In areas with less favourable conditions for agriculture, informal seed systems permit gene flow through pollen to play a crucial role in the development of new varieties. An important factor with great impact on cross-pollination is the plant breeding system, but so far this is little studied within the context of low-input farming systems. This research studied the chances of cross-pollination within and between rice fields in The Gambia. Size and time of flowering were measured for 28 rice fields in one village. The level of mixture was measured in 90 seed lots of rice collected from four villages. Based on the results, we suggest that in general cross-pollination between different rice genotypes occurs more often within fields than between fields. No clear relationship was found between the level of within-field mixture and socio-economic status of farmers. Some comparison was made with millet, which allowed the identification of various factors influencing pollen flow between different genotypes. Effective pollen flow (between genotypes) is a function of a number of factors, such as the rate of cross-pollination of a crop, number of off-types within fields, variety distinctiveness, farmer expert knowledge, length and reliability of the rainy season, growth duration of different varieties, availability of fields, pest pressure and number of varieties grown per field or per farmer. We hypothesize that a low cross-pollination rate is more favourable for the development of new varieties in farmer fields than a high cross-pollination rate.

The collected articles in this volume are discussed in their wider context.

The Triticeae tribe (Poaceae) includes several important cereal crops, cultivated forages, annual and perennial grass weeds and ecologically diverse native North American grasses. Elymus L. is the largest and most complex genus in the Triticeae tribe with approximately 150 polyploid perennial grass species occurring worldwide. The genomic constitutions of approximately 40% of the Elymus species are unknown. Molecular markers are needed to facilitate genetic analysis of diversity and functional traits in these species. We have developed simple sequence repeat (SSR) markers for use in Elymus based on Elymus expressed sequence tag sequences. To test the polymorphic content and transferability of these SSRs, 100 SSR primer pairs were tested on 84 plants representing seven North American Elymus, Pseudoroegneria and Pascopyrum species. The number of bands produced from each of the SSRs ranged from 1 to 11 with an average of 4.3 bands/SSR. A subset of the 23 most polymorphic SSRs produced 142 bands, an average of 6.2 bands/SSR. Binary data from the 100 SSRs successfully separated all individuals into their respective accessions in a neighbour-joining phylogram with a 100% confidence interval. Analysis of molecular variance showed that 29.9% of the total variation was within and 70.1% was among the accessions. These SSRs will be a useful tool for investigating genetic diversity, genome constitutions and molecular mapping in Elymus and other Triticeae grasses.

Plant genetic resources (PGR) include cultivars, landraces, wild species closely related to cultivated varieties, breeder's elite lines and mutants. The loss of genetic diversity caused by the practice of agriculture and the availability of genetic information has resulted in a great effort dedicated to the collection of PGR. Prior to the advent of molecular profiling, accessions in germplasm collections were examined based on morphology. The development of molecular techniques now allows a more accurate analysis of large collections. Next-generation sequencing (NGS) with de novo assembly and resequencing has already provided a substantial amount of information, which warrants the coordination of existing databases and their integration into genebanks. Thus, the integration and coordination of genomic data into genebanks is very important and requires an international effort. From the determination of phenotypic traits to the application of NGS to whole genomes, every aspect of genomics will have a great impact not only on PGR conservation, but also on plant breeding programmes.

