Spatial and temporal dynamics in genetic diversity in upland rice and late millet (<Emphasis Type="Italic">Pennisetum glaucum</Emphasis> (L.) R. Br.) in The Gambia

Ambiguity exists about the level of genetic diversity represented by farmer crop varieties, how it develops over time and how it relates to the diversity comprised by formal varieties. As part of an interdisciplinary technological/sociological study on farmer management of gene flow, upland rice (Oryza sativa L.) and late millet (Pennisetum glaucum (L.) R.Br.) from The Gambia were investigated for morphological and molecular variation. The goal of these analyses was to obtain insight into the level of crop genetic diversity of farmer’s materials planted in several case study villages in The Gambia. For both crops, samples were collected from villages and various research institutes. Based on variety names, different rice and millet varieties were expected to be used in different villages. In fact, there was a large overlap in genetic diversity for both crops, masked by the use of synonyms. The considerable similarity in rice genetic diversity between villages most likely results from the exchange of varieties between farmers. For millet this seems the result of development of varieties from the same gene pool. Some farmer varieties of rice, however, are apparent hybrid forms between the species O. sativa and O. glaberrima Steud., and farmer varieties in general displayed higher levels of genetic diversity than formal varieties. This indicates that, for rice, genetic diversity develops in farmers’ fields and may have potential use in formal breeding programs.     

Diversity in Phenotypic Profiles in Landrace Populations of Vietnamese Rice: A Case Study of Agronomic Characters for Conserving Crop Genetic Diversity on Farm

Phenotypic variation of agronomic characters in aromatic rice (Oryza sativa L.) was analyzed in order to elucidate the genetic diversity of the populations of rice landraces. Thirteen populations in Namdinh province, in the Red River Delta of Vietnam, were studied in both of farmers fields and an experimental field. Only small differences were found in agronomic characters among the populations, including populations containing different varieties. Variations among the populations in the frequency distributions of several characters suggested different degrees of diversity among the populations even among populations with the same variety name. The phenotypic profiles of farmers fields were different from those in an experimental field suggesting the environmental differences between them. One variety cultivated in the Myloc district had different phenotypic characters from the other varieties in the Haihau district more clearly in the experimental field. Since the small phenotypic variation in each of farm might be due to the genetic drift and selection by the farmers, on farm conservation of the landraces of rice is considered to be under a force to decrease phenotypic diversity. The present study suggests that the targeting several farms with different phenotypic profiles contribute to the conservation of regional genetic diversity of the landraces of rice.     

The dynamics of spatial and temporal population genetic structure of weedy rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> f. <Emphasis Type="Italic">spontanea</Emphasis> Baker)

Weedy rice (Oryza sativa f. spontanea Baker) is one of the most serious weeds in direct-seeded rice production; adversely affecting rice areas and yield in Thailand. The objectives of this study were to evaluate the level of morphological and agronomical variation and the level and pattern of genetic diversity and population structure of weedy rice populations in Thailand. Sixty-three weedy rice populations collected from three rice production areas of Thailand were sampled over four rice cultivation seasons to study phenotypic characteristics, genetic diversity and population structure. All analysis included comparison with seven cultivated rice varieties and seven local common wild rice populations. The results demonstrated considerable genetic and morphological variation, population structure, and changing dynamics of Thai weedy rice populations, both within and between regions and growing seasons. Phenotypic and genotypic variations and population structure of weedy rice populations changed temporally, with a trend over five years toward greater similarity to companion crop rice varieties. The ongoing gene flow, combined with ecological conditions created by farmers’ selection and agronomic practices, may enhance fitness and adaptability of weedy rice populations and stimulate the evolution of invasiveness in weedy rice plants. The adaptive evolution of weedy rice tended to parallel cultivated rice for high adaptation to the agronomic practices, possibly including selection for crop mimicry, which has led to the convergence of weedy populations phenotypically and genetically with the companion crop rice.     

