The present study is the first to compare the trait-level differentiation (Qst) and the molecular-level differentiation (Fst) between Malus× domestica and Malus sieversii. A set of 115 accessions representing M.× domestica (99) and M. sieversii (16) were genotyped using the International RosBREED SNP Consortium apple 8K SNP array and phenotyped for eight fruit quality traits in a clonally replicated experiment. A set of 3521 single nucleotide polymorphisms (SNPs) with an average call rate of 98% was retained following SNP data quality filters. About 86% of the total SNPs were polymorphic in M. sieversii, while all but three SNPs were polymorphic in M. × domestica. The patterns of linkage disequilibrium were different, especially at the longer distances, between the two species. No differentiation (Fst= 0) was observed for nearly 23% of the SNPs, but about 20% of the SNPs exhibited a high genetic differentiation (Fst≥ 0.15). A highly significant (P< 0.001) genome-level Fst= 0.12 was observed between M. × domestica and M. sieversii. The average estimated Qst value was 0.20 (range 0.08–0.40), and for three of the eight studied traits (crispness, flavour intensity and fruit weight), Qst value was more than twice the estimated genome-level Fst value. A higher Qst value than Fst value for four of the eight fruit quality traits indicated differential (or directional) selection for these traits in M. × domestica. The average posterior probability of assignment of M. × domestica accessions to the M. sieversii gene pool was 11%, supporting the hypothesis of M. sieversii being one of the progenitors of the domesticated apple.

Wild and managed bees are needed to move sunflower (Helianthus annuus L.) pollen, both to create hybrid seed and to encourage high, consistent yields when those hybrids are subsequently grown. Among floral traits that influence bee preference, floret size may be critical, as the depth of the corolla affects the accessibility of nectar. Sampling and observation of inbred maintainer (HA) lines were used to assess variation in floret size, and to measure any effects of floret size on pollinator visitation. Among 100 inbreds sampled, there was significant variation among the lines, with floret lengths of 6.8–9.9 mm. Floret length, measured before anthesis, was closely related to corolla depth during anthesis and was consistent between 2 years (environments). Pollinator observations on 30 inbred lines showed floret size explained a majority (52%) of the variation in wild bee preference, with a reduction in floret length of 2 mm more than doubling pollinator activity. Though honey bee, Apis mellifera L., colonies were located ≈ 60 m from the plots, near-zero honey bee activity in the sunflowers precluded an assessment of how strongly this managed pollinator is affected by floret length. Production of inbreds and hybrids with smaller florets could enhance sunflower pollination, but genetic markers for floret size are needed to facilitate selection, and an understanding of potential trade-offs also is required. Information on variation and heritability of other traits, such as pollen and nectar rewards, could help explain residual variation in wild bee visitation to sunflowers.

Soft wheat (Triticum aestivum L.) improvement could be enhanced by the identification of germplasm with superior end-use quality traits. Due to the geographic and historical separation of eastern and western US soft wheat germplasm ‘pools’, genetic differences in end-use quality may exist among cultivars arising from these two pools. To identify such differences, 30 US soft wheat cultivars were evaluated in ‘head-to-head’ trials over 3 years in Washington state. Cultivars were classified as: eastern soft red winter (SRW), eastern soft white winter (ESWW), western soft white (WSWW) and western Club. These four soft wheat cultivar classifications clearly differed systematically for some of the quality traits examined. The Club wheat cultivar group had the highest flour yield and flour ash. The Club group also had the lowest mixograph dough water absorption. Milling score (which incorporates break flour yield) was highest for Club and ESWW. Eastern soft red and white wheat cultivar groups had lower flour ash and alkaline water retention capacity (AWRC) compared to the western Club and soft white wheats; ESWW had the lowest AWRC of any classification. Cookie diameter was greatest for the ESWW group, followed by the SRW and Club groups (which were not significantly different), and then by the WSWW group. Individual cultivars with exceptional quality traits were also identified. These results indicate that the four US soft wheat germplasm pools differ, and they may be valuable genetic resources for ‘inter-pool’ wheat improvement.

Triticum boeoticum is a valuable gene source for tolerance to drought stress. In order to study the effect of drought stress on this plant, and to understand its adaptive mechanisms at the molecular level, 10 accessions of T. boeoticum were evaluated under non- and drought stress conditions. Evaluation of 31 different phenological, morpho-physiological and root-related traits showed that there were significant differences between accessions. Using the bi-plot resulting from the PCA, the studied traits and accessions were separated in different groups. The most tolerant (B5) and susceptible (B6) accessions to drought stress were identified, so these accessions were used for assessment of changes in the TaNAC2 and TaNAC69-1 transcription factors (TFs) expression. The results showed that in the most tolerant and susceptible accessions, TaNAC2 and TaNAC69-1 expression levels increased between non-stress and stress conditions significantly, but the increased level of these two genes expression in the most tolerant accession was much higher than the most susceptible accession. According to the obtained results, T. boeoticum can be a suitable and promising gene source for improving modern wheat. In addition, the results of TFs expression could improve our understanding about the complex mechanisms associated with drought tolerance in wheat, especially wild wheat.