The tribe Fabeae (formerly Vicieae) contains some of humanity's most important grain legume crops, namely Lathyrus (grass pea/sweet pea/chickling vetches; about 160 species); Lens (lentils; 4 species); Pisum (peas; 3 species); Vicia (vetches; about 140 species); and the monotypic genus Vavilovia. Reconstructing the phylogenetic relationships within this group is essential for understanding the origin and diversification of these crops. Our study, based on molecular data, has positioned Pisum genetically between Vicia and Lathyrus and shows it to be closely allied to Vavilovia. A study of phylogeography, using a combination of plastid and nuclear markers, suggested that wild pea spread from its centre of origin, the Middle East, eastwards to the Caucasus, Iran and Afghanistan, and westwards to the Mediterranean. To allow for direct data comparison, we utilized model-based Bayesian Analysis of Population structure (BAPS) software on 4429 Pisum accessions from three large world germplasm collections that include both wild and domesticated pea analyzed by retrotransposon-based markers. An analysis of genetic diversity identified separate clusters containing wild material, distinguishing Pisum fulvum, P. elatius and P. abyssinicum, supporting the view of separate species or subspecies. Moreover, accessions of domesticated peas of Afghan, Ethiopian and Chinese origin were distinguished. In addition to revealing the genetic relationships, these results also provided insight into geographical and phylogenetic partitioning of genetic diversity. This study provides the framework for defining global Pisum germplasm diversity as well as suggesting a model for the domestication of the cultivated species. These findings, together with gene-based sequence analysis, show that although introgression from wild species has been common throughout pea domestication, much of the diversity still resides in wild material and could be used further in breeding. Moreover, although existing collections contain over 10,000 pea accessions, effort should be directed towards collecting more wild material in order to preserve the genetic diversity of the species.

Anatolia (Asia Minor) is considered to be the cradle of viticulture, but wild grape accessions from this region have not been subjected to any genetic analysis. We present the first genetic characterization of wild grapes (Vitis vinifera subsp. sylvestris) from this region. Using 15 nuclear microsatellites, we genotyped 84 wild grape accessions collected from three Anatolian locations. The unweighted pair group method with arithmetic mean analysis revealed four genetic clusters that partially separated Anatolian wild grape populations. In general, accessions from geographically closer locations showed higher genetic similarities than those from more distant locations. In some cases, accessions from one population showed close genetic relationships to accessions from a different population. The genetic diversity between natural populations from both ends of the Mediterranean basin has shown higher genetic diversity in the Anatolian Peninsula than peripheral populations, suggesting that this area could be one centre of diversity of the species. The genetic relationship between wild and cultivated grapevine from Anatolian Peninsula indicated a clear separation between them. However, we cannot discarded a local genetic contribution. Overall, this study reveals useful information for management and potential utilization of Anatolian wild grape germplasm.

For maintaining food security and livelihood, farmers in marginal areas of production environments make use of high levels of crop genetic diversity. The exchange of seed and varieties among villagers, and also the relative isolation of local varieties in their production environments, contributes to the continued existence of locally adapted genotypes. In Tigray, one of the major barley-growing regions of Ethiopia, local varieties and local seed systems are dominant. The annual barley seed requirement is met with seed produced, saved and exchanged by farmers. In order to understand the flows of seed and varieties within and between villages, a study was conducted using a survey to gather information from 130 respondents in seven villages. Seed network analysis was used as an analytical tool to assess flows of seed and varieties and to identify farmers who play different roles in the seed system. Within the major seed exchange network, nodal or connector farmers linked seed subnetworks. The flow within villages was much more dominant than beyond. Rare varieties appeared to be sourced from farms that maintain a broad variety portfolio. Varieties seemed to disseminate informally across farms, in their target environments, following participatory varietal selection. The methodology of social seed network analysis proved to be a powerful tool for monitoring seed and variety flows. Furthermore, it identified farmers as critical partners in the conservation and on-farm management of plant genetic resources, recognized the role of plant breeders in participatory varietal selection and that of seed experts, engaged in strengthening local seed supply and in disseminating quality seed of superior varieties.

Inter simple sequence repeat markers were used to assess the genetic diversity and population genetic structure in 12 populations of Nothapodytes nimmoniana from Western Ghats of India. A total of 16 selected primers produced 103 discernible bands, with 76 (73.7%) being polymorphic. The Nei's gene diversity (h) ranged from 0.1166 to 0.2124, with an average of 0.1518 at the population level and 0.2965 at the species level indicating high genetic diversity. The Shannon's index (I) was estimated to be 0.2189 within populations (range 0.1703–0.2947) and 0.4352 at the species level. The analysis of molecular variance showed that the genetic variation was found mainly within populations (73%), but variance among populations was only 27% and its value, ΦPT = 0.271, P < 0.001, implied that high genetic differentiation among populations. In addition, Nei's differentiation coefficient (GST) was found to be high (0.4882) and the gene flow (Nm) was low (0.5242), confirming the high population genetic differentiation. The unweighted pair-group method using arithmetic average clustering elicited similar results. Based on this, we propose conservation strategy for this plant species.

