Regional distributions of crop diversity are important to take into account for the spatial design of in situ, farmer-participatory interventions in crop genetic management. Regional seed flows are an important factor in shaping geographical distributions of crop diversity. This study contributes to the insight in these seed flows, focusing on maize (Zea mays L.) in Chimaltenango, an area in the western highlands of Guatemala. A social survey of 257 households on different aspects of seed management produced information on cultivar naming, seed sources, reasons and causes of the discontinuation of seed lots, and important explanatory variables associated with different seed sources. A small portion of the reported seed lots originated from regional seed sources. The main motivation of regional seed exchange and the discontinuation of seed lots was to achieve change in plant characteristics of the crop, especially to obtain lower plants and shorter growing cycles. It is argued that farmer selection fails to achieve such change, and in fact leads to an equilibrium with high plants and long growing cycles. Seed exchange functions as an escape to this trend. Other factors of influence on seed exchange are altitude and ethnicity. The study also highlights the issue of geographical directionality in seed exchange patterns.

Cowpea is a drought-tolerant food legume grown in the savannah regions of the tropics and subtropics. The International Institute for Tropical Agriculture (IITA) holds the world collection of 15,003 cultivated cowpea from 89 countries in its genebank. In excess of 12,000 accessions were characterized for 28 agrobotanical descriptors. The entire collection was first stratified by country of origin and biological status. Land race accessions (10,227) with information on origin and characterization data were grouped using clustering procedures. The clustering analysis was based on Euclidean distances between and among accessions. Accessions within each country were then grouped hierarchically, according to their similarity. The number of clusters selected for countries varied from 2 to 20, depending on the size of collection for that country. A percentage number of accessions (5–25%) was chosen from each country, based on the size of the collection and its proximity to the centre of diversity. The number of accessions from each cluster in a country was then chosen randomly, based on the predetermined percentage. In countries where the numbers of accessions were few ( < 10), the percentage chosen from those countries would be higher and may go up to 100% to ensure that at least one accession was chosen from every country. Accessions with no characterization information were treated as a group, and accessions were chosen randomly, based on their geographical distribution. In the process of selection, 200 accessions that are known to be resistant to pests and diseases and not originally chosen through the selection processes were, nevertheless, kept as part of the core collection. Following these procedures, a total of 1701 accessions of landraces were chosen from the entire collection. Using the same procedures, a subset of 225 accessions was chosen from 1422 advanced cultivars and breeding or research lines. A third subset of 130 accessions was chosen from 838 accessions that either lack information on origin or biological status, and six accessions of wild and weedy forms from the available 64 wild and weed accessions were added. Thus a core collection of 2062 accessions of cowpea was constituted. The diversity in the core collection was similar to that of the entire collection and correlated traits that may be linked were also preserved in the core collection. This core collection of cowpea provides an opportunity for further exploitation of the cowpea germplasm for improvement of this crop.

Landraces (LRs) are important as a source of novel alleles for crop improvement, and their conservation is therefore necessary for food security. These genetic resources have suffered continuous erosion, especially in more accessible areas. We assess the loss of Nepali rice LRs and identify the factors influencing the probability of cultivating the most dominant LR via a logistic regression model. The majority of farmers cultivate LRs and modern varieties simultaneously. However, there has been a decrease in varietal diversity and a loss of some LRs over recent years, mainly because of their low yield, their sensitivity to diseases and pests, and their late maturity. The opportunity cost of maintaining the Satha landrace is higher on irrigated farms and for those farmers specializing in niche products. On the other hand, Satha is more likely to be cultivated by large-scale farmers and by those having a religious and/or a cultural attachment to this LR. Market-based incentives are less costly than publicly funded conservation programmes, and the superior taste of some LRs may allow them to be developed as niche products. However, to achieve this, public investment is needed to generate the necessary support infrastructure. In the more accessible Terai region, there is a particular need to introduce a flexible incentive mechanism to maintain LRs and to offset the negative effect of development intervention.

