Plant genetic resources in a touristic island: the case of Lefkada (Ionian Islands, Greece)

Lefkada is one of the islands of the Ionian Sea and disposes interesting biodiversity both in crop landraces and in wild relatives. It is also one of the most famous touristic attractions in the Eastern Mediterranean basin, thus traditional agriculture is under great pressure from tourism. Nevertheless, Lefkada’s mountainous relief has apparently preserved some diversity of landraces in upland villages. A collecting expedition was organized in September 2010 and a second (minor) in 2012 in order to assess the current status of landraces in a touristic island such as Lefkada. The results are discussed and compared with previous expeditions in the island. Landraces still cultivated, others that are considered lost, and information about their traditional uses are presented. Finally, the potential for the exploitation of landraces in Lefkada’s touristic environment is discussed.     

Genetic, morphological and cyanogen content evaluation of a new collection of Caribbean Lima bean (Phaseolus lunatus L.) landraces

Lima bean is a species cultivated broadly in the Americas and has been cultivated in the Caribbean for at least 500 years. In order to determine the genetic structure and diversity of Lima bean from the Caribbean, 50 landraces from Haiti, the Dominican Republic and Puerto Rico were collected and analyzed using 24 SSR markers. All landraces in this Caribbean collection were found to be of Middle-American descent. The genetic diversity (H_E) was highest in the landraces from Puerto Rico and lowest in Haitian landraces. The observed proportion of heterozygotes (H_O) was higher in the Haitian landraces and lowest in Puerto Rican landraces. Unweighted pair-group method with arithmetic averaging analysis showed that the landraces clustered into 3 clusters with all Haitian landraces grouping in one cluster. We also assessed the agro-morphological characteristics of the collection as well as the content of cyanogenic glucoside, linamarin, in leaves and dry seeds. Lima bean, which is a model crop for indirect plant defenses against herbivory, also possess linamarin as a source of direct plant defense. Upon tissue damage, linamarin is converted to toxic hydrogen cyanide. In our collection 44.6 % of the landraces had average seed HCN content ≤200 ppm which is the permitted level for Lima bean seed in the US. Our results also identified the landraces in this collection which have high linamarin levels in the leaves while having low levels in the seeds. Such landraces have the desirable combination of traits and will be the focus of our future plans for agronomic trait improvement though breeding.     

RAPD Polymorphism of the White-Flowered Gourd (Lagenaria siceraria (Molina) Standl. Landraces and its Wild Relatives in Kenya

The present study was performed to investigate genetic diversity of Kenyan landraces of the white-flowered gourd (Lagenaria siceraria), which exhibits tremendous morphological variation. RAPD analyses were performed on 53 landraces of the cultivated species L. siceraria and 42 accessions of three wild species (40 L. sphaerica, 1 L. abyssinica, and 1 L. breviflora). A total of 432 polymorphic bands were detected using 54 primers. The four species were clearly differentiated from one another. Intra-specific variations were investigated with L. siceraria and its wild relative L. sphaerica. Landraces of the cultivated species collected from different ethnic communities or regions were differentiated. Morphological variations were not associated with RAPD variations. Bitter landraces collected in Maasai communities showed two specific RAPD bands. In the wild species, accessions collected from the eastern and western sides of the Great Rift Valley were genetically differentiated from each other. In both species, genetic and geographical distance matrices computed among all pairs of accessions were significantly correlated, implying that the observed geographical variation can be explained by the 'Isolation by distance model'. Progeny plants derived from a common mother in L. siceraria showed a low level of segregation in RAPD pattern, suggesting that collected landraces are cultivated, maintaining their inherent traits although they are monoecious and insect-pollinated, whereas the wild relative L. sphaerica showed a higher level of segregation. The morphological diversity observed among landraces of L. siceraria is the result of human selection and their genetic identities are maintained by inbreeding probably resulting from frequent self-pollination.     