Guava (Psidium guajava) and araçá (Psidium spp.) plants are important for the Brazilian economy, as their fruit is both accepted by the consumers, and makes a beneficial contribution to the human diet thanks to their content in vitamin C, carotenoids and phenolic compounds. Here, we report the content in the fruit of free ascorbic acid, lycopene, β-carotene, flavonoids and phenolic compounds, and the total antioxidant activity present in a collection of guava and araçá accessions curated at the Embrapa Semiarido germplasm bank. Guava fruits with a red-coloured pulp flesh contained a significant amount of carotenoids, especially lycopene, and a high concentration of phenolic compounds. These compounds were largely responsible for the antioxidant activity of the araçá accessions. Among the guava accessions, phenolic compounds were also responsible for the antioxidant activity. High levels of free ascorbic acid were present in most accessions. In both guava and araçá, there is substantial potential to develop cultivars with a good level of consumer acceptability.

Extensive collections of lentil germplasm now exist in various genebanks around the world. This germplasm including wild Lens species has been used in plant introduction strategies and in efforts to widen the potential sources of increasing genetic diversity in the breeding programmes of lentil. Improved techniques are emerging to overcome hybridization barriers between species and as a result, interspecific hybrids have been successfully obtained between species. Several interspecific recombinant inbred line populations have been developed. Selected and backcrossed lentil lines are currently in advanced yield trial stages, and desirable traits such as yield, disease resistance and agronomic traits have been incorporated into cultivated lentil especially from Lens ervoides, generating a wider spectrum of variability. Secondly, further expansion of the overall pool of germplasm and examination of allelic variation at the nucleotide level will benefit lentil-breeding programmes by augmenting phenotype-based variation to further advance cultivar development. Genomic resources for lentil are limited now, but this situation is changing rapidly as the cost of genotyping has declined. As a result, two successive expressed sequence tags (EST) projects were undertaken under the NAPGEN EST project initiative (http://www.nrc-cnrc.gc.ca/eng/programs/pbi/plant-products/napgen/.htm) and an Agricultural Development Fund project initiative. We emphasize that creation of intraspecific and interspecific genetic populations, genetic maps, association maps, quantitative trait loci and marker-assisted selection technologies for implementation in the breeding programme will enhance deployment of genes responsible for traits of interest. The economical use of genomic technologies for use in germplasm resource management and genetic improvement is on the near horizon.

We now understand that many different types of DNA structural polymorphisms contribute to functional diversity of plant genomes, including single nucleotide polymorphisms, insertions of retrotransposons and DNA transposons, including Helitrons carrying pseudogenes, and other types of insertion–deletion polymorphisms, many of which may contribute to the phenotype by affecting gene expression through a variety of mechanisms including those involving non-coding RNAs. These polymorphisms can now be probed with tools such as array comparative genomic hybridization and, most comprehensively, genomic sequencing. Rapid developments in next generation sequencing will soon make genomic sequencing of germplasm collections a reality. This will help eliminate an important difficulty in the estimation of genetic relationships between accessions caused by ascertainment bias. Also, it has now become obvious that epigenetic differences, such as cytosine methylation, also contribute to the heritable phenotype, although detailed understanding of their transgenerational stability in crop species is lacking. The degree of linkage disequilibrium of epialleles with DNA sequence polymorphisms has important implications to the analysis of genetic diversity. Epigenetic marks in complete linkage disequilibrium (LD) with DNA polymorphisms do not add additional diversity information. However, epialleles in partial or low LD with DNA sequence alleles constitute another layer of genetic information that should not be neglected in germplasm analysis, especially if they exhibit transgenerational stability.

The recombinant inbred line mapping population Opata85 × Synthetic W7984 was used to map Jeli long terminal repeat retrotransposon insertion sites in the hexaploid wheat genome. Sequence-specific amplified polymorphism technique was applied to reveal Jeli insertions. Jeli was found to provide multiple genetic markers for common wheat. Our marker system revealed A-genome Jeli insertions, and therefore can be used for targeted analysis of the A genome.