The landraces of rice (Oryza sativa L.) possess wide diversity, which needs to be properly characterized for their use in genetic improvement. Replicated field studies were conducted in 1998, 1999 and 2000 at two sites in Nepal to determine diversity in 183 landraces of rice adapted to the lowlands and the hills in Nepal. Fourteen improved genotypes were also used for comparison. Thirteen agronomic traits were investigated. Shannon–Weaver diversity index (H) and Simpson's index of diversity (D) were estimated to determine the level of genetic richness among the landraces. The landraces differed significantly for all traits. Except for plant height and maturity, at least one of the landraces compared well with the performance of improved cultivars. A principal component analysis separated the lowland- and hill-adapted landraces into two broad groups.

Guinea yam (Dioscorea rotundata Poir.) is a dioecious vegetatively propagated tuber crop. It is widely cultivated by traditional techniques in West Africa, its area of origin. The genetic diversity of 146 accessions from Benin was analysed using 10 polymorphic simple sequence repeat (SSR) nuclear markers and agromorphological traits. An average of 8.4 alleles per locus was detected. The mean heterozygosity was 0.57 and the mean polymorphism information content (PIC) for polymorphic markers was 0.51. Some cultivars (23%) were found to have an identical genotype for the 10 markers. The structure of the genetic diversity observed in Benin is the result of farmers' crop management practices and their know-how. The cultivar diversity had a geographical component. We also noted major differentiation between early and late cultivars, with higher diversity in the early ones. Cultivars from northern Benin and early cultivars had the greatest allelic richness. SSR markers proved to be powerful tools for fingerprinting each cultivar and analysing their genetic relationships. The results of this study could be useful for defining a strategy for the conservation of genetic diversity in yams.

With the numbers of new varieties of potato obtaining Plant Breeders' Rights increasing yearly, the reliable maintenance of large culture collections is becoming more problematic. Additionally, the differentiation of cultivars based on morphological characteristics is a highly skilled and time-consuming task and for these reasons a rapid and robust method for variety differentiation has become highly desirable. By screening a number of microsatellite (simple sequence repeat, SSR) markers we have developed a set of six that can be used to differentiate over 400 cultivars, including those on the UK National List, but excluding somaclonal variants (e.g. Red King Edward and King Edward). The whole process from tuber to accurate identification can be carried out in a single day.

Spelt (Triticum spelta L.) is hulled wheat which was widely cultivated in Spain until the first half of the 20th century and is still cultivated in Asturias (northern Spain). Much of the variability of this species has been preserved, but little evaluation has been carried out. We describe the characterization of some of these spelt lines for several quantitative traits, including plant height and awnedness.

Quinoa (Chenopodium quinoa Willd.) is a staple food crop for millions of impoverished rural inhabitants of Andean South America where it has been cultivated for millennia. Interest in quinoa, due largely to its superior nutritional characteristics, is fuelling a growing export market and has led to an increased focus on genetic research and the development of quinoa breeding programmes throughout South America. The success of these breeding programmes will rely heavily on the development of core germplasm collections and germplasm conservation. We report the development of a set of fluorescence-tagged microsatellite molecular markers that can be used to characterize genetic diversity within quinoa germplasm and we use this set of 36 microsatellites markers to genetically characterize the diversity of 121 accessions of C. quinoa held in the USDA germplasm bank, 22 accessions from the CIP-FAO international nursery collection and eight accessions representing parents from genetic mapping populations. A total of 420 alleles were detected among the quinoa accessions with an average of 11 alleles detected per microsatellite locus. Genetic heterogeneity was observed in 32% of the quinoa accessions at a given locus and suggests that many of these accessions represent heterogeneous seed lots or landraces. Both unweighted pair-group method with arithmetic averages (UPGMA) and principle components analysis (PCA) analyses partitioned the quinoa accessions into two main clusters. The first major cluster consisted of accessions from the Andean highlands of Peru, Bolivia, Ecuador, Argentina and extreme northeastern Chile. The other main cluster contained accessions from both the lowlands of Chile and a set of USDA accessions with no known passport data, collected by Emigdio Ballón. Using the patterns of genetic diversity detected within the C. quinoa accessions we discuss hypotheses regarding quinoa's centre of diversity, including highland and lowland ecotype clustering patterns, origin of lowland varieties, origin of domestication, and diversity levels in the USDA and CIP-FAO collections.