Characterisation and Variation of Morphological Traits and Storage Proteins in Spanish Emmer Wheat Germplasm (<Emphasis Type="Italic">Triticum Dicoccon</Emphasis>)

Emmer wheat is hulled wheat that was wide cultivated in Spain at the past. Actually, the most of this germplasm is conserved in Germplasm Banks, and only two small populations have been found in Asturias (North of Spain) in a recent collecting mission. In this work, a collection of 31 Spanish emmer lines developed from identical number of accessions of two Germplasm Banks was analysed for morphological spike traits and seed storage protein composition. Up to seven different botanical varieties were detected, which suggest the presence of a wide diversity, although lower than the historically described 10 botanical varieties. At level of seed storage proteins, the lines showed a high diversity, although the new alleles were present with low frequency in materials with scarce agronomic interest for the farmers (var. atratum, var. lagascae or var. pycnurum). This last circumstance could translate in a lost of variability by genetic drift.     

A study of genetic diversity of sesame (<Emphasis Type="Italic">Sesamum indicum</Emphasis> L.) in Vietnam and Cambodia estimated by RAPD markers

Sesame (Sesamum indicum L.) is a traditional oil crop cultivated throughout South East Asia. To estimate the genetic diversity of this crop in parts at the region, 22 sesame accessions collected in Vietnam and Cambodia were analyzed using 10 RAPD markers. The 10 primers generated 107 amplification products of which 88 were polymorphic fragments (83%). Genetic diversity of all populations was H_t = 0.34 when estimated by Nei’s genetic diversity and species diversity was H′_sp = 0.513 when estimated by Shannon diversity index. Genetic distance ranged from 0.03 to 0.43, with a mean genetic distance of 0.23. The unweighted pair group method with arithmetic averages (UPGMA) cluster analysis for the 22 accessions divided the material in four groups. The dendrogram revealed a clear division among the sesame accessions based on their geographical region. Interestingly, some geographically distant accessions clustered in the same group, which might indicate the human factor involved in the spreading of sesame varieties. The high level of polymorphism shown suggests that RAPD techniques can also be useful for the selection of parents in sesame (Sesamum indicum L.) breeding program and for cultivar differentiation.     

Molecular differentiation,diversity, and folk classification of “sweet” and “bitter” cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis>) in Caiçara and Caboclo management systems (Brazil)

This study focuses the inter-relationships among the men, the use, and the intra-specific cassava diversity, under the perspective of this crop evolutionary dynamics. The origin, the use and the current local management of varieties with high and low cyanogenic potential are important questions around cassava domestication. We collected 169 local varieties identified as “sweet” or “bitter” cassava by traditional farmers from Atlantic Forest and Amazon (Medium Negro River Basin), Brazil. Using a population genetics and an ethnobotany approach, the diversity and the genetic structure of cassava were evaluated. We found a total of 115 vernacular names, and in the Atlantic Forest sample the average genetic diversity (H _S = 0.654) was higher for the sweet varieties than for bitter ones (0.582). The genetic differentiation coefficient (R _ST), used to estimate the diversity among groups, was 0.057 (P < 0.001), indicating that the divergence between the two groups is low. We obtained a low correlation between the morphological and genetic distances, and the congruence was high when the ethnoclassification and the genetic structure were considered. We discuss the adaptive advantages of the sweet varieties use, the current socio-economic changes in bitter varieties use, and the ecological history of these variety groups.     

The diversity and sustainable development of crop genetic resources in the Lancang River Valley

This paper reviews the status of crop genetic resources in Yunnan province of China from 1978 to 1999. Results are presented of same research in the field of the diversity of cultivated and wild crop. Yunnan is one of the centre of origin or genetic diversity of more than 200 cultivated and wild crops. There are over 500 cultivated plants which account for over 80% of the total in China and more than 650 species of wild crops. In addition, there are more than 440 species of main wild flowers. According to our recently researches there are abundant species, subspecies and varieties of crop genetic resources in Yunnan Province. The Lancang River Valley is the richest genetic diversity centre of rice, maize, wheat, barley, buckwheat, legumes, ramie, sugarcane, vegetable, tea, actinidia and so on. For example, there are 59 varieties (including all varieties of Oryza sativa L. in China) in 5933 accession of Yunnan indigenous rice. The Lancang River Valley is one of the centre for genetic diversity of rice resources and a rich region for elite and rare rice resources of Yunnan, too. In order to protect the highly endangered crop genetic resources in the Lancang River Valley, it is necessary and very important to set up a collection, conservation, utilization and research system, enhancing their protection and utilization, in situ- and ex situ-conservation, farm management and sustainable production.     

Genetic Variation and Population Structure in a Eurasian Collection of <Emphasis Type="Italic">Isatis tinctoria</Emphasis> L.