Diversity of common bean (Phaseolus vulgaris L.) germplasm from Portugal

Common bean (Phaseolus vulgarisL.) is a traditional crop in Portugal, where farmers growvarieties selected and maintained by themselves. A collection of 88landraces of common bean was evaluated for 17 quantitative andqualitative traits and the biochemical marker phaseolin to displaythe degree of variation of this germplasm. Agronomic data weresubjected to cluster analysis and several groups were identified,with three groups clustering most of the landraces. Regardingphaseolin variation the C and T banding patterns are the mostfrequent ones, so the origin of the Portuguese beans is thus probablythe Andean region of South America. These results give informationabout the origin, diversity and breeding value of the Portuguesegermplasm, that could be useful to widen the genetic base ofcurrently cultivated bean varieties in Europe.     

Genetic diversity of Spanish Cucurbita pepo landraces: an unexploited resource for summer squash breeding

Cucurbita pepo is a worldwide cultivated vegetable of American origin. Most of the widely grown commercial types are known as summer squashes and belong to the elongated forms of C. pepo ssp. pepo (Cocozelle, Vegetable marrow and Zucchini groups). These forms were developed in Europe after the arrival of the first American landraces through a process of selection and fixation that led to a loss of genetic diversity. Part of the genetic variability of the first American cultigens remains intact in diverse landraces that are still cultivated for self-consumption and sale in local markets. Using the first collection of genomic and EST-derived microsatellites that has just become available for the species, we compared the natural variation present in a collection of Spanish landraces with that of a set of commercial varieties and hybrids, representing current summer squash market offerings. A total of 194 alleles allowed us to distinguish all the genotypes, even those that were closely related. In general, Cocozelle and Vegetable marrow, groups with considerably long histories, were more variable than the Zucchini group, of more recent origin. We found significant genetic diversity among landraces. The variation present among landraces belonging to the Zucchini group was larger than that of the commercial cultivars. Cluster, principal coordinate and population structure results suggested that the variation of the Spanish landraces has not been extensively used in breeding. Commercial summer squashes can therefore benefit from this underexploited variability, especially from certain landraces that already display favourable commercial traits.     

Genetic erosion and in situ conservation of Lima bean (Phaseolus lunatus L.) landraces in its Mesoamerican diversity center

Lima bean (Phaseolus lunatus L.) is an important crop in traditional Mayan agriculture of the Yucatan Peninsula, Mexico, its Mesoamerican center of diversity. Genetic erosion in this species is currently a threat in this region out of 3 of 21 landraces dominate 71.24% of the cultivated area, and 12 are rare landraces grown only in 6.29%. Using 90 ISSR loci, we estimated the diversity and genetic relationships for 21 landraces to analyzing their risk of genetic erosion, and generate data for their in situ conservation. Total genetic diversity was high (h = 0.29), however it was lower than wild gene pool reported (h = 0.69). The abundant landraces had genetic diversity values lower (h = 0.13, I = 0.17) than the common (h = 0.26, I = 0.33) and rare landraces (h = 0.24, I = 0.27). However, the rare landraces are in a higher risk of genetic erosion due to local extinction. The cluster analysis showed no groups corresponding to morpho-phenological characteristics, geographic origin or traditional classification, which resulted from high inter-landraces gene flow levels. The molecular data confirmed that the domesticated Lima bean pool of the Yucatan Peninsula has a high risk of genetic erosion. If current tendencies in landrace cultivation continue, many will no longer be planted within two to three generations, with a consequent loss of their alleles. Programs urgently need to be established for in situ conservation of Lima bean landraces in this region.     

