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

Despite the economic and cultural importance of the indigenous “Amerindian” yam Dioscorea trifida, very little is known about their origin, phylogeny, diversity and genetics. Consequently, conventional breeding efforts for the selection of D. trifida genotypes resistant to potyviruses which are directly involved in the regression of this species have been seriously limited. Our objective of this paper is to contribute to the clarification of the cytogenetic status, i.e., inheritance and chromosome number. Our results provide genetic evidence supporting tetrasomic behaviour of the genome of D. trifida based on chromosomal segregation pattern analysis using eight SSRs markers in three different crosses. This is the first reliable evidence of an autopolyploid species in the genus Dioscorea. The second major result in this study is the revealing of a new base chromosome number in the botanical section Macrogynodium to which D. trifida belongs. To date, our assumptions about the ploidy level of yams are based on the observations that the basic chromosome number is 10 or 9, and D. trifida was described as octoploid. The chromosome number of D. trifida accessions was also assessed using somatic chromosomic count techniques. Flow cytometry did not show significant variation of 2C DNA content among 80 accessions indicating homogeneity of the ploidy level of the cultivated D. trifida. This suggests that autotetraploidy is well established as well as the rule for the cultivated pool of D. trifida, even if the direct diploid ancestor remains to be identified. The data presented in this paper are significant and important for the effective breeding and conservation of the species and for elucidating the phylogeny and the origins of the yam and the evolution of the genus Dioscorea.     

Development of DNA microsatellite markers in tropical yam (Dioscorea sp.)

We developed new simple sequence repeat (SSR) markers in different species of yam (Dioscorea sp.). A microsatellite‐enriched bank was created from Dioscorea alata, Dioscorea abyssinica and Dioscorea praehensilis. Sixteen polymorphic loci were characterized. Several of these markers are transferable to species of other Dioscorea sections.     

Tuber Germination and Early Growth in Four Edible Dioscorea Species

The gross morphology and the sequence of anatomical events duringtuber germination in D. alata, D. esculenta, D. rotundata andD. trifida yams are compared with particular reference to theorigin of the organ of renewed growth, the primary nodal complex.The significance of this organ in yam phylogeny and ontogenyis briefly discussed. Dioscorea species, yams, tuber germination, nodal complex     

Segregation patterns of isozyme loci and microsatellite markers show the diploidy of African yam Dioscorea rotundata (2n=40)

The cultivated yam species Dioscorea rotundata (2n=40) has been considered by most authors as a tetraploid species with a basic chromosome number of ten. In this paper, we analysed the segregation of two isozyme loci and six microsatellite markers in the progeny of a self-fertilised monoecious plant. For the eight markers, segregation patterns could be explained by only two genetic models: diploidy or tetraploidy with two null alleles. Given the nature of studied markers, the most parsimonious hypothesis was that the parental plant was diploid. These results, data from a diversity survey and results of other authors led to the conclusion that D. rotundata is a diploid species.     

Development and characterization of microsatellite markers in a clonal plant,Dioscorea japonica Thunb.

We developed 10 microsatellite loci from genomic DNA of a dioecious clonal plant, Dioscorea japonica. Out of 384 clones, 148 contained microsatellite repeats. Polymerase chain reaction primer pairs were designed for 95 of these clones from their sequence data, of which, 10 pairs produced successful amplification. Thirty‐eight individuals were genotyped for allelic diversity. We detected three to nine alleles per locus, and the expected heterozygosity ranged from 0.461 to 0.851.     