Isatis tinctoria L. is a biennial species which was cultivated in Europe until the 18th century to produce indigo, a pigment used for dyestuffs. Today there is renewed interest in this ancient crop because of a market demand for natural dyes. Cultivation of the species appears to be particularly suitable for marginal areas. Information about the evolutionary and genetic patterns of I. tinctoria is needed if varieties or to be developed in future breeding programs. The aim of this study was to assess the genetic variation and similarity levels among and within natural populations of I. tinctoria from Europe and central Asia. Fifteen populations were used to carry out the genetic analyses with AFLP and SAMPL molecular markers. Data collected were analysed by the UPGMA method and were used to perform AMOVA. The results are consistent with the hypothesis that the crop originated in an eastern centre of origin and moved westward giving rise to a gene pool that is quite different from the original. The wide within-population variation revealed by this study suggests that effective breeding work to develop varieties suitable for marginal environments can be carried out easily.     

Origin and evolution of Chinese waxy maize: evidence from the <Emphasis Type="Italic">Globulin-1</Emphasis> gene

Waxy maize is a special type of cultivated maize and has grown in China for long history. However, the evolution and origin of waxy maize still remain unknown. We analyzed the origin and evolution of waxy maize by sampling DNA sequences from four taxa with eight populations: waxy maize and other maize cultivars from Southwest China or America (Zea mays L. ssp. mays), parviglumis (Z. mays L. ssp. parviglumis Iltis et Doebley), three more distant species within this genus (Z. luxurians (Durieu et Ascherson) Bird, Zea perennis (Hitchcock) Reeves et Mangelsdorf, and Zea diploperennis Iltis, Doebley et Guzman), and a representative of sister genus (Tripsacum dactyloides L.). We sequenced 20 sequences and downloaded 26 sequences from NCBI for the glb1 locus, which encodes a nonessential seed storage protein. Within the Zea genus samples, the waxy maize has the minimum sequence diversity, which contains 31.1% of the level of diversity of parviglumis and 58.5% of the level of diversity of normal maize from Southwest China. Sequence variation within glb1 locus is consistent with neutral evolution in all four taxa according to Tajima’D test. From the NJ tree for glb1 sequences waxy maize formed two main groups which are intermixed with normal maize sequences. These results suggest that the Chinese waxy maize originate from a single gene mutation from normal maize. Combined with the history of maize dispersal in China we can even think that Chinese waxy maize was divergenced from Chinese flint maize.     

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.     

Biodiversity of <Emphasis Type="Italic">Secale strictum</Emphasis> in Iran measured using microsatellites

The mountain rye Secale strictum is native to the Middle East and is the progenitor of the cultivated rye. Regarding lack of information about the genetic diversity of this species in Iran, this study was aimed to evaluate its genetic variation and to examine the patterns of diversity related to the varieties and geography. Fifteen wheat and rye derived microsatellite markers were used to achieve this aim. High levels of diversity, with an average number of 6.1 alleles per locus (ranging up to 11) and high level polymorphism with polymorphism rate averaging 0.624 (between populations) and 0.357 (within populations) were observed among 125 individuals from 19 populations collected from various regions of Iran. The Northwestern populations showed the highest and the Northern populations showed the lowest polymorphism and diversity. One population of the Northwest of the country was notably closer in its allele range to the S. cereale accessions used as outgroup. No taxon or geographic specific marker was detected, suggesting high gene flow between the populations, however some groupings which can be related to the geographic regions and varieties, were evident. The analysis of molecular variance attributed same portions of genetic diversity to the within and between populations with no significant variation among different geographic regions. The results of this study indicated that the Iranian genepool of Secale strictum is valuable to search for new useful alleles for crop improvement.     

Farmers’ unconscious incorporation of sexually-produced genotypes into the germplasm of a vegetatively-propagated crop (Oxalis tuberosa Mol.)

