Identification of some Benin Republic's Guinea yam (Dioscorea cayenensis/Dioscorea rotundata complex) cultivars using Randomly Amplified Polymorphic DNA

DNA from twenty-three late maturing cultivars of Guinea yams (D. cayenensis/D. rotundata complex) from the Benin Republic that could not be separated using isozyme markers, were examined using randomly amplified polymorphic DNA (RAPD) markers with decamer primers of arbitrary sequence. All the twelve primers tested were informative and yielded 63 amplified DNA bands from which 47 (75%) were polymorphic. Although no single primer produced polymorphic bands in all cultivars, the great majority of the cultivars were separated with the combinations of polymorphic bands generated by various primers. Putative duplicates and cultivar misclassifications were identified. Many morphologically distinct cultivars were close. The dwarf cultivar Tam-Sam considered as derived from Tabane, appeared more distant from the latter than was believed. RAPD analysis was found as a practical tool for the identification of duplicates toward establishment of an accurate core collection of Guinea yams in Benin Republic and in the other countries of the African yam belt.     

Using isozyme polymorphism to assess genetic variation within cultivated yams (Dioscorea cayenensis/Dioscorea rotundata complex) of the Republic of Benin

Four hundred and sixty-seven accessions of cultivated Guinea yam (Dioscorea cayenensis/Dioscorea rotundatacomplex) collected from different localities of Benin Republic were analysed to study isoenzymatic variability in seven enzyme systems: aspartate aminotransferase (AAT), esterase (EST), glucose-6-phosphate dehydrogenase (G6PDH), isocitrate dehydrogenase (IDH), phosphoglucomutase (PGM), phosphoglucoisomerase (PGI), and shikimate dehydrogenase (SKDH) using starch gel electrophoresis. Polymorphism was observed in all of the enzyme systems and a total of 62 electromorphs of different frequency and variability patterns were recorded. Different combinations of banding patterns of these systems led to identification of 227 different cultivars within the 467 accessions analysed. For an old and vegetatively propagated crop (with a considerable number of vernacular names) such as yam, and for which a high rate of duplication is expected, the 227 cultivars were found to be good enough to be considered as the adequate number of accessions representing the diversity in the germplasm analysed. Cluster analysis (UPGMA) produced a most likely division of the 467 accessions into two groups corresponding to D. rotundata Poir. and D. cayenensis Lam., supporting the concept that the two forms of guinea yam represent different genetic entities. The different clusters formed within the white yams (D. rotundata) did not exactly conform to the known cultivar groups. Additional polymorphic enzymes are needed for an accurate isozyme-based genetic discrimination of most of the cultivar groups.     

PCR Marker-based Analysis of Wild and Cultivated Yams (<Emphasis Type="Italic">Dioscorea</Emphasis> spp.) in Nigeria: Genetic Relationships and Implications for <Emphasis Type="Italic">ex situ</Emphasis> Conservation

Reliable characterization of the variation among wild and cultivated yams in Nigeria is essential for improved management and efficient utilization of yam genetic resources. RAPD and double stringency PCR (DS-PCR) analyses were used to investigate genetic relationships and the extent of redundancy among 30 accessions of two cultivated, and 35 accessions of four wild yam species collected from Nigeria. Twenty-five selected random decamer and two microsatellite primers were used individually and in combination to generate DNA profiles for each accession of the six Dioscorea species. The number of amplified fragments varied from 7 to 18 fragments per primer/primer combination. Different levels of intraspecific genetic diversity were found, with Dioscorea rotundata Poir. being the most variable. Based on identical profiles for the RAPD and DS-PCR primers, 12 duplication groups consisting of a total number of 37 accessions were observed in the present study. An UPGMA analysis grouped the majority of plants according to the species. Cultivated yams belonging to the D. cayenensis–rotundata species complex, which were classified into seven morphotypes/varietal groups, could be clearly separated into two major groups corresponding to D. rotundata Poir. and D. cayenensis Lam. D. cayenensis cultivars exhibited a low level of intraspecific variation and were genetically close to the wild species Dioscorea burkilliana J. Miège. D. rotundata cultivars classified into six varietal groups showed a high degree of DNA polymorphism and were separated into two major groups that appeared most closely related to Dioscorea praehensilis Benth. and Dioscorea liebrechtsiana de Wild. We propose, based on these results, that cultivars classified into D. cayenensis should be considered as a taxon separate from D. rotundata. The implications of intraspecific variability for the ex situ conservation of wild and cultivated yam germplasm in Nigeria are discussed.     

