotic behavior of allotetraploid peanut using 380 SSR markers and 90 F2 progeny derived from the cross between Arachis hypogaea cv Fleur 11 (AABB) and ISATGR278-18 (AAKK), a synthetic allotetraploid that harbors a K-genome that was reported to pair with the cultivated B-genome during meiosis. Segregation analysis of SSR markers showed 42 codominant SSRs with unexpected null bands among some progeny. Chi-square tests for these loci deviate from the expected 1:2:1 Mendelian ratio under disomic inheritance. A linkage map of 357 codominant loci aligned on 20 linkage groups (LGs) with a total length of 1728 cM, averaging 5.1 cM between markers, was developed. Among the 10 homeologous sets of LGs, one set consisted of markers that all segregated in a polysomic-like pattern, six in a likely disomic pattern and the three remaining in a mixed pattern with disomic and polysomic loci clustered on the same LG. Moreover, we reported a substitution of homeologous chromosomes in some progeny. Our results suggest that the homeologous recombination events occurred between the A and K genomes in the newly synthesized allotetraploid and have been highlighted in the progeny. Homeologous exchanges are rarely observed in tetraploid peanut and have not yet been reported for AAKK and AABB genomes. The implications of these results on peanut breeding are discussed.

Next-generation sequencing based genotyping, cytometry and phenotyping for understanding diversity and evolution of Guinea yams

Genotyping by sequencing (GBS) is used to understand the origin and domestication of guinea yams, including the contribution of wild relatives and polyploidy events to the cultivated guinea yams. Patterns of genetic diversity within and between two cultivated guinea yams (Dioscorea rotundata and D. cayenensis) and five wild relatives (D. praehensilis, D. mangenotiana, D. abyssinica, D. togoensis and D. burkilliana) were investigated using next-generation sequencing (genotyping by sequencing, GBS). Additionally, the two cultivated species were assessed for intra-specific morphological and ploidy variation. In guinea yams, ploidy level is correlated with species identity. Using flow cytometry a single ploidy level was inferred across D. cayenensis (3x, N = 21), D. praehensilis (2x, N = 7), and D. mangenotiana (3x, N = 5) accessions, whereas both diploid and triploid (or aneuploid) accessions were present in D. rotundata (N = 11 and N = 32, respectively). Multi-dimensional scaling and maximum parsimony analyses of 2,215 SNPs revealed that wild guinea yam populations form discrete genetic groupings according to species. D. togoensis and D. burkilliana were most distant from the two cultivated yam species, whereas D. abyssinica, D. mangenotiana, and D. praehensilis were closest to cultivated yams. In contrast, cultivated species were genetically less clearly defined at the intra-specific level. While D. cayenensis formed a single genetic group, D. rotundata comprised three separate groups consisting of; (1) a set of diploid individuals genetically similar to D. praehensilis, (2) a set of diploid individuals genetically similar to D. cayenensis, and (3) a set of triploid individuals. The current study demonstrates the utility of GBS for assessing yam genomic diversity. Combined with morphological and biological data, GBS provides a powerful tool for testing hypotheses regarding the evolution, domestication and breeding of guinea yams.

Rapid metabolic discrimination and prediction of dioscin content from African yam tubers using Fourier transform-infrared spectroscopy combined with multivariate analysis

To determine whether or not FT-IR spectroscopy could be used for taxonomic and metabolic discrimination of African yam lines, tuber samples from African and Asian yam species were subjected to FT-IR. Most remarkable spectral differences between African and Asian yams were found in the 1750-1700 cm(-1) region, polysaccharide (1200-900 cm(-1)) and protein/amide I and II (1700-1500 cm(-1)) regions of FT-IR spectra. A hierarchical dendrogram based on partial least square-discriminant analysis (PLS-DA) of FT-IR data from 7 African yam species show phylogenetic relationship. In addition, the content of dioscin, a steroidal saponin found in yam tuber, was predicted using a PLS regression model with regression coefficient R(2)=0.7208 indicated that prediction model had average accuracy. Thus, considering these results we suggest that FT-IR combined with multivariate analysis could be applied as a novel tool for metabolic evaluation and high-throughput screening of African yam lines with higher content of dioscin.

Physicochemical, functional, and macromolecular properties of waxy yam starches discovered from "Mapuey" (Dioscorea trifida) genotypes in the Venezuelan Amazon

"Mapuey" tubers in Venezuela are staple food for indigenous peoples from the Caribbean coast and Amazon regions. Noticeable differences between genotypes of yam starches were observed. Granules were large, triangular, or shell-shaped with monomodal particle size distribution between 24.5 and 35.5 μm. Differential scanning calorimetry (DSC) analyses revealed onset gelatinization temperatures from 69.1 to 73.4 °C with high gelatinization enthalpy changes from 22.4 to 25.3 J g(-1). All X-ray diffractograms of starches exhibit B-type crystallinity. Crystallinity degrees varied from 24% to 40%. The highest crystallinity was found for the genotype having the highest amylose content. Iodo-colorimetric, amperometric, and DSC amylose determinations varied from 1.4 to 8.7%, 2.2 to 5.9%, and 1.4 to 3.5% for Amazonian genotypes, in comparison with commercial Mapuey starches: 12.0, 9.5, and 8.7%, respectively. Solubility and swelling power at 90 °C varied from 2.1 to 4.4% and 20.5 to 37.0%, respectively. Gel clarity fluctuated from 22.4 to 79.2%, and high rapid visco analyzer (RVA) viscosity was developed at 5% starch suspension (between 1430 and 2250 cP). Amylopectin weight average molar mass M(w), radius of gyration R(G), hydrodynamic coefficient ν(G), and apparent molecular density d(Gapp) were determined using high-performance size exclusion chromatography (HPSEC) and asymmetrical flow field flow fractionation (A4F) techniques coupled with multiangle laser light scattering (MALLS) on the Dioscorea trifida genotypes exhibiting the lowest and highest amylose contents. Amylopectins showed very similar molecular conformations. M(w) values were 1.15 × 10(8) and 9.06 × 10(7) g mol(-1) using HPSEC and A4F, respectively, thus, 3-5 times lower than those reported with the same techniques for other yam species, and very close to those of potato and cassava amylopectins. This discovery of a new natural amylose-free starch in the neglected yam "Mapuey" could present some potential for the food industry.