Geographic variation in tetraploid wheat (Triticum turgidum spp. turgidum convar. durum) landraces from two provinces in Ethiopia

There is considerable wealth of genetical and morphological variation in tetraploid wheat collected from Ethiopia by past expeditions. Several authors have speculated on the reasons for this concentration of diversity so far removed from the centre of origin of wheats in West Asia. The present study reports results of evaluation carried out on material collected in the early 1970's from Ethiopia. The landraces from the two provinces Shewa and Tigray were found to be distinctly different. This divergence was attributed to the differences in environmental conditions between them. Wide differentiation among landraces within each province was also present. The Ethiopian farmer's practice of growing composite cultivars in the field has resulted in bulk samples of Ethiopian landraces containing several agrotypes. The proportion of total variance due to differences among agrotypes within landraces was by far the greatest found in this study, followed in most cases by the variation among landrace populations within provinces which exceeded, in turn, the variation between province gene pools. The optimal strategy for further germplasm collections and implications for improvement and conservation in locally-based community gene banks are discussed.     

Market-based incentives for conserving diversity on farms: the case of rice landraces in Central Tarai,Nepal

Market-based incentives are one means of encouraging farmers to grow landraces that are also of social value, thereby contributing to the conservation of crop genetic diversity on farms – and in principle, the cheapest. This study uses a participatory, market systems approach supplemented by baseline data from an ongoing project to analyze markets for rice landraces and modern varieties in Nepal. Nepal is located in the area of origin and diversity for Asian rice. With the exception of traditional Basmati rice (which is of high aromatic quality), most rice landraces are traded through small-scale informal channels. Traders earn higher profits handling modern varieties than landraces, with the exception of Basmati, which competes with modern varieties. The superior consumption qualities of Basmati are valued in markets, but conserving these landraces may not have great social value. Furthermore, farmers who grow Basmati are clearly better off than those who do not. Findings raise questions about the role of market-based incentives for conserving landraces on farms, the costs entailed in establishing a structure to generate them, and about efficiency vs. equity considerations in the design of conservation programs.     

Genetic diversity in Chinese sorghum landraces revealed by chloroplast simple sequence repeats

A collection of sorghum, including more than 12,000 Chinese landraces, has been constructed and maintained in China. However, the genetic diversity of Chinese sorghum landraces has not been fully investigated, and the origin of Chinese sorghum is still in dispute. In this study, the complete chloroplast genome sequence of sorghum line Tx623B was searched for simple sequence repeats (SSRs). 31 SSR loci with at least 10 mononucleotide repeats or five dinucleotide repeats were identified, and primer pairs for 27 loci were designed. Chloroplast DNA variation in cultivated sorghum was investigated by using these primer pairs on 185 Chinese sorghum landraces and 70 cultivated sorghum accessions from other countries. Among the 27 loci, 14 were polymorphic. The number of alleles per polymorphic locus ranged from 2 to 5 with an average of 2.79. Allelic data at 14 polymorphic loci were combined to give 12 haplotypes. The average allelic diversity index across the 14 polymorphic loci and corresponding haplotype diversity were markedly lower for Chinese sorghum landraces than were those for accessions from other countries. However, Chinese sorghum landraces shared a predominant allele at each polymorphic locus and a predominant haplotype with foreign accessions. Our results indicate that Chinese landraces experienced a severe maternal bottleneck during the introduction process with a predominant haplotype being present in 171 of 185 accessions analyzed. Except for one rare exception, haplotypes found in Chinese landraces were either identical or closely related to those found in foreign accessions and could not be separated clearly from them by cluster analysis. Our results are consistent with the hypothesis of African origin of Chinese sorghum.     

Genetic diversity analysis of yams (Dioscorea spp.) cultivated in China using ISSR and SRAP markers