Diversity,conservation and related wild species of Fonio millet (<Emphasis Type="Italic">Digitaria</Emphasis> spp.) in the northwest of Benin

Fonio (Digitaria exilis (Kipp.) Stapf, white fonio; Digitaria iburua Stapf, black fonio), is one of the oldest native, but neglected, cereal crops of cultural, nutritional and economic importance of West Africa. To gather key information that will help to preserve its diversity in Benin and develop modern and well-adapted varieties that could meet both farmers’ and consumers’ needs, a participatory research appraisal survey was conducted in 15 villages randomly selected in the fonio production zone of Benin. Altogether 15 farmer-named landraces were recorded and further grouped into five morphotypes of which four belong to D. exilis and one to D. iburua. The number of landraces inventoried varied from one to five per village (three on average) and from one to three per household. Their distribution and extent are presented and their importance in terms of genetic resources conservation is discussed. Farmers’ preferences for fonio varieties were assessed and eight preference criteria (earliness, culinary characteristics, ease of processing, productivity, facility of harvesting, grains size, storability, and drought tolerance) were identified and prioritised according to the gender. The traditional seed supply system and on-farm seed maintenance were investigated. Two plant species (Digitaria horizontalis Willd. and Digitaria longiflora (Retz.) Pers.) were reported by farmers as putative parents of cultivated fonio. Of these, only Digitaria longiflora has interesting agronomic traits (erect habit; stem long, big, strong and resistant to lodging; panicle long and rich in grains; large sized seeds) that are useful for the improvement of cultivated fonio. In the entire study area, the crop is under threat. Therefore, concerted efforts should be deployed to preserve its diversity and increase its use to combat food insecurity and malnutrition in Benin.     

Ecogeographical distribution of wild, weedy and cultivated Sorghum bicolor (L.) Moench in Kenya: implications for conservation and crop-to-wild gene flow

The potential gene flow between a crop and its wild relatives is largely determined by the overlaps in their ecological and geographical distributions. Ecogeographical databases are therefore indispensable tools for the sustainable management of genetic resources. In order to expand our knowledge of Sorghum bicolor distribution in Kenya, we conducted in situ collections of wild, weedy and cultivated sorghum. Qualitative and quantitative morphological traits were measured for each sampled wild sorghum plant. Farmers’ knowledge relating to the management of sorghum varieties and autecology of wild sorghum was also obtained. Cluster analysis supports the existence of several wild sorghum morphotypes that might correspond to at least three of the five ecotypes recognized in Africa. Intermediate forms between wild and cultivated sorghum belonging to the S. bicolor ssp. drummondii are frequently found in predominantly sorghum growing areas. Crop-wild gene flow in sorghum is likely to occur in many agroecosystems of Kenya.     

The influence of European and American wild germplasm in hop (<Emphasis Type="Italic">Humulus lupulus</Emphasis> L.) cultivars

Microsatellite variation at the nuclear and chloroplast genomes was evaluated for wild European and wild American hops, in order to assess the genetic diversity and origin of cultivated hops. Seven nuclear loci and 32 chloroplast loci were used in the analysis of 182 hop accessions including wild European (68), wild American (48), and cultivars (66). A total of 116 alleles were identified using 7 nuclear microsatellites showing different averages of polymorphism and distribution in the wild American and European accessions and cultivars. Two main groups were established as revealed by several statistical analyses; one including European wild accessions and cultivars and a second group consisting of American wild accessions. Three polymorphic chloroplast microsatellite loci were detected, six alleles were scored which defined a total of five haplotypes that were exclusive or presented different distribution between American and European wild accessions. A major influence of the wild European haplotypes was detected among hop cultivars. To the best of our knowledge, this is the first work reporting the use of chloroplast microsatellites in hops.     