Clonal propagation and sexual reproduction have diametrically opposite effects on the genetic diversity of crops, permitting, respectively, the conservation of existing genotypes or the creation of new diversity. Oxalis tuberosa Mol. (“oca”) exhibits a heteromorphic self-incompatibility system and is traditionally propagated clonally but is capable of sexual reproduction. In this study we investigated the influence of sexual reproduction on the in situ genetic diversity of a vegetatively propagated crop, taking oca as a model plant. The occurrence of sexual reproduction in natural conditions and its use by farmers were studied through surveys and interviews, while the effect of sexual reproduction on the in situ genetic diversity was evaluated using microsatellite analysis. Plantlets issuing from sexual reproduction were encountered in five of the nine visited communities. The interviews indicated that six out of the nine interviewed farmers were likely, albeit unconsciously, incorporating clonal lineages issuing from sexual reproduction into their varieties. The microsatellite analysis indicated a strong effect of such incorporations on the genetic diversity of the plant varieties. Assignment tests confirmed the allogamy of oca. “Complex varieties”, made up of individuals exhibiting genetically differentiated genotypes, were most likely the result of recent crossing. Unconscious incorporation of new genotypes into the cultivated oca germplasm is therefore highly likely, raising the question of its potential occurrence in other vegetatively propagated crops. These findings could have an important effect on the adaptive potential of oca, especially in light of the genetic erosion that threatens the crop.     

Abundant genetic diversity in cultivated <Emphasis Type="Italic">Codonopsis pilosula</Emphasis> populations revealed by RAPD polymorphisms

Genetic diversity of seven cultivated populations of Codonopsis pilosula Nannf. from Longxi County, Gansu Province of China was estimated using randomly amplified polymorphic DNA (RAPD) markers. The 17 selected RAPD primers amplified 205 polymorphic bands out of a total of 235 (87.2%). Nei’s gene-diversity statistics and population differentiation parameters based on AMOVA analysis indicated that the cultivated C. pilosula populations remained a high level of genetic diversity with Hs = 0.299 and I = 0.450. A greater proportion of genetic diversity was found within (77%) rather than among (23%) the populations. In addition, we also detected that populations from different altitudes had a considerable genetic differentiation after 40 years of cultivation at the same site. Populations from higher altitude had lower genetic diversity than those from lower altitude. Our results suggested that irregular and sparse cultivation practices, i.e., random collecting, preserving, and planting seeds of the medicinal species without deliberate selection, might be an efficient way to conserve genetic resources of medicinal plants, in addition to their effective uses.     

Effects of conventionally bred and <Emphasis Type="BoldItalic">Bacillus thuringiensis</Emphasis> (<Emphasis Type="BoldItalic">Bt</Emphasis>) maize varieties on soil microbial biomass and activity

Genetically modified (GM) maize containing genes from the soil bacterium Bacillus thuringiensis (Bt) was cultivated on 29% of the total maize production area worldwide in 2009. Most studies to date compare Bt-maize varieties with their near isogenic lines; however, there is little information on the variability of conventional maize breeding lines and how the effects of Bt varieties are ranked within. In our study on the potential risks of Bt-maize varieties, we analyzed tissue quality and compared the effects of ten conventional and GM maize varieties on soil microbiological properties in a replicated climate chamber experiment. All maize varieties were cultivated twice in the same soil microcosm. Shoot yields and soluble C in leaf tissue of Bt varieties were higher than the ones of non-Bt. Soil dehydrogenase activity was reduced by 5% under Bt varieties compared to non-Bt, while most of the other soil microbial properties (soil microbial biomass, basal respiration) showed no significant differences between Bt and non-Bt varieties. The leaves and roots of one Bt variety were decomposed to a greater extent than the ones of its near isogenic line; the conventional breeding lines also showed higher values. Changes in crop and soil parameters were found when comparing the first and the second crops, but the effects of repeated cropping were the same for all tested varieties. For the studied parameters, the variation among non-Bt-maize varieties was similar to the difference between Bt and non-Bt varieties.     

Studying the extent of genetic diversity among Gossypium arboreum L. genotypes/cultivars using DNA fingerprinting

Genetic diversity is an area of concern for sustaining crop yield. Information on genetic relatedness/diversity among Gossypium arboreum L. cultivars/genotypes is scanty. We have used random amplified polymorphic DNA (RAPD) analysis to assess the genetic divergence/relationship among 30 genotypes/cultivars of G. arboreum. Of 45 primers surveyed, 63% were polymorphic. Out of the total number of loci amplified, 36% were polymorphic. The calculated genetic similarity between the cultivars/genotypes was in the range of 47.05–98.73%. Two genotypes, HK-244 and Entry-17, were the most distantly related. The average genetic relatedness among all the genotypes was 80.46%. However, most of the cultivated varieties showed a close genetic relationship, indicating a narrow genetic base in comparison to the non-cultivated germplasm. The calculated coefficients were used to construct a dendrogram using the unweighted pair group of arithmetic means (UPGMA) algorithm, which grouped the genotypes/cultivars into two major and three smaller clusters. The study is the first comprehensive analysis of the genetic diversity of G. arboreum germplasm and identifies cultivars that will be useful in extending the genetic diversity of cultivated varieties and future genome mapping projects.     