Yam (Dioscorea spp.) is widely cultivated in China and many landraces are maintained by local farmers. However, there is little information available about their diversity and species identity. In this study, inter simple sequence repeat (ISSR) and sequence related amplified polymorphism (SRAP) techniques were used to assess genetic diversity within 21 yam landraces from seven cultivated populations. We observed high level of polymorphism among these landraces, specifically, 95.3 % for ISSR and 93.5 % for SRAP. Analysis of molecular variance revealed a significantly greater variation among the four yam species (40.39 %) and their populations (35.78 %) than within the populations (23.83 %). The unweighted pair group method arithmetic averages clusters and principal component analysis for 21 landraces formed four well-separated groups containing landraces of each of the four species, namely, Dioscorea opposita Thunb., Dioscorea alata L., Dioscorea persimilis Prain et Burkill, and Dioscorea fordii Prain et Burkill. The ISSR and SRAP primers were highly discriminatory among the 21 landraces; all 21 landraces could be easily differentiated using these primers. The average mean of gene flow (Nm = 0.1081) estimated from high genetic differentiation (Gst = 0.8222) suggested that gene flow among the populations was relatively restricted. The lack of genetic diversity within individual yam species suggests that it is critical to develop long-term strategies for enhancing genetic diversity within various yam species.     

Agro-morphological diversity of Spanish traditional melons (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) of the Madrid provenance

The variability of 14 landraces belonging to a Madrilean village historically specialized on melon cultivation, Villaconejos, was evaluated based on 58 quantitative and qualitative morphological traits. These landraces were compared to a reference array composed of 14 accessions which represented the main varieties cultivated in Spanish fields. Individual data related to plant, fruit, seed and phenology have been analysed using a multivariate analysis. This analysis showed intra- and inter-varietal diversity, as emphasized the most discriminant morphological traits in order to define similarities. Villaconejos accessions were morphologically distinct from the reference accessions (RA). Only the landraces belonging to Piel de Sapo market class showed common morphological affinities with the RA, grouping with them. The majority of Villaconejos traditional varieties clustered in five different groups, with no RA within, showing distinctive morphological singularities not described previously. Two of these groups showed some particularities in fruit traits, which are appreciated as quality marks for Spanish consumers. These results indicate that these accessions must be conserved as valuable genetic resources to enrich the Inodorus genetic bases for future breeding proposes worldwide. Furthermore, it should be considered the opportunity of promoting their cultivation under the shelter of a Protected Geographical Indication as a high quality melon. Finally, the discovering of such a high variability presented in a very small area, gives a clue for focusing, with an elevated probability of success, future surveys in similar ancestral European villages which in the past times, also supplied more populated cities with their farming products.     

Estimating genetic erosion in landraces — two case studies

Summary The results of collecting missions in Albania in 1941 and 1993 and in South Italy in 1950 and in the eighties allowed a comparison to be made of the material cultivated. The number of landraces still cultivated recently, as compared to their former number, was the basis for the estimation of genetic erosion. Genetic erosion (GE) was calculated as GE=100%-GI (Genetic integrity). Genetic erosion was found to be 72.4% in Albania and 72.8% in South Italy, respectively. These results prove the high degree of genetic erosion in landraces from different parts of the Mediterranean area. Apart from the economic conditions, several other factors are responsible for genetic erosion, among them breeding system, crop type (i.e., garden or field crop) and crop group (e.g., cereals, vegetables and pulses).The results show that in the areas investigated there are still landraces for in situ conservation. Ex situ conservation in genebanks proved to be a possibility. An integration process is necessary to prevent losses in crops which are difficult to propagate under ex situ conditions. The complementarity of both conservation methods is stressed.     

Genetic diversity of potato landraces from northwestern Argentina assessed with simple sequence repeats (SSRs)

Andean potato varieties are cultivated in the northwest of Argentina and constitute the most important staple food for the local farmers. The genetic diversity of 155 accessions conserved at the Genebank of Balcarce (INTA) was tested using four microsatellites. Three commercial potato varieties of Tuberosum group and one accession of Curtilobum group were used as outgroups. The presence of bands was scored for each microsatellite and for each accession and the data were analysed by principal coordinate analysis. The polymorphism information content was obtained for each molecular marker from banding patterns. Analysis of molecular variance was carried out with a variable number of accessions for each landrace, from different departments and sites within departments. More than one genotype was detected in the majority of the potato landraces. Some accessions within each landrace did not differentiate. AMOVA revealed that most of the genetic variation occurred among sites within departments and among local varieties. These findings are discussed considering the agricultural practices carried out in the Andean farming system.     