Sequence characterization of microsatellites in diploid and polyploid Ipomoea

 The objectives of the present study were to evaluate the inheritance and nucleotide sequence profiles of microsatellite genetic markers in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.] and its putative tetraploid and diploid ancestors, and to test possible microsatellite mutation mechanisms in polyploids by direct sequencing of alleles. Sixty three microsatellite loci were isolated from genomic libraries of I. batatas and sequenced. PCR primers were designed and used to characterize microsatellite loci in two hexaploid I. batatas populations, a tetraploid Ipomoea trifida population, and a diploid I. trifida population. Nine out of the sixty three primer pairs tested yielded a clearly discernible, heritable banding pattern; five showed Mendelian segregation. All other primer pairs produced either smeared banding patterns, which could not be scored, or no bands at all in I. batatas. All of the primers which produced discernible banding patterns from I. batatas also amplified products of similar size in tetraploid and diploid I. trifida accessions. The sequence analysis of several alleles in the three species showed differences due to mutations in the repeat regions consistent with small differences in the repeat number. However, in some cases insertions/deletions and base substitutions in the microsatellite flanking regions were responsible for polymorphisms in both polyploid and diploid species. These results provide strong empirical evidence that complex genetic mechanisms are responsible for SSR allelic variation in Ipomoea. Four I. batatas microsatellite loci showed polysomic segregation fitting tetraploid segregation ratios. To our knowledge this is the first report of segregation ratios for microsatellites markers in polyploids. Received: 4 January 1999 / Accepted: 4 January 1999     

Organ- and Age-Specific Differences of Dioscorea polystachya Compounds Measured by UPLC-QTOF/MS

Dioscorea polystachya, named Chinese yam, is widely cultivated as a functional food and natural medicine in China. There is currently little information about the chemical characteristics of Dioscorea polystachya in different organs (tuber cortex and tuber flesh) and at various ages. In this study, an ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) was used to profile chemical compounds in Dioscorea polystachya. As a result, thirty-eight compounds were detected in yam tuber cortex and tuber flesh. More compounds were detected in yam tuber cortex than in tuber flesh. Compounds such as dehydroepiandrosterone, allantoin and flavonoids were selected as biomarker candidates. Dehydroepiandrosterone was found more abundant in tuber flesh, while allantoin and flavonoids showed higher levels in tuber cortex. Furthermore, the levels of dioscin, malvalic acid and sucrose differed significantly among age groups and were highest in the tubers at 2 years. While the levels of allantoin, adenosine and glutamine increased with the growing years and were highest at 4 years. Thus, 2-year old Dioscorea polystachya tubers could be harvested to prepare dioscin, malvalic acid and sucrose supplements. The 4-year-old Dioscorea polystachya tubers would be the best choice for obtaining a large amount of allantoin and adenosine in industrial production.     

Intracellular Localization of a Class IV Chitinase from Yam

Genomic DNA encoding a class IV chitinase was cloned from yam (Dioscorea opposita Thunb) leaves in previous research (Biosci. Biotechnol. Biochem., 68, 1508–1517 (2004)). But this chitinase had an additional sequence composed of eight amino acids (a C-terminal extension) at the C-terminal, compared with class IV chitianses from other plants. In order to clarify the role of this C-terminal extension in cellular localization, plants and suspension-cultured cells of Nicotiana tabacum were transformed with either the cloned yam class IV chitinase gene carrying the C-terminal extension or its truncated gene by the Agrobacterium-mediated method, and then their localization was investigated. The results suggest that the C-terminal extension of yam class IV chitinase plays a role as a targeting signal for plant vacuoles. This is the first report presenting the existence of vacuolar type class IV chitinase.     

Rapid assessment of resistance of tissue-cultured water yam (Dioscorea alata) and white guinea yam (Dioscorea rotundata) to anthracnose (Colletotrichum gloeosporioides Penz.)

Yam anthracnose is caused by the pathogen Colletotrichum gloeosporioides Penz. and has been identified as the most important biotic constraint to yam production worldwide. Rapid assessment of the disease is vital to its effective diagnosis and management. In this study, tissue-cultured yam plantlets of five lines of Dioscorea alata and nine of D. rotundata were rapidly assessed for their reactions to two isolates of yam anthracnose. The plantlets, obtained from meristem of the nodal cuttings, were grown for 8?weeks on Murashige and Skoog (MS) basal medium, acclimatised for 3?weeks, hardened for an additional 3?weeks, arranged in screen house in completely randomised design and sprayed with spore inocula prepared from 7?day-old culture of the two strains of Colletotrichum gloeosporioidies Penz. The relative resistance of the different Dioscorea spp. was evaluated using three disease indices – severity at seventh day after inoculation, SD7; area under disease progress curve, AUDPC; and disease severity rate, Rd. A modified rank-sum classification method put TDa 1425 and TDr 2040, with rank sum of 2.0 each, as resistant. TDr 2121, TDr 2287 and TDr 2048 were susceptible with rank sum of 27.50, 25.50 and 24.50, respectively. Dioscorea alata TDa 1425 and Dioscorea rotundata TDr 2040 were recommended in areas endemic with yam anthracnose, and also as parent lines while breeding for resistance to anthracnose.     

