This article focuses on advances in both basic and applied research on soybean germplasm resources collected from China and dispersed to the world. Many landraces developed over the course of the 4500 years since its domestication in the Huangdi period. Systematic germplasm collection was begun in the early 20th century by Professor Shou Wang, and since then over 170,000 accessions have been conserved worldwide. Evaluation with respect to key morphological characteristics, pest resistance, abiotic stress tolerance and nutritional quality attributes has been widely carried out. In addition, genetic diversity has been assessed at the DNA level, and used to establish core collections for both cultivated (Glycine max) and wild (Glycine soja) soybean. Some core sets have targeted the most used parental lines, and others have focused on specific traits, such as resistance to the soybean cyst nematode or to soybean mosaic virus, or enhanced phosphorus use efficiency. The recent acquisition of the soybean genome sequence should accelerate the utilization of not only the Chinese soybean germplasm collection, but also those maintained elsewhere in the world.

Rocket (Eruca spp. and Diplotaxis spp.) is widely cultivated as a green vegetable in Mediterranean countries, Europe, United States and Brazil, but few rocket cultivars are available and limited variety selection has taken place. Plant genetic resources and germplasm are fundamental sources for plant breeding, and the assessment of the genetic diversity among germplasm accessions is useful to facilitate the more efficient use of plant genetic resources. The objective of this study was to characterize phenotypic diversity and relationships among genotypes of Eruca and Diplotaxis originating from 11 countries across three regions (Europe, Africa and Asia). Principal component analyses explained over 85% of total variation for 51 qualitative and quantitative agromorphological traits. Cluster analyses divided the accessions into five major clusters according to plant traits, siliqua properties and geographical origin of genotype with a few exceptions. These findings indicate a number of useful traits in the gene pool and a wide range of phenotypic variation that provides a good source of diversity for use in modern Eruca breeding programmes.

Apple cultivars are an integral part of the Latvian State Program for Preservation and Sustainable Use of Genetic Resources for Food and Agriculture. Latvian apple (n = 109) cultivars of local origin, nominated as National Plant Genetic Resources, were analyzed with eight simple sequence repeat (SSR) markers recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR) Malus/Pyrus working group and a marker for scab resistance gene (Vf). All SSR loci exhibited a high level of polymorphism – 12 to 39 alleles, 18.75 in average, with high observed heterozygosity (Ho) ranging from 0.64 to 0.89 and a mean of 0.78. The gene diversity (polymorphism information content value) varied from 0.79 to 0.90, with an average of 0.86. All cultivars could be distinguished with the tested set of SSR loci, with a high frequency of rare (38%) or unique (26%) alleles. For the Vf gene, all three possible genotypes (VfVf, Vfvf and vfvf) were detected for 1, 6 and 102 varieties, respectively. The analyzed germplasm showed high genetic diversity, particularly landraces, while the modern cultivars clustered mainly into two groups. Cluster analysis did not reveal a clear pattern with well-defined groups, but confirmed some relationships based on known or putative pedigrees, as well as suggesting the possible parentage of some cultivars.

The primary mission of germplasm collections is to preserve genetic diversity, but germplasm is preserved so that it can be used. Historically, the standard practice is that all germplasm accessions should be maintained as collected, so that even self-pollinated accessions are maintained as heterogeneous seed lots. In theory, this seems like an ideal strategy for preserving genetic diversity, but in practice, it is simply not workable. Heterogeneous accessions are in constant risk of change and loss. It is possible to mitigate the risk factors, but they can only be lessened and not eliminated. Maintaining pure-lined accessions for self-pollinated species not only eliminates the problems associated with genetic drift and natural selection, but also enhances the accuracy of the evaluations and fosters effective germplasm utilization. Neither the current potential to characterize entire germplasm collections with tens of thousands of DNA markers nor the future potential of whole genome sequencing to completely characterize the diversity of all accessions in collections can be fully realized for self-pollinated species unless accessions are homogeneous and homozygous. In this manuscript, the case is made for pure-lining self-pollinated germplasm accessions using the USDA Soybean Germplasm Collection, which has maintained pure-lined accessions for over 50 years, as an example. There is also an analysis of the extensive seed distribution from this collection to indicate the value of a diverse collection of genotypes.

