The beautiful hills: half a century of vanilla (Vanilla planifolia Jacks. ex Andrews) breeding in Madagascar

Genetic Resources and Crop Evolution - An ambitious vanilla (Vanilla planifolia Jacks. ex Andrews) breeding program was started in Madagascar in the early 1950s to control Fusariosis, a serious...     

Assessment of genetic diversity and phylogenetic relationships in Asparagus species related to Asparagus officinalis

Eight species of the genus Asparagus, members of the group of European species closely related to A. officinalis, were analysed using internal transcribed spacer (ITS), and expressed sequence tag-derived simple sequence repeat (EST-SSR) markers, as well as cytological observations of their hybrids, to study their phylogenetic relationships and the possibility of broadening the narrow genetic base of cultivated varieties. Phylogenetic analysis using ITS data revealed two major clades: clade I consisting of A. acutifolius and clade II (referred to in this study as the ‘officinalis group’) comprised of sequences derived from species closely related to A. officinalis; but the different species within the ‘officinalis group’ could not be clearly separated. In contrast, cluster analysis of EST-SSR marker data showed six major clades and clearly separated each population, grouping most of the genotypes from each population together. That is, EST-SSR markers were found to be more informative than ITS markers about the relationships within the ‘officinalis group’, indicating that EST-SSR markers are more useful than ITS sequences for establishing phylogenetic relationships at the intrageneric level. All the crosses carried out at the same ploidy level were successful. The high crossability, together with the regular meiotic behaviour and high pollen and seed fertility observed in the interspecific hybrids analysed, suggest relatively close relationships between the species studied. We conclude that the group of species classified in the ‘officinalis group’ are in the primary gene pool, indicating that these species could be used to increase the genetic diversity of the cultivated species. In addition, the tetraploid landrace “Morado de Huétor” could be employed as a bridge to generate new cultivated germplasm.     

Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars

The US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository in Corvallis, Oregon, preserves more than 800 accessions of hazelnut (Corylus), including C. avellana cultivars and representatives of 10 other recognized shrub and tree species. Characterization and study of genetic diversity in this collection require cross-transferable markers, such as trinucleotide microsatellite or simple sequence repeat (SSR) markers and universal chloroplast SSR markers. We developed new SSR markers and evaluated 114 Corylus accessions representing 11 species and 44 interspecific hybrids. Eight of 23 SSRs generated easy-to-score alleles in all species and seven were highly polymorphic. For those seven, the average heterozygosity was moderate at 0.49, and mean allele number, genetic diversity and polymorphism information index were high at 11.71, 0.79 and 0.76, respectively. The three most polymorphic SSRs were CaC-C008, CaC-C040 and CaC-C118. Neighbor-joining (NJ) clustering and structure analysis agreed with classical taxonomic analysis and supported inclusion of C. maxima within the large polymorphic species, C. avellana. Analysis also indicated that C. californica is a distinct species rather than a botanical variety of C. cornuta. Six universal cpSSRs were polymorphic in Corylus and generated 21 distinct chlorotypes with an average of 3 alleles per locus. Diversity at these cpSSRs was high and ranged from 0.33 to 0.64, with an average of 0.54. Incongruence in NJ topologies between the nuclear and chloroplast markers could be attributed to chloroplast capture related to hybridization during the ancestral diversification of the genus, or to homoplasy. The phylogeographical relationships among the 21 chlorotypes in the 11 Corylus species support Asia as a refugium where several hazelnut lineages survived during glaciation and from which they continued to evolve after dispersal from Asia through the Mediterranean to Europe, and across the Atlantic and/or the Bering land bridge to North America.     

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.     

Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region

The Capsicum genus is native to tropical America and consists of 27 species, five of which are used as fresh vegetables and spices: Capsicum annuum L., Capsicum chinense Jacq., Capsicum frutescens L., Capsicum baccatum L. and Capsicum pubescens R. et P. The study of the relationships among species of cultivate Capsicum species will be useful for breeding new cultivars or hybrids. This study is focused on the genetic diversity and relationships of these species that were collected in the Andean region. Ten microsatellites and four AFLP combinations were used to characterize 260 Capsicum accessions. The AFLP tree turned out to be informative regarding relationships among species. The data clearly showed the close relationships between C. chinense and C. frutescens. Moreover, C. cardenasii and C. eximium were indistinguishable as a single, morphologically variable species. Our data showed C. baccatum and C. praetermissum to be distinct species that form a compact group. In the present work, AFLP fingerprinting indicated that C. chacoense was placed in the C. baccatum complex and showed C. tovarii as a separate species. In addition, SSR data indicated that there is intraspecific differentiation in the species C. chinense, C. baccatum and C. pubescens, as the PCoA-based clustering showed a clear geographic division related to country. Even though Bolivia is considered to be the nuclear area for these species, we have found similar variability in Ecuador and Peru for several Capsicum species.     

Sampling effects on the assessment of genetic diversity of rhizobia associated with soybean and common bean

Biological nitrogen fixation plays a key role in agriculture sustainability, and assessment of rhizobial diversity contributes to worldwide knowledge of biodiversity of soil microorganisms, to the usefulness of rhizobial collections and to the establishment of long-term strategies aimed at increasing contributions of legume-fixed N to agriculture. Although in recent decades the use of molecular techniques has contributed greatly to enhancing knowledge of rhizobial diversity, concerns remain over simple issues such as the effects of sampling on estimates of diversity. In this study, rhizobia were isolated from nodules of plants grown under field conditions, in pots containing soil, or in Leonard jars receiving a 10⁻² or a 10⁻⁴ serially-diluted soil inoculum, using one exotic (soybean, Glycine max) and one indigenous (common bean, Phaseolus vulgaris) legume species. The experiments were performed using an oxisol with a high population (10⁵ cells g⁻¹ soil) of both soybean rhizobia, composed of naturalized strains introduced in inoculants and of indigenous common-bean rhizobia. BOX-PCR was used to evaluate strain diversity, while RFLP-PCR of the ITS (internally transcribed spacer) region with five restriction enzymes aimed at discriminating rhizobial species. In both analyses the genetic diversity of common-bean rhizobia was greater than that of soybean. For the common bean, diversity was greatly enhanced at the 10⁻⁴ dilution, while for the soybean dilution decreased diversity. Qualitative differences were also observed, as the DNA profiles differed for each treatment in both host plants. Differences obtained can be attributed to dissimilarity in the history of the introduction of both the host plant and the rhizobia (exotic vs. indigenous), to host-plant specificity, rhizobial competitiveness, and population structure, including ease with which some types are released from microcolonies in soil. Therefore, sampling method should be considered both in the interpretation and comparison of the results obtained in different studies, and in the setting of the goals of any study, e.g. selection of competitive strains, or collection of a larger spectrum of rhizobia. Furthermore, effects of sampling should be investigated for each symbiosis.     

The role of shoot residues vs. crop species for soil arthropod diversity and abundance of arable systems

Removal of crop residues has become common practice in arable systems, however, little is known about how soil arthropod communities change in response to reduced resource availability and habitat complexity associated with residue removal. We added maize residues to wheat and maize fields and investigated soil arthropod diversity and abundance over the period of one year. Residue addition did not affect the diversity and little affected the abundance of soil arthropods in wheat and maize fields with the latter being restricted to few taxonomic groups, suggesting that at least in the short-term soil arthropods benefit little from crop residue-mediated increase in food supply and habitat structure. Contrasting the minor effects of residue addition, densities of soil arthropods were much higher in wheat than in maize fields, presumably due to more dense and more continuous coverage by plants, and higher input of root residues. Furthermore, in wheat fields density of arthropods more strongly varied with season, presumably due to more pronounced pulses of root exudates and root residues entering the soil in wheat as compared to maize fields in summer and winter, respectively. Low density and little variation in densities of soil arthropods in maize fields reflect that environmental conditions and resource supply varied little with crop coverage and season. Overall, the results point to low importance of aboveground crop residues for soil arthropod communities and highlight that belowground plant resources, i.e. root exudates and root residues are the major driver of soil arthropod communities of arable systems. Thus, at least in short term removal of crop residues for e.g., biofuel production is likely to be of minor importance for soil arthropod communities. In contrast, changing crop species from wheat to maize markedly reduces the density of soil animals threatening the ecosystem functions they provide.     