This study discusses some of the important aspects of laws/regulations formulated for the protection of plant varieties in Union for the Protection of New Varieties of Plants (UPOV) member states, European Community countries and India. The study also provides an insight into some of the unique features of Indian sui generis system for the protection of plant varieties. During this study, the registration of crop notified in India and in some selected UPOV member countries has been examined. Since India is not an UPOV member state, the system of plant variety protection (PVP) is independent of international scenario but aims for similar standards. The study provides useful information in order to analyse the implementation of PVP laws in UPOV member states and India. Some important features were selected for carrying out a comparative analysis. These include Intellectual Property Rights protection (patent/breeder's right), types of varieties protected, methods of testing, criteria for protection, duration of protection, exemptions (researcher/farmer's exemption), infringement and penalty and compulsory license.

Lentil is recognised as the most nutritious rabi pulse and, with respect to acreage, it ranks next to chickpea. It is grown throughout northern and central India. A large percentage of Indians are vegetarian and lentil has long been part of India's indigenous diet, and is a common source of protein. Of about 60 varieties released in India to date, 13 have been developed by hybridization, mostly from parents not distantly related. The narrow genetic base of the presently cultivated varieties and losses due to biotic and abiotic stress factors remain the main cause of concern. Introgression of genes between microsperma and macrosperma groups of lentil from closely related species like L. culinaris subspp. Orientalis and use of biotechnological tools, wherever necessary, have been recommended by various workers to broaden the genetic base of this crop. Direct selection for grain yield through important component traits such as pods/plant, seeds/pod, number of clusters/plant, harvest index, biological yield, early maturing and breeding for better yield quality have been suggested. Realizing the significance of plant germplasm, special efforts have been made by the national bureau to collect the genetic resources of lentil from different states of India. A large number of accessions were characterised and evaluated for various agro-morphological traits, using the lentil minimal descriptor. The core collection comprising 287 promising accessions recorded variation for seed yield and its important component traits; variation was also observed for important morphological traits, using mutation breeding approaches. These genetic resources of lentil have also been screened for tolerance to several biotic stresses and a few lines showed immunity against rust, blight and fusarium wilt and these have been utilized as donors in cross-breeding programmes. On the other hand, wild Lens species revealed substantial genetic diversity for phenological and agro-morphological characters, including some important diseases of lentil. From these genetic resources, potential donors of desirable traits have been selected after evaluation and characterization and have been utilized in the genetic improvement of cultivars.

Cowpea, an indigenous crop to sub-Saharan Africa, is found mainly in the dry savanna regions along with cereals such as millets and sorghum. Cowpea is grown primarily for human consumption of the grains, which are rich in protein, carbohydrates and contain some minerals. The development and deployment of cowpea varieties with higher nutritional value will be of immense benefit to consumers. As a first step in the enhancement of mineral content in cowpea grains, several germplasm lines (1541) of different origins and obtained from the genetic resources unit at IITA were sown in the experimental field in Minjibir, Kano State, Nigeria. The grains were analysed for protein and nine mineral contents. However, in this study, we shall report data on crude protein, Fe, Zn, Ca, Mg, K and P. The data generated from the chemical analysis were subjected to the ‘mixture of normal distributions’ clustering method, which distributed the cowpea lines into nine groups. Groups G7 and G9 contained 174 genotypes and these were characterized by high mineral concentrations. The mean nutritional content values for group G9 were 24.7% for protein, and 58.9, 41.5, 1107, 2132, 15,282 and 5664 mg/kg for Fe, Zn, Ca, Mg, K and P, respectively. On the other hand, the 363 lines making up groups G2, G3 and G6 showed low amounts of nutrients in their grains. Some of the lines in G7 and G9 would be good as parents to use in breeding programmes that aimed at developing nutrient-dense cowpea varieties.