The Dilatata group of Paspalum is a polyploid complex native to the grasslands of temperate South America. A pentaploid apomictic biotype of P. dilatatum is a widely recognized forage grass; however, the complex includes apomictic tetra- and hexaploids along with sexual allotetraploids (P. urvillei, P. dasypleurum, P. dilatatum ssp. flavescens, and biotypes Virasoro and Vacaria of P. dilatatum) which are suspected to be hybrids between different combinations of biotypes. Fifteen primer pairs for nuclear microsatellite loci were developed from a (CA)n-enriched genomic library. A single, low stutter, robust two-step PCR profile was used for all the primer pairs. Twelve primer pairs were analysed for their variability and transferability among all the sexual biotypes of the Dilatata group and the common apomictic pentaploid. Six primer pairs amplified more than one locus, and sequence and segregation evidence suggest that the additional bands correspond to homeologous loci. No close linkage was found among the 16 loci amplified in the tetraploids. One variable chloroplast microsatellite is also reported. All loci were successfully amplified from most members of the Dilatata group and variability was recorded for all the biotypes analysed. The set of loci reported here provide highly variable markers for intra-biotypic population studies, biotype-specific markers for the analysis of hybrid apomicts and a biotype-specific chloroplast marker.

Legume flavonoids have received considerable attention due to their beneficial effects on human health. Flavonoid content in the seeds of 36 germplasm accessions of guar [Cyamopsis tetragonoloba (L.) Taub.] was quantified by high-performance liquid chromatography (HPLC). On a per 100 g basis, the seed contained, on average, 1.114 mg (0–2.355) daidzein, 0.700 mg (0–1.685) genistein, 0.553 mg (0–1.250) quercetin and 14.460 mg (10.70–19.82) kaempferol. A significant positive correlation was observed between the content of daidzein and genistein; however, significant negative correlations existed between the content of kaempferol and daidzein and of kaempferol and genistein. Compared to soybean seeds, guar seeds contained very low amounts of daidzein and genistein, but a high amount of kaempferol. The information about the levels of flavonoids in guar seeds will be useful to breeding programmes for improving guar seed quality. Furthermore, the high kaempferol content of guar seeds may expand its nutraceutical and pharmaceutical utilization.

Groundnut is one of the most important oilseed crops in the world. Bacterial wilt, caused by Ralstonia solanacearum E. F. Smith, is one of the major biotic constraints to groundnut production particularly in South-East Asia and East Africa. Several sources of resistance to bacterial wilt have been identified through field screening of groundnut germplasm. The aim of the present study was to quantify the genetic diversity among selected bacterial wilt-resistant lines, in comparison with the levels of variation observable within the cultivated A. hypogaea gene pool. Thirty-two SSR markers were used to assess the degree of molecular polymorphism between 46 selected genotypes revealing 107 alleles, of which 101 (99.4%) were polymorphic with gene diversity scores ranging from 0.103 to 0.669, averaging 0.386. Cluster and multidimensional scaling analysis revealed two distinct groups within the germplasm broadly corresponding to the two subspecies (hypogaea and fastigiata) of A. hypogaea. However, accessions of varieties peruviana and aequatoriana grouped together with the varieties from subsp. hypogaea, rather than grouping with the other varieties of subsp. fastigiata. Analysis of molecular variance (AMOVA) revealed that 15% of the total observed variation was accounted for by disease response groups. This analysis will be useful in the selection of parental genotypes for mapping populations and breeding programmes attempting to broaden the genetic base of future groundnut cultivars. In particular, this opens up significant opportunities for the development of intraspecific mapping populations that will be highly relevant to modern groundnut breeding programmes.