Sustainable utilization of plant genetic resources for food and agriculture has been increasingly discussed at both national and international forums. Besides exploitation, conservation of plant genetic resources has become an integral part of these discussions. Conservation aims at maintaining the diversity of living organisms, their habitat and the interrelationship between organisms and their environment. For achieving such goals, appropriate conservation strategies have to be adopted. Determining the genetic makeup of a particular plant species is of critical importance when planning a suitable conservation strategy. In this study, we sequenced the chloroplast trnK intron, matK and rbcL gene aimed at understanding the rarity of Nymphaea tetragona, a critically rare and endangered plant of India found at only one location. We extended our investigation to other Nymphaea species such as N. nouchali, N. pubescens and N. rubra that are commonly available throughout India. Interestingly, matK gene of N. tetragona revealed high number of non-synonymous substitutions. Molecular evolutionary analysis indicated that three of these sites may be under mild selective pressures. Such adaptive changes at the DNA and protein sequence level of matK gene may have been associated with the colonization of N. tetragona, suggesting that it could have migrated from China.

Ginger (Zingiber officinale Rosc.), originated in the Indo-Malayan region, is now widely distributed across the tropics of Asia, Africa, America and Australia. It was domesticated in India and China, which represent the centre of origin of the species. Cultivated ginger though sterile, exhibits variations in rhizome and vegetative characters. The crop is gaining importance as a curative agent for a variety of ailments. Yield and quality traits (such as essential oil, fibre and oleoresin contents) along with volatile and non-volatile constituents are important determinants of the commodity's end product. Cultivar diversity for yield and morphological features is well known in ginger with few primitive types having excellent quality. However, the common name(s) of ginger cultivars are confusing and have resulted in geographical bias in its ex situ conservation. Most of the molecular/biochemical marker studies reported in ginger show low levels of polymorphism in contrast to plentiful phenotypic variability recorded in the species. The large influence of environmental factors on the content of key compounds, lack of seed set and confusion of the common names are the leading constraints to further varietal improvement of ginger. As tailor-made ginger varieties assume future significance these aspects will have relevance.

Here, we present a brief overview of the main studies conducted on the common bean (Phaseolus vulgaris L.) in Europe and other countries outside its centres of origin. We focus on the proportions of the Andean and Mesoamerican gene pools, and on the inter-gene pool hybridization events. In Europe, for chloroplast microsatellites, 67% of European germplasm is of Andean origin. Within Europe, interesting trends have been seen; indeed, the majority of the Andean type is found in the three macro-areas of the Iberian Peninsula, Italy and central-northern Europe, while, in eastern and south-eastern Europe, the proportion of the Mesoamerican type increased. On a local scale, the contribution of the Mesoamerican type is always low. On other continents, various situations are seen using different markers: in China and Brazil, the Mesoamerican gene pool prevails, while in an African sample, overall, both gene pools are equally represented, with differences in individual countries. The frequency of European bean genotypes deriving from at least one hybridization event was 44% with an uneven distribution. Interestingly, hybrids tend to have intermediate seed size in comparison with ‘pure’ Andean or Mesoamerican types. On other continents, very few hybrids are found, probably because of the different marker systems used.

Given the increasing importance of data quality for the ex situ conservation and utilization of plant genetic resources (PGR), an indicator was created that quantifies the level of completeness of passport data. This passport data completeness index (PDCI) uses the presence or absence of data points in the documentation of a genebank accession, taking into account the presence or value of other data points. For example, a wild accession should have a well-defined collection site but no variety name. Any type of accession, wild, landrace, breeding material or modern variety, can attain a maximal score of ten for this index. The applicability of this index was tested on the complete contents of EURISCO, the European catalogue of ex situ maintained PGR containing over one million records. Analysis of the PDCI of the material in EURISCO provided valuable insight in the data quality of European collections. The PDCI can be used to identify datasets that might need additional attention and improvement or datasets that need more careful interpretation than others.