Castanea spp. biodiversity conservation: collection and characterization of the genetic diversity of an endangered species

Centuries of co-evolution between Castanea spp. biodiversity and human populations has resulted in the spread of rich and varied chestnut genetic diversity throughout most of the world, especially in mountainous and forested regions. Its plasticity and adaptability to different pedoclimates and the wide genetic variability of the species determined the spread of many different ecotypes and varieties in the wild. Throughout the centuries, man has used, selected and preserved these different genotypes, vegetatively propagating them by grafting, for many applications: fresh consumption, production of flour, animal nutrition, timber production, thereby actively contributing to the maintenance of the natural biodiversity of the species, and providing an excellent example of conservation horticulture. Nonetheless, currently the genetic variability of the species is critically endangered and hundreds of ecotypes and varieties are at risk of being lost due to a number of phytosanitary problems (canker blight, Chryphonectria parasitica; ink disease, Phytophthora spp.; gall wasp, Dryocosmus kuriphilus), and because of the many years of decline and abandonment of chestnut cultivation, which resulted in the loss of the binomial male chestnut. Recently, several research and experimentation programmes have attempted to develop strategies for the conservation of chestnut biodiversity. The purpose of this paper is to give an overview of the status of biodiversity conservation of the species and to present the results of a 7?year project aimed at the individuation and study of genetic diversity and conservation of Castanea spp. germplasm.     

Influence of soil and host plant crop on the genetic diversity of Azospirillum amazonense isolates

The genetic structure of Azospirillum amazonense populations isolated from the rhizosphere soil and washed and surface-sterilised roots of rice, maize and sorghum plants, cropped simultaneously in two different soils (clay loam and sandy loam) was characterised. Genetic diversity was measured by restriction fragment length polymorphism of the amplified 16S–23S rDNA intergenic spacer region (RISA-RFLP) and cluster analysis. Four genetically distinct clusters of isolates were observed with 78% similarity, suggesting that the A. amazonense population was heterogeneous at the strain level regardless of the soil type or host plant. Analysis of molecular variance (AMOVA) demonstrated that the host plant had a highly significant selective effect on the genetic structure of this species, especially on those isolates intimately associated with them, but also to a lesser extent on isolates from the rhizosphere and washed roots. The soil type also had a highly significant selective effect on A. amazonense genetic diversity, especially for those isolates from the rhizosphere soil. The selective effect of the soil type combined with that of the host plant suggests that environmental factors, such as soil texture and composition of exudates provided by C₃ or C₄ plants, play major roles in the overall genetic structure of A. amazonense populations associated with these cereals.     

Contribution to the knowledge of the genetic diversity and taxonomy of some Iranian Trifolium species

Genetic Resources and Crop Evolution - Trifolium (Fabaceae) is widely distributed with more than 255 species. The current study contributed to the knowledge of the diversity and genetic population...     

Assessment of genetic diversity of Musa species accessions with variable genomes using ISSR and SCoT markers

Genetic Resources and Crop Evolution - Assessing the effectiveness of different molecular markers is essential for identification of appropriate ones for crop improvement and conservation, hence,...     

Soil sustainability changes in organic crop rotations with diverse crop species and the share of legumes

There have been few long-term field studies on greenhouse gases measurement in organic crop rotations under temperate climatic conditions. Little is known about the extent to which the share of legumes in a crop rotation of organic farming affects the potentials for CO₂ emission and soil organic carbon sequestration. The current study was aimed to investigate soil physicochemical state and soil net CO₂ exchange rate in diverse organic crop rotations with different crop species and proportions of legumes. Four 5-year duration crop rotations were investigated. The best soil sustainability of the arable layer was found in a crop rotation enriched with red clover (Trifolium pratense L.). This rotation resulted in the highest soil mesoporosity and the lowest microporosity, ensured the best supply of plant-available water and revealed high soil resistance to dry conditions. Red clover secured the highest soil organic C sequestration, caused the increase in reserves of total N and available K, and slackened the decrease of soil-available P sources. Red clover-based cropping system exhibited the highest soil net CO₂ exchange rate during five experimental years. The effect of crop rotation, consisting of phacelia (Phacelia tanacetifolia Benth.), peas (Pisum sativum L.) and yellow lupin (Lupinus luteus L.), on soil sustainability was weaker than the effect of rotation with red clover. Non-legume rotations, i.e. binary (two-crop) rotation and the crop rotation involving four spring and one winter species, can be regarded as miners of soil nutrient resources rather than contributors. These rotations did not promote soil sustainability because the soil lost large amounts of macronutrients and caused 26–33% lower soil net CO₂ exchange rate, compared with leguminous rotations. For future, it could be recommended for ecological farming to rely more on crop rotations with red clover to improve ecosystems functioning.     