AFLP analysis of genetic diversity in five accessions of Polish runner bean (<Emphasis Type="Italic">Phaseolus coccineus</Emphasis> L.)

Runner bean (Phaseolus coccineus L.) is traditionally cultivated in Poland for dry seeds. The national collection of runner bean maintained in the National Center for Plant Genetic Resources gathers 152 accessions, which are mainly landraces originated in Poland (68%), Ukraine (17%) and Slovakia (10%). The collection contains valuable genetic resources for bean breeders and research. The aim of this study was to describe the level and structure of genetic diversity of three landraces and two commercial cultivars of runner bean from the national collection in order to assess their genetic potential for breeding. Amplified Fragment Length Polymorphism analysis included five combinations of selective primers. Analysis of seven genetic diversity parameters reveled fair amount of genetic variation both in landraces and cultivars. High genetic diversity of commercial cultivars relative those of landraces suggests that the breeding process leading to their release was rather moderate and most likely included domestic gene pool of runner bean. Low gene diversity and low Nei’s genetic distance values as well as intergradations among accessions in the PCoA may indicate reduced variability P. coccineus grown in Poland as a result of its migration pathways.     

Sustainability of the traditional management of Agave genetic resources in the elaboration of mezcal and tequila spirits in western Mexico

Over the last 30 years, cultivation of Agave tequilana Weber var blue for industrial production of tequila, has generated soil erosion, chemical pollution, displacement of traditional food crops and traditional Agave landraces used for preparing “mezcals” in the Appellation of Origin Tequila area. It is also associated with harmful cycles 8–10 years long of surplus-shortfall availability of raw material. Mezcal is the common traditional name given in Mexico to spirits like tequila, prepared with Agave tissue. We examined the traditional strategies of management of the Agave genetic resources for elaborating mezcal and tequila spirits by people of southern Jalisco, Mexico, analyzing the bases of their sustainable management, compared with management of the industrial tequila system. We found that mezcal spirits are prepared with different landraces of A. angustifolia Haw. and A. rhodacantha Trel. which are cultivated as living fences within the “milpa”, the traditional Mesoamerican multi-crop system. The whole system allows simultaneous production of agricultural, livestock and forest resources, permitting the adjustment of mezcal production to demand. Agave borders and terraces are laid out perpendicular to slopes to increase rainfall capture and filtration, and decrease soil erosion. The high species richness creates niche heterogeneity, substantially reducing pest and disease incidence. Genetic and morphological analyses indicated that traditional management and selection of A. angustifolia landraces have produced high genetic diversity (H_BT = 0.438 ± 0.003) and structure (θ^B = 0.408) when compared with wild populations (H_BT = 0.428 ± 0.015; θ^B = 0.212). Morphological differentiation is associated to artificial selection pressures. Differential precocity of Agave landraces and scaled planting favors continuous, year round spirit production. Growers directly market their mezcals, and a portion of the profits is reinvested in the parcel to ensure system continuity. The technological advantages of the traditional mezcal system could attenuate some challenges caused by the tequila industrial agriculture.     

AFLP analysis of genetic diversity in leafy kale (<Emphasis Type="Italic">Brassica oleracea</Emphasis> L. convar. <Emphasis Type="Italic">acephala</Emphasis> (DC.) Alef.) landraces,cultivars and wild populations in Europe

AFLP markers were used to characterize diversity and asses the genetic structure among 17 accessions of kale landraces, cultivars and wild populations from Europe. The range of average gene diversity in accessions was 0.11–0.27. Several landraces showed higher levels of diversity than the wild populations and one cultivar had the lowest diversity measures. The landraces that were most genetically diverse were from areas where kales are known to be extensively grown, suggesting in situ conservation in these areas as a supplement to storage of seeds in gene banks. An analysis of molecular variance (AMOVA) showed that 62% of the total variation was found within accessions. For most accessions, genetic distance was not related to geographic distance. Similarities among accessions were probably not caused by recent gene flow since they were widely separated geographically; more likely the relationship among them is due to seed dispersal through human interactions. Our results indicate that a kale population found in a natural habitat in Denmark was probably not truly wild but most likely an escape from a cultivated Danish kale that had subsequently become naturalized.     