Evidence of diploidy in the wild Amerindian yam, a putative progenitor of the endangered species Dioscorea trifida (Dioscoreaceae)

The fundamental question about Dioscorea trifida (Dioscoreaceae), the most important Amerindian yam, that remains unresolved concerns its evolutionary origin, since no wild relative has been reported. In this paper we report the existence of D. trifida’s wild relative for the first time. The diploidy of wild D. trifida (2n = 40) is clearly demonstrated by flow cytometry, chromosome counts, and microsatellite pattern analysis, whereas the cultivated form was previously shown to be autotetraploid (2n = 80). In the coastal region where the wild and cultivated forms are sympatric, tetraploid and triploid cytotypes coexist within the same populations. In the sites where the wild and cultivated forms are allopatric, the wild diploid cytotype predominates. AFLP (amplified fragment length polymorphism) analyses gave an initial idea of the position of the wild forms in relation to the cultivated forms. All the wild and cultivated types form a monophyletic group structured into two major subgroups corresponding to the tetraploid cytotype of the cultivated form and the diploid cytotype of the wild form. The triploid cytotypes of the wild form are in an intermediary position. Wild accessions are grouped on the basis of their geographic origin. The data presented in this paper are significant for the effective breeding and conservation of D. trifida and to assess its genetic diversity and population structure for the general understanding of the evolution and domestication of the species.

Revision of ploidy status of Dioscorea alata L. (Dioscoreaceae) by cytogenetic and microsatellite segregation analysis

Dioscorea alata is a polyploid species with several ploidy levels and its basic chromosome number has been considered by most authors to be x = 10. Standard chromosome counting and flow cytometry analysis were used to determine the chromosome number of 110 D. alata accessions of the CIRAD germplasm collection. The results revealed that 76% of accessions have 2n = 40 chromosomes, 7% have 2n = 60 chromosomes and 17% have 2n = 80 chromosomes. Progenies were produced from 2n = 40 types of D. alata and the segregation patterns of six microsatellite markers in four different progenies were analysed. The Bayesian method was used to test for diploid versus tetraploid (allo- and autotetraploid) modes of inheritance. The results provided the genetic evidence to establish the diploidy of plants with 2n = 40 chromosomes and to support the hypothesis that plants with 2n = 40, 60 and 80 chromosomes are diploids, triploids and tetraploids, respectively, and that the basic chromosome number of D. alata is x = 20. The findings obtained in the present study are significant for effective breeding programs, genetic diversity analysis and elucidation of the phylogeny and the species origin of D. alata.

Dilemmas caused by endogenous pararetroviruses regarding the taxonomy and diagnosis of yam (Dioscorea spp.) badnaviruses: analyses to support safe germplasm movement

The discovery of endogenous pararetroviral sequences (EPRVs) has had a deep impact on the approaches needed for diagnosis, taxonomy, safe movement of germplasm and management of diseases caused by pararetroviruses. In this article, we illustrate this through the example of yam (Dioscorea spp.) badnaviruses. To enable progress, it is first necessary to clarify the taxonomical status of yam badnavirus sequences. Phylogeny and pairwise sequence comparison of 121 yam partial reverse transcriptase sequences provided strong support for the identification of 12 yam badnavirus species, of which ten have not been previously named. Virus prevalence data were obtained, and they support the presence of EPRVs in D. rotundata, but not in D. praehensilis, D. abyssinica, D. alata or D. trifida. Five yam badnavirus species characterised by a wide host range seem to be of African origin. Seven other yam badnavirus species with a limited host range are probably of Asian-Pacific origin. Recombination under natural circumstances appears to be rare. Average values of nucleotide intra-species genetic distances are comparable to data obtained for other RNA and DNA virus families. The dispersion scenarios proposed here, combined with the fact that host-switching events appear common for some yam badnaviruses, suggest that the risks linked to introduction via international plant material exchanges are high.

Phylogenetic position of Oxygyne shinzatoi (Burmanniaceae) inferred from 18S rDNA sequences

The genus Oxygyne comprises three species disjunctly distributed in Africa and Japan and is the least examined genus of the Burmanniaceae due to the scarcity of living material. We obtained living samples of Oxygyne shinzatoi and examined the phylogenetic position of this species on the basis on the 18S rDNA sequence. Oxygne shinzatoi was consistently found to belong to the monophyletic group of tribe Thismieae, but its position in the tribe differed depending on the criteria applied (maximum parsimony, maximum likelihood, Bayesian inference). Distance analysis from the most recent common ancestor indicated that O. shinzatoi had the lowest substitution rate among the species of tribe Thismieae. Combined with recent knowledge of basic chromosome numbers and substitution rate characteristics, O. shinzatoi can be considered to be one of the basal taxon of tribe Thismieae.

A genetic linkage map of water yam ( Dioscorea alata L.) based on AFLP markers and QTL analysis for anthracnose resistance

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.