Genetic structure and differentiation among grapevines (<Emphasis Type="Italic">Vitis vinifera</Emphasis>) accessions from Maghreb region

Three gene pools representative of Vitis vinifera L. subsp. vinifera (=subsp. sativa Beger) growing in the Maghreb regions (North Africa) from Tunisia (44), Algeria (31) and Morocco (18) and 16 wild grape accessions (Vitis vinifera L. subsp. sylvestris (Gmelin) Beger) from Tunisia were analysed for genetic diversity and differentiation at twenty nuclear microsatellites markers distributed throughout the 19 grape chromosomes. 203 alleles with a mean number of 10.15 alleles per locus were observed in a total of 109 accessions. Genetic diversities were high in all populations with values ranging from 0.6775 (Moroccan cultivars) to 0.7254 (Tunisian cultivars). F _st pairwise values between cultivated grapevine populations were low but found to be significantly different from zero. High F _st pairwise values were shown between wild and cultivated compartments. Two parent offspring relationships, two synonyms and two clones of the same cultivar were detected. The rate of gene flow caused by vegetative dissemination of cultivated grapevine plants was not sufficient to genetically homogenise the pools of cultivars grown in different regions. The Neighbour Joining cluster analysis showed a clear separation according to geographical origins for the cultivated grapevines gene pools and revealed a high dissimilarity between cultivated and wild grapevine. However, three cultivars (Plant d’Ouchtata 1, Plant de Tabarka 3 and Plant d’Ouchtata 3) are very close to wild accessions and may result from a hybridisation between cultivated and wild accessions. The high level of differentiation between cultivated and wild accessions indicates that the cultivated accessions do not derive directly from local wild populations but could mostly correspond to imported materials introduced from others regions during historical times or derived from crossing between them.     

Genetic Diversity of the Greater Yam (<Emphasis Type="Italic">Dioscorea alata</Emphasis> L.) and Relatedness to <Emphasis Type="Italic">D. nummularia</Emphasis> Lam. and <Emphasis Type="Italic">D. transversa</Emphasis> Br. as Revealed with AFLP Markers

Amplified fragment length polymorphism markers were used to assess the genetic relatedness between Dioscorea alata and nine other edible Dioscorea. These species include D. abyssinica Hoch., D. bulbifera L., D. cayenensis-rotundata Lamk. et Poir., D. esculenta Burk., D. nummularia Lam., D. pentaphylla L., D. persimilis Prain. et Burk., D. transversa Br. and D. trifida L. Four successive studies were conducted with emphasis on the genetic relationship within D. alata and among species of the Enantiophyllum section from Vanuatu. Study 1 was carried out to select a set of polymorphic primer pairs using 11 combinations and eight species belonging to five distinct sections. The four most polymorphic primer pairs were used in study 2 among six species of the Enantiophyllum section. Study 3 focussed mainly on the genetic relationship among 83 accessions of D. alata, mostly from Vanuatu (78 acc.) but also from Benin, Guadeloupe, New Caledonia and Vietnam. The ploidy level of 53 accessions was determined and results indicated the presence of tetraploid, hexaploid and octoploid cultivars. Study 4, included 35 accessions of D. alata, D. nummularia and D. transversa and was conducted using two primer pairs to verify the taxonomical identity of the cultivars `langlang', `maro' and `netsar' from Vanuatu. The overall results indicated that each accession can be fingerprinted uniquely with AFLP. D. alata is an heterogeneous species which shares a common genetic background with D. nummularia and `langlang', `maro' and `netsar'. UPGMA cluster analysis revealed the existence of three major groups of genotypes within D. alata, each assembling accessions from distant geographical origins and different ploidy levels. The analysis also revealed that `langlang', `maro' and `netsar' clustered together with the cultivar `wael' (D. transversa) from New Caledonia. Results are discussed in the paper.     