Population evaluation in crop wild relatives for <Emphasis Type="Italic">in situ</Emphasis> conservation: a case study for raspberry <Emphasis Type="Italic">Rubus idaeus</Emphasis> L. in the Leningrad region,Russia

Many crop wild relatives are usually widely distributed species, and in this relation a question arises about selecting populations of special importance for conservation. Using Rubus idaeus as an example, we propose a compound selection of wild populations for in situ conservation. Twelve raspberry populations in the Leningrad region have been evaluated from the point of view of their significance for in situ conservation. To exclude the run-wild forms from the evaluation process, we tried to identify them applying a mathematical model developed by statusmetry method. The constructed model is based on morphological features of leaves of primocanes and helps to distinguish the wild forms from the cultivated and run-wild ones. The wild raspberry populations were screened for plants with features useful for cultivated raspberry improvement such as waxy cover presence, yellow fruiting plants, spinelessness, fruiting primocanes and others. The diversity of wild raspberry populations was assessed by variation of morphological features, presence of botanical varieties and polymorphism of seed storage proteins. The results of viability status assessment for the chosen populations reflect the perspectives of their development and permit to determine the strategy and measures for optimal conservation.     

Genetic diversity of some accessions of Cucurbita maxima from Spain using RAPD and SBAP markers

Increasing the knowledge of the molecular diversity of a crop is essential for extending its genetic base, identifying cultivars and selecting parental varieties for breeding programs. In this sense, Cucurbita maxima Duch. is poorly characterised. Nineteen accessions of this species and 8 related Cucurbita accessions were included in a genetic diversity analysis. For this purpose, Random Amplified Polymorphic DNA markers (RAPDs), which analyse neutral variability, and Sequence-Based Amplified Polymorphism (SBAPs), which preferentially amplify coding regions of the genome, were used. While the UPGMA cluster and the principal coordinates analysis obtained using RAPDs did not group the different accessions according either to fruit morphological criteria or to passport data (origin and agro-climatic conditions), the principal coordinates analysis obtained using SBAPs grouped the different pumpkin accessions fundamentally according to the type of use (human consumption, animal fodder or ornamental). This passport trait is reported to be associated with agronomic breeding characters of interest. The usefulness of both types of markers for discriminating accessions of breeding interest is discussed.     

RAPD-based Analysis of Genetic Diversity and Selection of Lingonberry (<Emphasis Type="Italic">Vaccinium vitis-idaea</Emphasis> L.) Material for <Emphasis Type="Italic">ex situ</Emphasis> Conservation

Random amplified polymorphic DNA markers were used to assess relatedness and genetic diversity for 15 lingonberry (Vaccinium vitis-idaea) populations. Seven primers yielding 59 polymorphic bands were used to analyse 13 populations, representing ssp. vitis-idaea from Sweden, Finland, Norway, Estonia and Russia, and two populations, representing ssp. minus from Japan and Canada. A cluster analysis and a multidimensional scaling analysis (MDS) showed similar phenetic patterns among populations, with a pronounced geographic grouping in most cases. Significant correlations were obtained between geographic and genetic distances for the entire set of populations as well as for the 13 ssp. vitis-idaea populations. Mean within-population diversity was 0.206 when estimated with Lynch and Milligan's index, and 0.431 when estimated with Shannon's index, which is in agreement with the mixed mating system reported for lingonberry. Within-population variability accounted for 68.6% of the total variance when all populations were included, and for 78.8% when only populations of ssp. vitis-idaea were analysed. Two different approaches were applied to the selection of plant material for a potential gene bank: (1) a hierarchical sampling strategy based on a cluster analysis and (2) the Maximum genetic diversity program, developed for the establishment of core collections. Random sampling was undertaken for comparisons with the selected data sets. The most diverse and representative set of lingonberry specimens was obtained when samples were selected with the Maximum diversity program.