Serological detection of yam viruses in farmers' fields in Ogun State,Nigeria

A field survey was conducted in eight local government areas (LGA) of Ogun state, Nigeria to assess the incidence of viral diseases of yams in the areas. Leaf samples were collected from 90 yam plants which were either symptomatic or asymptomatic. These were bulked into 45 during serological tests and the viruses indexed include yam mosaic virus (YMV); Dioscorea alata bacilliform virus (DaBV) and cucumber mosaic virus (CMV). DaBV was the most prevalent virus on the field with incidence of 48.9% (22/45) followed by YMV which occurred in 42.2% (19/45). CMV had the lowest percentage of incidence; 2.2% (1/45). Of all the LGAs visited, Abeokuta north and Abeokuta south had the highest incidence of YMV and DaBV, respectively. Mixed virus infections were also detected.     

Infection of yam tubers by Aspergillus niger in relation to isolate, yam species, and temperatures

Infection of yam (Dioscorea spp.) tubers by a range of geographical isolates of Aspergillus niger from yam and other hosts was tested on tubers imported into the UK, using a standard inoculation procedure. A yam isolate of A. niger from Nigeria was generally more aggressive than one from Barbados or from isolates from different hosts. There were inconsistent differences in infection between different portions of the tubers. Infection and weight loss of yam tubers were evaluated at temperatures ranging from 18 to 36°C, using the Nigerian and Barbados isolates. Mean percentage infection increased across the temperature range for the Nigerian isolate; for the Barbados isolate, infection increased with temperatures only from 18 to 30°C. Comparison of different yam species in relation to A. niger infection is difficult due to lack of information on cultivar and provenance.     

Field Studies on Cross-protection against Japanese yam mosaic virus in Chinese yam (Dioscorea opposita) with an Attenuated Strain of the Virus

An attenuated strain of Japanese yam mosaic virus (JYMV), designated T‐3, was evaluated for its cross‐protection efficacy against virulent (native) strains of JYMV in Chinese yam (Dioscorea opposita) grown in farmers’ fields in Japan. Native strains of JYMV were detected by a polymerase chain reaction‐based assay in all the Chinese yam plants grown from virus‐free tubers in the first growing season in the fields. In contrast, the virus was detected in only one of fifty plants grown from tubers preinoculated with T‐3 during the experiments for 6 years, suggesting that T‐3 consistently cross‐protected against native JYMV in Chinese yam in the field. Chinese yam plants preinoculated with T‐3 produced significantly greater yield of tubers per plant compared with non‐inoculated plants.     

Isolation, characterisation and identification of a potyvirus from Dioscorea alata L. (water yam) in Nigeria

A yam potyvirus was isolated from Dioscorea alata samples collected in Nigeria. The virus was not transmissible mechanically but was transmitted by Aphis craccivora to four cowpea cultivars (Ife Brown, IT84S-2114, IT82E-10 and TVu2657), and from which it could be mechanically transmitted between the cowpea cultivars. In infectivity- tests using cowpea extracts, the virus had a dilution end point of 10^-4, a thermal inactivation point of 60–65°C and longevity in vitro of 2 days at room temperature. The virus coat protein had an estimated molecular weight of 32 100 daltons. The virus was identified as an isolate of Dioscorea alata virus (DAV; syn. yam virus 1) due to its biological characteristics and its serological reaction with antiserum raised against DAV. The virus is not related to yam mosaic virus, but distantly related to blackeye cowpea mosaic virus and cowpea aphid-borne mosaic virus.     