Genetic diversity and relationships between wild and cultivated olives (<Emphasis Type="Italic">Olea europaea</Emphasis> L.) in Sardinia as assessed by SSR markers

The genetic relationships within and between wild and cultivated olives were examined and clarified in an isolated and restricted area, such as the Mediterranean island of Sardinia. Wild (21 individuals) and cultivated olive trees (22 local cultivars from a germplasm collection and 35 ancient trees) were genotyped by means of 13 SSR loci. Five cases of synonymy were observed and nine distinct genotypes were identified in the collection. Five novel genotypes were also detected among the ancient trees. Differences on the allelic composition and heterozygosity levels were found between wild and cultivated trees. Model-based clustering method classified the olive trees into two major gene pools: (a) wild genotypes and (b) local cultivars from the collection and from heritage olives. Regarding the cultivated plant material, we observed that: (a) most of the Sardinian cultivars shared the same allelic profiles with the ancient cultivated trees and (b) the majority of these cultivars and all the novel genotypes were not related to any other cultivars included in this study. These findings as well as the detection of unique alleles and a certain wild genetic background at some cultivars revealed by the Bayesian analysis may indicate their autochthonous origin. The synonymy cases found between local cultivars and Italian mainland cultivars indicate interchange of genetic material among these growing areas, suggesting thus a possible allochthonous origin. The information obtained can assist in the management of an olive collection and sheds some light on the survival of true oleasters and the origin of Sardinian cultivars.     

Diversity of cassava (Manihot esculenta Crantz) cultivars and its management in the department of Bouenza in the Republic of Congo

Cassava (Manihot esculenta Crantz) is one of the most produced and consumed food crops in the Republic of Congo. To assess the diversity and understand the traditional management of its cultivars in the department of Bouenza, twenty-one villages randomly selected from nine ethnic zones were surveyed using participatory rural appraisal. Altogether, 86 land races cultivars were recorded and further grouped into 36 types based on their agronomic and culinary characteristics. The number of cultivars accessed varied from 6 to 21 per village (13 on average) and from 1 to 11 (4 on average) per household. Their distribution and extent analysis revealed some worrying rates of cultivar loss in the range of 7.41–66.67% (32.06% on average) per village. The reasons of cultivars abandonment, the folk nomenclature and the traditional cutting supply system and planting techniques were documented and their importance in terms of genetic resources conservation and utilisation are discussed. Twenty farmers’ cultivar preference criteria were identified and prioritised. Their relative importances were examined across ethnic groups. Among them, the most important were yield, taste, cossette quality and root size which account for 72.39% of the total responses. The study revealed that most of the farmers did not consider the importance of the sexual reproduction in the cultivar diversification and the impact of cassava mosaic disease on the productivity of the infested plants. Awareness efforts and extension of the study to other cassava production zones were recommended for food security needs in Congo. To clarify synonym, morphological classification and molecular analysis were also suggested.     

Genetic Nature of Yams (Dioscorea sp.) Domesticated by Farmers in Benin (West Africa)

‘Domestication’ is a traditional farmers’ practice reported for yams (Dioscorea sp.) in Benin (West Africa). It involves introducing ‘spontaneous’ (naturally occurring) yams, supposedly wild (D. abyssinica and D. praehensilis), in varieties of the D. cayenensis–D. rotundata cultivated species complex. In this study, we established the genetic nature of ‘predomesticated’ yam plants using the amplified fragment length polymorphism (AFLP) technique. A total of 213 accessions, consisting of 32 predomesticated yams, 70 D. cayenensis–D. rotundata, 86 D. abyssinica and 25 D. praehensilis yams were analysed. Using 91 AFLP markers, three groups of accessions were distinguished, broadly corresponding to the above botanical species. Of the 32 predomesticated accessions, 16% were clustered with D. praehensilis, 37% with D. abyssinica and the remaining 47% with D. cayenensis–D. rotundata. These results demonstrated the use of wild plants by farmers in their domestication process, and suggested that plants derived from intervarietal and interspecific hybridisation may also be subject to this process. This study has shown that through domestication farmers influence and increase the genetic diversity in yam by using sexual reproduction of wild and possibly cultivated yams.     