Assessment of genetic diversity and genetic relationships among 29 populations of <Emphasis Type="Italic">Azadirachta indica</Emphasis> A. Juss. using RAPD markers

Randomly amplified polymorphic DNA (RAPD) analysis was employed to assess genetic divergence among 29 neem accessions collected from two agro-ecological regions of India (11 agro-climatic sub-zones), which cover three states, Punjab, Haryana and Rajasthan. Out of 24, 10-mer random primers used for studying genetic divergence, 14 were polymorphic, generating a total of 73 amplification products with an average of 5.21 products per polymorphic primer and estimated gene diversity of 0.49. Genetic relationships among accessions were evaluated by generating a similarity matrix based on Jaccard’s coefficient, ranging from 0.70 to 0.96. The phenetic dendrogram generated by UPGMA analysis grouped accessions into five clusters. RAPD performed within accessions (individual seedlings collected from the same mother plant) showed no variation indicating homogeneous population within accessions. Primers OPA-18, OPC-08 and OPI-03 were found most informative based on their resolving power. The degree of genetic variation detected among the 29 accessions with RAPD analysis suggests that RAPD can be used for studying genetic diversity in neem. The study also demonstrated that neem germplasm collected from northwestern plains of India shows no eco-geographical isolation based on sub-zones because accessions collected from different sub-regions are grouping together in the genetic tree.     

An assessment of the genetic integrity of ex situ germplasm collections of three endangered species of Coffea from Madagascar: implications for the management of field germplasm collections

Madagascar has 59 species of Coffea, of which 42 are listed as Critically Endangered, Endangered, or Vulnerable by criteria of the Red List Category system of the World Conservation Union. In an attempt to assess the conservation value of ex situ collections of Malagasy coffee species, a study was undertaken using the field genebank collections maintained at the Kianjavato Coffee Research Station. Three species were selected for this purpose, C. kianjavatensis, C. montis-sacri, and C. vatovavyensis, and for comparative purposes extant, in situ populations of the same species were studied. Parentage analyses of ex situ propagated offspring of C. kianjavatensis and C. montis-sacri were performed to assess if crossing with other Coffea species maintained in the field genebank is compromising the genetic integrity of the collection. For these three species, higher genetic diversity was observed in the ex situ populations compared to the in situ populations, highlighting the importance of preserving the plants currently in ex situ collections. Parentage analyses of seed-propagated offspring of C. kianjavatensis and C. montis-sacri revealed that cross contamination with pollen from other Coffea species in the ex situ field genebank is occurring. These results have significant implications for the conservation management of wild Coffea species and for the management of ex situ genebanks.     

Molecular diversity, genetic structure and mating system of Calopogonium mucunoides Desv.

Calopogonium mucunoides Desv. is a species native of South and Central America that is used as green manure and a pasture crop. The molecular genetic diversity was characterized in 195 C. mucunoides accessions from a germplasm collection using 17 microsatellite markers. Outcrossing rate was estimated after the evaluation of six microsatellite loci in 200 genotypes originated from 10 open-pollinated progenies (20 genotypes per progeny). Six genetic clusters were identified in the germplasm collection by the STRUCTURE software analysis, neighbor-joining tree comparisons and principal component analysis, which highly correlated with the geographic locations where these accessions were originated or collected. These results were confirmed using AMOVA. The largest portion of the genetic variation was observed among clusters (64.38%). The results indicated that: multilocus outcrossing rate (t _m ) was 16.3%, suggesting a mixed mating system with a predominance of autogamy; single locus outcrossing rate (t _s ) was 11%; difference (t _m ?t _s ) was 0.054, indicating that only 5.4% of outcrossing occurred among related individuals; paternity correlation (r _p ) was 33% suggesting a low probability of finding full sibs among the progeny; parental coefficient of inbreeding (F _m ) was 5.0%, indicating a low degree of inbreeding in each parent. A core collection for C. mucunoides was assembled to capture the allelic diversity found in this study. The complete allelic diversity was represented by only 15 accessions. These results should be useful for exploiting the genetic resources of C. mucunoides and could influence future conservation efforts and breeding programs.     