Concentrated Distribution of Wild Yam Patches: Historical Ecology and the Subsistence of African Rainforest Hunter-Gatherers

Availability of annually reproducing wild yam species (Dioscorea praehensilis and Dioscorea semperflorens) is considered to be a key factor for the viability of forest hunter-gatherer subsistence in the African rainforests. I here describe the habitat and distribution of wild yam patches, and discuss possible human impacts on the formation of wild yam patches, which currently support long-term forest expeditions by Baka hunter-gatherers in southeastern Cameroon. An analysis of canopy photographs shows that annual yams favor a habitat of canopy gaps which receive sufficient sunlight. However, the fact that annual yams patches are limited to specific locations even though gaps in the canopy occur throughout the forest, combined with the mostly vegetative reproductive system of the yams, suggests annual yams do not propagate extensively in the wild. Moreover, areas with abundant annual yam patches that are presently situated far from any villages contain several abandoned village sites. Since the Baka often transplant parts of yam tubers to encourage their spread, it seems that human activities may have contributed to the formation of locally concentrated annual yam patches.     

Isolation and characterization of microsatellite loci in the threatened brook lamprey Lethenteron sp. N

A microsatellite‐enriched genomic library was obtained for the threatened brook lamprey, Lethenteron sp. N, and from it 16 dinucleotide markers were successfully isolated and characterized. These markers were found to have between 1 and 6 alleles with heterozygosity ranging from zero to 0.79. Cross‐species amplification was successful, with eight loci amplifying products in the counterpart cryptic species, Lethenteron sp. S, as well as 15 loci in Lethenteron japonicum. One out of 10 primer pairs previously reported also amplified products in all the three species.     

Antifungal properties of yam (Dioscorea alata) peel extract

The extraction of natural antifungal compounds from the peels of yam (Dioscorea alata) and the effect of these compounds on both the vegetative and reproductive structures of some yam rot pathogens were studied. Four prominent antifungal components were obtained; one of the components was fully characterized and identified as β-sitosterol. The antifungal activity of the compounds toward the germination of spores of two yam pathogens showed an inhibition of less than 57% at a concentration of 50 mg/L while inhibition on the elongation of germ-tubes ofFusarium moniliforme was as high as 82% at the same concentration. However, the ED₅₀ for inhibition of germ-tube elongation in the yam compounds for the same organism was below 32 mg/L. The role of the yam compounds at high concentrations in disease resistance is discussed.     

基于ISSR的豚草和三裂叶豚草遗传多样性研究

[目的]研究不同地理种群的豚草和三裂叶豚草的遗传多样性水平和遗传结构。[方法]应用筛选的13条ISSR引物对8个豚草居群和7个三裂叶豚草居群共240个样品进行分子标记。[结果]8个豚草居群128个样品,共扩增出304条带,多态性位点比率为98.68%;Shannon''s信息指数为0.6716,Nei''s基因多样性指数为0.4788。7个三裂叶豚草居群112个样品,共扩增出266条带,多态性位点比率为95.86%;Shannon''s信息指数为0.6593,Nei''s基因多样性指数为0.4670。豚草和三裂叶豚草各居群遗传距离较近。[结论]豚草和三裂叶豚草在居群间具有一定的遗传稳定性;居群内具有丰富的遗传多样性。豚草和三裂叶豚草遗传变异主要来源于居群内部。豚草各居群遗传距离和地理距离有显著相关性,三裂叶豚草各居群遗传距离和地理距离无显著相关性。     

Lactic acid fermentation of Chinese yam (Dioscorea batatas Decne) flour and its pharmacological effect on gastrointestinal function in rat model