The Weedy Rice Complex in Costa Rica. I. Morphological Study of Relationships Between Commercial Rice Varieties,Wild <Emphasis Type="Italic">Oryza</Emphasis> Relatives and Weedy Types

Weedy rice is a complex of Oryza morphotypes widely distributed in commercial rice fields, which interfere with rice cultivation, seed production, industrial processing and commercialization of this crop in several countries. The objective of this study was to characterize the weedy rice complex of Costa Rica by comparing it with the cultivated and wild rice species found in the country. A collection of weedy rice accessions, representative of the morphotypes found in the country, was established and characterized. Their morphometric relationships were established by comparing 27 morphological traits with commercial rice cultivars, landraces and wild Oryza species and by performing a multivariate analysis. Twenty-one weedy rice morphotypes were identified among 735 weedy accessions by using a three-digit code based on seed characters. Three principal components (PCs) explained 66.25% of the variation observed. The first PC accounted for 36.21% of the variation and separated CCDD genome type Oryza latifolia and O. grandiglumis from AA genome species O. sativa, O. glumaepatula, O. rufipogon and O. glaberrima. The second (18.9%) and third (11.14%) PCs separated the weedy morphotype groups from the AA genome species O.sativa, O. glaberrima and O. rufipogon. The weedy morphotypes were scattered between the indica commercial rice varieties, the cluster landraces–glaberrima and O. rufipogon. Additionally, a group of morphotypes showed intermediate characteristics between O. sativa and O. rufipogon, suggesting that hybridization could have taken place in the past between these species. None of the morphotypes collected in Costa Rica clustered with the allotetraploids CCDD species or O. glumaepatula.     

Traditional leafy vegetables and their use in the Benin Republic

Seventy-three villages randomly selected in 29 ethnic areas and three regions or agro-ecological zones of Benin were investigated by a participatory rural appraisal survey to assess the diversity of the species used as traditional leafy vegetables (TLVs). In total, 187 plant species belonging to 141 genera and 52 families were recorded. Among these, 47 (25.13%) were cultivated and 140 (74.87%) were gathered from the wild. Herbs (64.78%) were the most numerous followed by shrubs (19.78%) and trees (15.50%). The Shannon–Weaver diversity index calculated was 3.232. The total number of TLVs used highly varies, across ethnic groups, from 15 (Toli tribe) to 58 (people Mahi) with, on average, 36 species per ethnic group. The relative proportions of the wild and cultivated species used also vary with the tribes but on average appeared almost the same. Of the species inventoried, 18 of national importance were found among which Solanum macrocarpon, Corchorus olitorius, Amaranthus cruentus and Gymnanthemum amygdalinum ranked first. The matrix scoring technique yielded 12 criteria of different natures used to define preference. Among these, four (taste, ease of preparation, availability and quantity of required condiments) were the most important and represent, all together, more than 72% of responses. Despite the diversity of species used as leafy vegetables, they were all basically consumed in the same way. Sauces were the main type of preparation and involved all the species. The perceived nutritional and medicinal (curative, regulative and stimulative) properties of the species as well as their cultural significance were documented. Some TLVs are known and consumed by all or many ethnic groups while many others were simply ethnospecific or used by only a few peoples. However, no correlation was found between the distribution of the utilisation of the species and their degree of consumption which all depend on the eating habits of the peoples. Cluster analysis revealed that peoples sharing a common geographical space and/or cultural identity or origin seem to consume almost the same types of TLVs and cluster together. Given the large quantity of evidence of the importance of the TLVs, there should be a systematic effort to improve their understanding and their uses to reduce if not alleviate rural poverty and malnutrition in Benin.     

Spontaneous gene flow and population structure in wild and cultivated chicory, Cichorium intybus L.

Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted consequences. With the purpose to identify and quantify crop-wild gene flow in chicory, we analysed introgression in 19 wild chicory populations and 16 accessions of chicory varieties and landraces distributed across Northern, Central and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North–South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin. The results indicated, however, that the structuring between the two groups of wild and cultivated types was weak. As crop and wild recipients are genetically close and genes are transferred between the two types rather frequently, focus on mitigating crop-wild gene flow should be increased, before transgenic varieties are cultivated openly.     

Phaseolin diversity in wild Lima bean (Phaseolus lunatus L.) in American centres of origin

Summary Phaseolin variability was analyzed in 86 wild Phaseolus lunatus accessions, representing a wide geographical distribution from Mexico to Argentina, to determine geographical patterns of variability. The collection can be divided into two major groups. One group consists of accessions from Mexico, Central America, Cuba, Columbia, Argentina showing two Mesoamerican (M) phaseolin pattern types, already described in cultivated materials, as well as a variety of additional banding patterns. This suggests that at least two genotypes in the Mesoamerican gene pool were involved in a domestication process and spread throughout the world. The other group, consisting of wild Andean (A) forms from Northern Peru and belonging to the Andean gene pool, showed, among others, two A pattern types comparable to those found in cultivated large-seeded accessions.     

Evidence for two gene pools of the Lima bean,Phaseolus lunatus L., in the Americas

Summary The lima bean,Phaseolus lunatus L., is a bean species with a broad distribution in the Americas that rivals that of common bean (P. vulgaris). In order to better understand the organization of genetic diversity and the pattern of domestication in lima bean, a review was conducted of the available information on the geographic distribution of wild and cultivated forms of this species. In addition, one-dimensional SDS polyacrylamide gel electrophoresis of seed proteins was also conducted on a sample of 84 wild, 6 weedy, and 426 cultivated forms. Results show that wild forms can be divided into two groups, one with smaller seeds and a very extensive distribution that includes Mexico, Central America, and the eastern slope of the Andes, and the other with a more circumscribed distribution on the western slope of the Andes in Ecuador and northern Peru. Electrophoretic analyses of seed proteins confirmed this subdivision and, additionally, showed that the large-seeded cultivars had been domesticated from the large-seeded wild lima beans in western South America. For the small-seeded lima bean cultivars, it was not possible to determine a domestication center as the most abundant protein pattern in the cultivars also had a widespread distribution in the small-seeded wild progenitor. Electrophoretic analyses showed, however, that domestication led to a reduction of genetic diversity in the small-seeded, Mesoamerican group, but not in the large-seeded group. The latter may be due to insufficient sampling of the larger-seeded, wild germplasm.     

Intra-specific DNA polymorphism in pineapple (<Emphasis Type="Italic">Ananas comosus</Emphasis> (L.) Merr.) assessed by AFLP markers

Pineapple (Ananas comosus (L.) Merr.) cultivars, often derived from somatic mutations, are propagated vegetatively. It has been suggested by isozyme data that there is little genetic variation among Smooth Cayenne cultivars. A thorough investigation of the genetic variation within the cultivated speciesAnanas comosus, particularly among commercial cultivars, will provide critical information needed for crop improvement and cultivar protection. One-hundred and forty-eight accessions ofA. comosus and 14 accessions of related species were evaluated with AFLP markers. The average genetic similarity ofA. comosus was 0.735 ranging from 0.549 to 0.972, suggesting a high degree of genetic variation within this species. With AFLP markers, discrete DNA fingerprints were detected for each commercial cultivar, breeding line, and intra-specific hybrid. Self-incompatibility, high levels of somatic mutation, and intraspecific hybridization may account for this high degree of variation. However, major cultivar groups of pineapple, such as Cayenne, Spanish, and Queen, could not be distinctively separated. These cultivar groups are based on morphological similarity, and the similar appearance can be caused by a few mutations that occurred on different genetic background. Our results suggest that there is abundant genetic variation within existing pineapple germplasm for selection, and discrete DNA fingerprinting patterns for commercial cultivars can be detected for cultivar protection. The genetic diversity and relationships of fourAnanas species are also discussed.