Fifty morphological characteristics, fruit production over 3 years (from 1999 to 2002) and the amplified fragment length polymorphism (AFLP) technique were used to analyse a set of 48 guava (Psidium guajava L.) accessions cultivated in Mexico, in order to characterize their genetic relationships. Germplasm was collected from the Calvillo-Cañones region and planted in Huanusco, Mexico. The study included two P. cattleianum (Sabine) and two P. friedrichsthalianum (Berg-Niedenzu) accessions from Costa Rica as outgroups. Principal component analysis (PCA) explained less than 30% of total variation and 14 characteristics from trees (1), leaves (2) and fruits (11) were the most informative. PCA analysis separated the germplasm into three major groups of accessions based on fruit size and weight, stem diameter and leaf size. Significant differences in fruit yield were detected among accessions and years, where P. guajava produced 36 kg/year/tree of fresh fruit while P. cattleianum and P. friedrichsthalianum showed fruit yield lower than 7 kg/year/tree. The fruit yield broad sense heritability was 0.25. The AFLP analysis produced two clusters of Psidium accessions, the first included P. cattleianum and P. friedrichsthalianum, and the second P. guajava accessions. This is the first report about the use of AFLP marker methodology for the genetic characterization of Mexican native guava germplasm and the results based on phenotypic and productive characteristics suggest that germplasm was selected from open pollinated trees.

The composition of essential oils obtained from leaves of Acorus calamus growing wild in 19 different locations was analysed by gas chromatography and gas chromatography–mass spectrometry. In total, 84 constituents have been identified, representing at least 86% of the total essential oil. The essential oils were dominated by the presence of phenolic compounds: (Z)-asarone (15.7–25.5%) and (Z)-methyl isoeugenol (2.0–4.9%). Other identified major components were (E)-caryophyllene, α-humulene, germacrene, linalool, camphor and isoborneol. All oils were found to have a similar composition. However, a hierarchical cluster analysis of the quantitative data revealed significant differences between some accessions. Minimal inhibitory concentrations (MIC) of four selected leaf essential oils were determined by a screening test with the broth dilution method. Of the 17 species of fungi, bacteria and yeasts tested, Mycobacterium ssp. and Bacillus subtilis were most susceptible to essential oils. Oils displayed low anti-fungal activity and their inhibitory activity was lower than the standard antibiotics. Oils differed in their activities against the various microorganisms tested.

Eruca vesicaria subsp. sativa (syn. E. sativa) is a cruciferous vegetable and oilseed crop that is high in erucic acid. It occurs throughout the Mediterranean region and western Asia, and has been naturalized elsewhere as a crop/weed escape. It is closely related to subsp. vesicaria and subsp. pinnatifida, which are endemic to Spain and north-western Africa, respectively. This study evaluated patterns and levels of diversity in the three subspecies based on 234 amplified fragment length polymorphisms (AFLP), and evaluated agronomic and seed quality data in a field trial in western Canada. AFLP data revealed three main clusters: ‘Sativa’ (33 accessions of subsp. sativa), ‘Vesicaria’ (nine accessions of subsp. vesicaria) and a ‘Pinnatifida’ cluster (one accession of subsp. pinnatifida and three Moroccan accessions of subsp. sativa). The Sativa cluster separated into Mediterranean and Asian groups, likely reflecting differences in origin (wild versus cultivated) or primary usage, vegetable versus seed oil. The origin of the introduced Mexican population was confirmed as subsp. sativa. The highest levels of diversity were found in the Sativa cluster (88% AFLP polymorphisms) and the least in the Vesicaria (56%) and Pinnatifida (39%) clusters. Extensive variation was observed among the 159 subsp. sativa accessions evaluated in the field trial, and overall findings indicated a favourable agronomic potential.

Aegilops markgrafii is a useful source of genes encoding both resistance to biotic stress and high seed lysine content. Bread wheat/Ae. markgrafii introgression lines expressing leaf rust resistance were developed from a cross between a leaf rust-resistant Ae.markgrafii accession and the susceptible bread wheat cultivar ‘Alcedo’. The content of introgressed segments present in five sister introgression lines was assessed with the help of chromosome-specific simple sequence repeats (SSRs). One of the lines was used as a parent of a 140 individual F2 mapping population, by crossing with the leaf rust-susceptible bread wheat cv. ‘Borenos’. The population was tested for susceptibility or resistance to leaf rust, and linkage analysis indicated the presence of a quantitative trait locus (QLr.ipk-2A) originating from the Ae. markgrafii parent, mapping to the distal segment of chromosome arm 2AS.