Clovers (Trifolium species) are a large and widespread genus of legumes. Recent work supports the Mediterranean origin of the genus in the Early Miocene period, and centres of diversity for clovers occur in the Eastern Mediterranean, East Africa and South America. A number of clovers are of agricultural importance as forage species in grassland agriculture around the world, particularly in temperate areas. White clover (Trifolium repens L.) is the most important legume of grazed pastures, and red clover (T. pratense) is widely cut and conserved as a winter feed. We consider the current state of collected resources in clovers, which have been collated in the most important databases. These are European Internet Search Catalogue (EURISCO), germplasm resources information network and system-wide information network for genetic resources together with the collection held at AgResearch, New Zealand. In total, collections have been made of 204 species with 48 species having more than 100 accessions in these databases. As expected, the majority of accessions are of the agriculturally important species. The geographical origin of collected material is outlined and, for the major species, accessions are broken down according to their status, e.g. wild population, breeders' lines. We then describe some of the ways in which genetic resources of white and red clovers and their relatives have been used in the breeding of these species. These include introgression of stress tolerance traits, targetting improvements in resource use efficiency and increasing seed yield.

WRKY transcription factors are one of the largest families of transcriptional regulators and form an integral part of signalling webs which modulate many plant processes, such as abiotic stress tolerance. In the present paper, an innovative method has been applied to identify novel WRKY-1 alleles involved in the responses to salt and drought stresses in Triticum durum. This technique involves scanning for sequencing variations in cDNA-derived PCR amplicons, using high-resolution melting (HRM) followed by direct Sanger sequencing of only those amplicons which were predicted to carry nucleotide changes. HRM represents a novel advance in detection of single-nucleotide polymorphisms (SNPs) by measuring temperature-induced strand separation of short PCR amplicons. The use of this approach is still limited in the field of plant biology. Here, HRM analysis has been applied to the discovery and genotyping of durum wheat SNPs. Specific primers have been designed, starting at multi-alignment of WRKY-1-conserved portions. The PCR amplicons, containing single SNPs, produce distinctive HRM profiles, and by sequencing the PCR products identified, SNPs have been characterized and validated. The results showed that all the revealed SNPs are located on salt-tolerant varieties, confirming their value in breeding activities.

Knowledge of the genetic diversity of germplasm of breeding material is invaluable in crop improvement programmes. Frequently, qualitative and quantitative data are used separately to assess genetic diversity of crop genotypes. While assessing diversity based on qualitative and quantitative traits separately, there may occur a problem when the degree of correspondence between the clusters formed does not agree with each other. This study compares five different procedures of clustering based on the criterion of weighted average of observed proportion of misclassification in black gram genotypes using qualitative, quantitative traits and mixture data. The INDOMIX- and PRINQUAL-based clustering procedures, i.e. INDOMIX and PRINQUAL methods in conjunction with the k-means clustering procedure, show better performance compared with other clustering procedures, followed by clustering based on either quantitative or qualitative data alone. The use of the INDOMIX- and PRINQUAL-based procedures can help breeders in capturing the variation present in both qualitative and quantitative trait data simultaneously and solving the problem of ambiguity over the degree of correspondence between clustering based on either qualitative or quantitative traits alone.

Mango (Mangifera indica L.) is an important fruit crop with a long cultivation history in Myanmar. This study evaluated the genetic variation within two economically important traditional varieties, ‘Yin Kwe’ and ‘Sein Ta Lone’, and the relationship between genetic variation and propagation practices. Genetic variation was estimated by genotyping 94 individuals with 12 single sequence repeat markers. ‘Yin Kwe’ (n = 53) showed higher levels of observed heterozygosity (Ho = 0.59) and average genetic distance among individuals (Da = 0.29) than did ‘Sein Ta Lone’ (n = 41; Ho = 0.45; Da = 0.09). The differences between the two varieties at the DNA level were significant (Fst = 0.44). The broader genetic background in ‘Yin Kwe’ compared with ‘Sein Ta Lone’ was also demonstrated by neighbour-joining and principal coordinates analyses. Differences in variety uses and propagation practices were determined by interviewing local specialists in Lower Myanmar (southern Myanmar). ‘Yin Kwe’ was often used as a rootstock for ‘Sein Ta Lone’. Clonal propagation by grafting was observed frequently for ‘Sein Ta Lone’ but never for ‘Yin Kwe’. The differences in genetic variation between these two varieties might have been caused by the propagation practices for each variety, which result from their respective uses.