To develop a health-aid preparation of Chinese yam (Dioscorea batatas Decne), lactic acid fermentation was attempted using a mixed starter comprising ofLactobacillus acidophilus, Streptococcus thermophilus, andBifidobacterium bifidus. The anaerobic fermentation of a 5% Chinese yam flour suspension gave a uniform suspension of pH 4.35, containing 7.76×10⁶ CFU/mL lactic acid bacteria (LAB), and which was found to be acceptable to the panel from a sensory assessment. During the administration of the lactic acid fermented (LAF) Chinese yam to Sprague Dawley rats for 6 weeks, a smaller body weight gain, but greater excretion of feces were observed, implying the creation of a healthy gastrointestine on the administration of LAF Chinese yam, which was also confirmed by the gastrointestinal motility of the feed in rats fed on LAF Chinese yam. The constipation induced by loperamide was further suppressed in a rat group fed on a LAF Chinese yam diet, which was qualified from healthy gastrointestinal flora established by LAB. A serochemical analysis revealed a slight improvement in the blood glucose, neutral lipid and total cholesterol concentrations on administration of LAF Chinese yam, suggesting LAF Chinese yam could be served as a healthy-aid preparation, even for hyperglycemia or hyperlipidemia patients.     

Promiscuous arbuscular mycorrhizal symbiosis of yam (Dioscorea spp.), a key staple crop in West Africa

Yam (Dioscorea spp.) is a tuberous staple food crop of major importance in the sub-Saharan savannas of West Africa. Optimal yields commonly are obtained only in the first year following slash-and-burn in the shifting cultivation systems. It appears that the yield decline in subsequent years is not merely caused by soil nutrient depletion but might be due to a loss of the beneficial soil microflora, including arbuscular mycorrhizal fungi (AMF), associated with tropical “tree-aspect” savannas and dry forests that are the natural habitats of the wild relatives of yam. Our objective was to study the AMF communities of natural savannas and adjacent yam fields in the Southern Guinea savanna of Benin. AMF were identified by morphotyping spores in the soil from the field sites and in AMF trap cultures with Sorghum bicolor and yam (Dioscorea rotundata and Dioscorea cayenensis) as bait plants. AMF species richness was higher in the savanna than in the yam-field soils (18–25 vs. 11–16 spp.), but similar for both ecosystems (29–36 spp.) according to the observations in trap cultures. Inoculation of trap cultures with soil sampled during the dry season led to high AMF root colonization, spore production, and species richness (overall 45 spp.) whereas inoculation with wet-season soil was inefficient (two spp. only). The use of D. cayenensis and D. rotundata as baits yielded 28 and 29 AMF species, respectively, and S. bicolor 37 species. AMF root colonization, however, was higher in yam than in sorghum (70–95 vs. 11–20%). After 8 months of trap culturing, the mycorrhizal yam had a higher tuber biomass than the nonmycorrhizal controls. The AMF actually colonizing D. rotundata roots in the field were also studied using a novel field sampling procedure for molecular analyses. Multiple phylotaxa were detected that corresponded with the spore morphotypes observed. It is, therefore, likely that the legacy of indigenous AMF from the natural savanna plays a crucial role for yam productivity, particularly in the low-input traditional farming systems prevailing in West Africa.     

Tuber formation and development of <Emphasis Type="Italic">Dioscorea cayenensis–Dioscorea rotundata</Emphasis> complex <Emphasis Type="Italic">in vitro</Emphasis> effect of polyamines

Tuberisation was obtained in vitro on yam (Dioscorea cayenensis–Dioscorea rotundata complex). The effect of exogenous polyamines on tuber formation and development (length and weight of microtubers) was investigated and discussed in relation with changes in endogenous polyamines. Application of exogenous polyamines, inhibitors of their metabolism, and polyamines precursors in various concentrations positively affected microtuber formation by yam nodal cuttings and their further development. In control conditions, 3 wk are needed to obtain 100% of tuberisation. With low concentrations of putrescine (10⁻⁵ or 10⁻⁶ M), tuber formation occurred earlier. Polyamine endogenous level and metabolism can be significantly affected by exogenous polyamines, but modifications of endogenous free polyamines could not be directly correlated to the tuber formation process. Increases in endogenous putrescine and auxins were observed in tubers showing a better development in the presence of putrescine. These results can be used for optimising in vitro conditions for mass production of larger microtubers of the D. cayenensis–D. rotundata complex.