Molecular markers have been used to study genetic diversity within a set of Lablab purpureus accessions collected from the southern states of India. Amplified fragment length polymorphism (AFLP) molecular marker studies using a total of 78 L. purpureus accessions with nine primer combinations showed there was very little genetic diversity within the L. purpureus accessions from the southern Indian germplasm collection as compared to a set of 15 accessions from other international germplasm collections that included African accessions. The set of 15 were selected from a random amplified length polymorphism (RAPD) marker study and chosen on the basis of widest genetic distance. Further molecular analysis with polymerase chain reaction (PCR) markers from 97 expressed sequence tag (EST) and gene-specific primer pairs, designed from a range of legume sequences, concurred with the AFLP analyses. Both of these approaches provide a wealth of markers for diversity and mapping studies. The 97 sequence-specific primer pairs tested in L. purpureus resulted in 70% amplification success, with 44% of primer pairs amplifying single bands and 10% double bands. Markers generated from these EST and genomic sequences provide useful cross-reference to comparative legume genomics that will potentially have long-term benefit to legume plant breeding.

The allelic diversity within oil palm populations (45 native ones from 10 African countries, three breeding populations and one collection of semi-wild material) was determined using 16 microsatellite markers. A total of 209 alleles were detected, with a mean number of 13.1 alleles per locus. The mean effective number of alleles per locus (Ae) was 3.3 ± 1.3. Although the Duncan's multiple range test only separated the group of populations from Madagascar from the rest on the basis of Ae, the presence of unique and rare alleles and high values of Ae suggest that 23 of the African populations should be conserved to secure allelic diversity.

Genetic resource conservation is widely acknowledged as important. The implementation of conservation requires an insight into the distribution of genetic diversity at the scale of small regions or villages. We present an analysis of rice diversity at such a scale, in a region where traditional farming still prevails. Regional allelic diversity was comparable to that noted worldwide for Asian rice (Oryza sativa), but not as high for African rice (O. glaberrima). Each village pooled more than half of the regional allelic diversity. Genetic differentiation between varieties from the same village accounted for 70% of the regional variation. The differentiation associated with lowland and upland rice-growing ecosystems was 23%, while that associated with differences between villages within the same ecosystem was 7%. In the upland ecosystem, geographical distance had a significant effect on the FST between pairs of villages. In the lowland ecosystem, differences in soil salinity between villages affected FST. Genetic diversity within a single village may have up to three components: an ancient glaberrima component shared with neighbouring or ethnically related villages; a relatively ancient sativa component which was hardly or no longer shared with other villages due to local differentiation; and a recently introduced sativa component shared with other villages. Genetic resource conservation could be achieved, in terms of allelic diversity, through stratified sampling according to described genetic differentiation factors, whereas current farming systems must be preserved to ensure conservation of the diversity of allelic associations.

Bacterial blight (BB) of rice is a widespread disease in tropical Asia, contained largely through the deployment of race-specific resistance genes. Although more than 25 BB resistance genes have been identified, none are effective individually against all the pathotypes prevalent in north-western India. The response of a set of 327 accessions of 13 wild Oryza species and cultivated African rice, O. glaberrima, was evaluated to infection with seven pathotypes of Xanthomonas oryzae pv. oryzae over a period of 3–4 years. Of these, 67 were resistant or moderately resistant to all pathotypes. These comprised 13 accessions of O. glaberrima, 5 of O. barthii, 10 of O. rufipogon, 4 of O. longistaminata, 22 of O. nivara, 6 of O. officinalis, 2 of O. rhizomatis and 5 of O. minuta. Inheritance studies, molecular mapping and transfer of some of these genes into O. sativa ssp. indica are in progress.