Exploring the population genetics of genebank and historical landrace varieties

Landrace accessions have long been recognized as an important source of genetic diversity for crop species, and landraces are stored in genebanks across the world as genetic resources for future crop development. Landraces are also an important part of the human cultural heritage and as such they have been used for genetic studies to make inferences about historical agriculture. However, surprisingly little is known about the within-accession diversity of landrace crops of different species. In order to evaluate the diversity of Swedish landraces we used microsatellite markers to genotype accessions of four species (barley, pea, oats and rye), both extant genebank material and 114-year-old seed samples of similar geographic origin and type. We found consistently high levels of within-population genetic diversity in the historical material, but varying and often lower diversity levels in the genebank accessions. We also make tentative conclusions about how representative the genebank material is to what was originally cultivated in its reported area of origin and suggest that the true identity of the genebank accessions is unclear and that historical seed collections should be a more appropriate material for the study of historical agriculture.     

Diversity characterisation of broccoli (Brassica oleracea L. var. italica Plenck) landraces for their on-farm (in situ) safeguard and use in breeding programs

Brassica oleracea L. is an important species that originated in the eastern Mediterranean area. From there, B. oleracea L. subsp. capitata (L.) DC. convar. botrytis (L.) Alef. var. italica Plenck (broccoli) was introduced into Italy where considerable diversification took place. Several landraces of broccoli, which are highly appreciated by local people for their organoleptic traits, are presently cultivated in both large fields and home gardens. In this study, 10 landraces, 4 synthetics derived from landraces and 4 of the most used F1 hybrids were characterised for morpho-physiological and molecular traits with the principal aim of feeding information into the landrace protection schemes being developed in Italy and into breeding programs. The landraces and derived synthetics are well differentiated from each other and from the F1 hybrids for important agronomic and genetic traits. The principal component analysis based on analysis of morpho-physiological traits showed that overall the 2 main components accounted for 67.74 % of the total variation. The neighbour joining tree, based on 23 microsatellite markers, grouped accessions into 2 main clusters. One includes one synthetic variety and 2 F1 hybrids, while the other cluster includes all the other accessions. There were also several sub clusters. Most of the materials examined showed within-accession diversity. The information gathered in this study can be used to protect landraces through the schemes presently being developed in Italy and to register them in the European common catalogue of “conservation varieties”. In situ (on-farm) conservation of landrace diversity is discussed with reference to landrace use.     

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.     

Origin of cultivated Tatary buckwheat (Fagopyrum tataricum Gaertn.) revealed by RAPD analyses

The phylogenetic relationships among cultivated landraces and natural populations of wild subspecies of Tatary buckwheat were investigated at the individual level by constructing a phylogenetic tree based on RAPD markers. As the PCR templates, DNA of individuals rather than bulked samples, was used. Ten individuals from 10 cultivated landraces, 71 individuals from 21 natural populations of wild subspecies, and 7 individuals from 3 weedy Tatary buckwheat were provided for RAPD analyses. Three groups were recognized: (1) all cultivated landraces and wild subspecies from central Tibet and northern Pakistan; (2) 10 individuals of wild subspecies from northwestern Yunnan; (3) the remaining individuals of wild subspecies from northwestern Yunnan and all individuals of wild subspecies from Sichuan. Group (2) was phylogenetically closely related to group (1). The origin of cultivated Tatary buckwheat, the hybrid origin of weedy Tatary buckwheat and of the wild populations from central Tibet and northern Pakistan are discussed. We arrive at the conclusion that cultivated Tatary buckwheat probably originated in northwestern Yunnan in China.