Evaluation of genetic diversity and relationships within an on-farm collection of Perilla frutescens (L.) Britt. using microsatellite markers

The present study demonstrates utilization of 11 microsatellite markers to explore genetic diversity held in Perilla frutescens (L.) Britt. landrace accessions growing on farms in different parts of Korea and Japan and to assess their genetic relationships. All microsatellite loci were polymorphic and produced a total of 96 alleles ranging from 4 to 20, with an average of 8.7 alleles per locus. Of the 96 alleles found, a total of 15 unique landrace-specific alleles were observed at 9 different loci. The locus GBPFM203 provided the highest number of alleles (20), of which five were unique and each specific to a particular landrace accession. The occurrence of unique, accession-specific alleles presented molecular evidence for the generation of new alleles within on-farm collection of Perilla. The mean values of observed (H _O) and expected heterozygosity (H _E) were 0.39 and 0.68, respectively, indicating a considerable amount of polymorphism within this collection. A genetic distance-based phylogeny grouped the two Perilla varieties, var. frutescens and var. crispa (Thunb.) Decne into two distinct groups. Accessions belonging to var. frutescens could also be divided into two subgroups at a close genetic distance (GD = 0.432). The overall clustering pattern did not strictly follow the grouping of accessions according to their geographic origins. These observations are indicative of extensive germplasm exchange among farms from different geographical regions. The genetic similarity observed among the Perilla landraces may be useful for future Perilla crop variety identification, conservation, and improvement programs.     

AFLP assessment of diversity in sweetpotato from Latin America and the Pacific region: Its implications on the dispersal of the crop

Although originally domesticated in tropical America, the sweetpotato [Ipomoea batatas (L.) Lam.] has a long history of cultivation in the Pacific region. While the post-Columbus dispersal of sweetpotato to Asia and the Pacific is well documented, the hypothesis that there was a prehistoric transfer of sweetpotato by Peruvian or Polynesian voyagers from Peru to Oceania has long been a controversial issue. The objective of this study was to assess the genetic diversity and interrelationships of sweetpotato landraces from the Pacific region and Latin America, and test the hypothesis of human transfer of this crop to the Pacific Island in prehistoric times. Seventy-five sweetpotato landraces from Peru, Ecuador, Mexico, the Philippines, Papua New Guinea (PNG) and 5 Oceania countries were analyzed using amplified fragment length polymorphism (AFLP). Multidimensional scaling (MDS) and analysis of molecular variance (AMOVA) revealed a large genetic variation in the Oceania gene pool, far greater than that in Peru-Ecuador. The Mexican cultivars were grouped together with those of Oceania. In contrast, there is little association between the Peru-Ecuador germplasm and that of Oceania. These results suggest that Peru-Ecuador may not be the source of the Oceania sweetpotato germplasm. Natural dispersal from Mesoamerica is an alternative explanation, to the Kumara hypothesis, for the origin of the Oceania sweetpotato.     

The use of characterisation data to establish the Indian mungbean core collection and assessment of genetic diversity

A representative core set of well characterised Indian mungbean collection was developed using information on passport, characterisation and evaluation data. Initial diversity groups of the accessions comprising the whole collection were formed based on six major crop growing zones and a separate group for a few accessions from diverse exotic sources. Principal components score strategy was found to be most useful in maximising the selection inertia than strictly random sampling in all individual groups. A total of 152 accessions were extracted and the validity of their representativeness was established by comparing its diversity with that of the whole collection. Shannon diversity index for qualitative characters and certain statistical parameters for quantitative variables were used for measuring the diversity of the accessions in the core set and that of the whole collection. The representative core set was subjected to multivariate analysis for assessment of genetic diversity and also the variation patterns for discriminating among accessions to facilitate the users for easy accessibility, and effective and efficient utilisation of the material.