The legume Arachis hypogaea, commonly known as peanut or groundnut, is a very important food crop throughout the tropics and sub-tropics. The genus is endemic to South America being mostly associated with the savannah-like Cerrado. All species in the genus are unusual among legumes in that they produce their fruit below the ground. This profoundly influences their biology and natural distributions. The species occur in diverse habitats including grasslands, open patches of forest and even in temporarily flooded areas. Based on a number of criteria, including morphology and sexual compatibilities, the 80 described species are arranged in nine infrageneric taxonomic sections. While most wild species are diploid, cultivated peanut is a tetraploid. It is of recent origin and has an AABB-type genome. The most probable ancestral species are Arachis duranensis and Arachis ipaënsis, which contributed the A and B genome components, respectively. Although cultivated peanut is tetraploid, genetically it behaves as a diploid, the A and B chromosomes only rarely pairing during meiosis. Although morphologically variable, cultivated peanut has a very narrow genetic base. For some traits, such as disease and pest resistance, this has been a fundamental limitation to crop improvement using only cultivated germplasm. Transfer of some wild resistance genes to cultivated peanut has been achieved, for instance, the gene for resistance to root-knot nematode. However, a wider use of wild species in breeding has been hampered by ploidy and sexual incompatibility barriers, by linkage drag, and historically, by a lack of the tools needed to conveniently confirm hybrid identities and track introgressed chromosomal segments. In recent years, improved knowledge of species relationships has been gained by more detailed cytogenetic studies and molecular phylogenies. This knowledge, together with new tools for genetic and genomic analysis, will help in the more efficient use of peanut's genetic resources in crop improvement.

The N.I. Vavilov Institute of Plant Industry (VIR) holds and maintains collections of various crop plants among the largest and oldest worldwide. Among them, small berry trees have gained attention because of their potential for human health. Small berries, usually containing various valuable compounds such as vitamins or antioxidants in significant quantities, could be used for easily improving the human diet. Subsets of VIR collections of raspberry (Rubus idaeus L.) and blue honeysuckle (Lonicera caerulea L.) were investigated for genetic diversity. Ninety-five raspberry accessions were genotyped with eight nuclear simple-sequence repeat (microsatellite) markers. Results indicated a fair level of genetic diversity, but also a structure of three main groups in the collection. Blue honeysuckle accessions were genotyped with five intersimple-sequence repeat markers, yielding more than 1100 polymorphic fragments across the 194 accessions. Statistical analysis of these data showed that the subspecies level was key in explaining blue honeysuckle diversity. This study shows that the collections constitute important resources that could be used for either direct consumption goals or breeding of new cultivars. Results may also be used to establish recommendations for efficient conservation of these genetic resources.

Woad (Isatis tinctoria L.) was the most important source of natural blue indigo, a pigment used mainly for dyestuff until the beginning of the 20th century, when the increased use of synthetic dyes by the industry lead to a decrease in the interest of natural dyes and to the abandonment of dye crops. The aim of this study was to characterize, according to morphological and agronomical traits, 11 woad accessions from different countries and to quantify the indigo precursor content by high-performance liquid chromatograph-diode array detection (HPLC-DAD). Qualitative traits revealed a low variability and a great variation was observed in quantitative traits. Principal component analysis (PCA) diagrams divided the accessions into four groups, primarily according to their geographic origin. The first three components of the PCA accounted for 76.8% of the total variation. Reciprocal interactions between indigo precursors and fresh leaf weight were compared through genetic diversity, with significant differences in isatan B (0.5–5.1 g/kg), indoxyl (0.3–2.0 g/kg) and residual indigo (0.3–0.5 g/kg). This information, together with genetic data, can be used to assist local farmers to re-introduce Isatis species in the European agricultural system, not only indicating the higher indigo yielding genotypes, but also the most suitable harvest time.

Woad (Isatis tinctoria L.) was introduced in Europe in ancient times to produce indigo, a natural blue pigment used mainly for dyestuff. This species was cultivated in Portugal until the beginning of the 20th century, especially in the inner North and South. A set of nine inter-simple sequence repeat (ISSR) markers generated 177 reproducible fragments, of which 171 were polymorphic. The mean number of fragments/accession was 111, ranging between 100 (Portugal-Coimbra) and 124 (Poland). The total polymorphism observed was 0.3272, the average polymorphism was 0.1784 and the gene differentiation between accessions was 0.4546. Polymorphism ranged between 53.8% (Austria) and 73.1% (Belgium). The genetic relationship among woad accessions was obtained with unweighted pair group method with arithmetic mean dendrogram based on a molecular marker, clearly clustering the woad accessions according to their geographic origin. The genetic diversity observed in this collection shows that there is a considerable potential for its improvement and that ISSR could be used to evaluate intra- and inter-accession similarities in I. tinctoria species.