Grapevine cultivar identification is based mainly on two complementary methodologies: microsatellite (simple sequence repeat (SSR)) DNA analysis and traditional ampelography. Here, we report a direct multiplex PCR approach that allows the simultaneous amplification of 11 SSR loci from crude samples, i.e. bypassing DNA extraction, by using an engineered DNA polymerase improved to tolerate plant PCR inhibitors. Many different plant tissues were successfully amplified: leaf, root, wood, berry flesh and skin, stalk and must, from wine and table grape varieties, and rootstocks. The direct multiplex PCR that we propose is quicker and cheaper than the methodologies used until now, and provides accurate results. Thus, SSR DNA analysis becomes economically more accessible to a larger number of potential users in addition to research institutes.

Crop wild relatives (CWR) are valuable resources for crop breeding due to their close genetic relationship to the cultivated plants and their wide genetic variation, allowing the introgression of desirable traits into the crops, such as resistance to plant pests and diseases or adaptability to climate change. Mexico is a centre of agrobiodiversity, including CWR, but climate change, and other factors, are contributing to the loss of important Mexican CWR genetic diversity. The in situ and ex situ conservation status of Mexican priority CWR were assessed through a gap analysis as part of a national CWR conservation strategy for Mexico, to ensure the long-term preservation and improve the availability of these genetic resources. A set of 310 priority CWR taxa, previously identified as part of the national CWR inventory for Mexico, were analysed. Species distribution modelling and ecogeographic diversity analyses were used to detect gaps in in situ and ex situ conservation at taxon and ecogeographic levels. Priority target sites were identified throughout the country for complementary in situ and ex situ conservation of these taxa. The results obtained allow us to make recommendations for immediate conservation actions, thus helping to mitigate the threats to Mexican agrobiodiversity and enhance both national and global food security.

Frost damage was evaluated in 1-year-old olive trees in the cultivars ‘Arbequina’, ‘Cornicabra’, ‘Empeltre’, ‘Frantoio’, ‘Hojiblanca’, ‘Manzanilla Cacereña’, ‘Nevadillo de Jaén’, ‘Picual’, ‘Picudo’ and ‘Verdial de Badajoz’ in Madrid, Spain. Temperatures fell to −6.5 and −10.5°C on 11 November and 16 December 2001, respectively. In May frost damage was visually assessed. The olive trees were pruned to the ground and dry matter was quantified in shoots and leaves with and without signs of frost damage. In August resprouting was visually evaluated. Visual assessment overestimated frost damage compared to the quantitative evaluation. Leaves had a lower resistance to frost than shoots. Shoot frost resistance was linearly correlated to the cultivar's resprouting capacity. Significant differences in frost resistance were found between cultivars. ‘Cornicabra’ and ‘Arbequina’ had a low percentage of frost-damaged shoots and a high resprouting capacity after frost. The cultivars which were the least resistant to frost were ‘Empeltre’, ‘Frantoio’ and ‘Hojiblanca’. These cultivars had a high percentage of frost-damaged shoots and almost no resprouting capacity. ‘Picual’, ‘Picudo’, ‘Verdial de Badajoz’, ‘Manzanilla Cacereña’ and ‘Nevadillo de Jaén’ had an intermediate frost resistance.

Heat stress greatly limits the productivity of wheat in many regions. Knowledge on the degree of genetic diversity of wheat varieties along with their selective traits will facilitate the development of high yielding, stress-tolerant wheat cultivar. The objective of this study were to determine genetic variation in morpho-physiological traits associated with heat tolerance in 30 diverse wheat genotypes and to examine genetic diversity and relationship among the genotypes varying heat tolerance using molecular markers. Phenotypic data of 15 traits were evaluated for heat tolerance under non-stress and stress conditions for two consecutive years. A positive and significant correlation among cell membrane stability, canopy temperature depression, biomass, susceptibility index and grain yield was shown. Genetic diversity assessed by 41 polymorphic simple sequence repeat (SSR) markers was compared with diversity evaluated for 15 phenotypic traits averaged over stress and non-stress field conditions. The mean polymorphic information content for SSR value was 0.38 with range of 0.12–0.75. Based on morpho-physiological traits and genotypic data, three groups were obtained based on their tolerance (HHT, MHT and LHT) levels. Analysis of molecular variance explained 91.7% of the total variation could be due to variance within the heat tolerance genotypes. Genetic diversity among HHT was higher than LHT genotypes and HHT genotypes were distributed among all cluster implied that genetic basis of heat tolerance in these genotypes was different thereby enabling the wheat breeders to combine these diverse sources of genetic variation to improve heat tolerance in wheat breeding programme.

Within the cultivated peanut species (Arachis hypogaea L.), there are two subspecies comprising six botanical varieties, and the effect of botanical taxon on oil content and fatty acid composition variability is unclear. To gauge the variability, 83 peanut accessions were analyzed for oil content (expressed at 0% moisture) and fatty acid composition. We found that within the subsp. hypogaea, var. hypogaea contained a much higher amount of oil in seeds than did the var. hirsuta Köhler (520 vs. 473 g/kg, P < 0.05); within the subsp. fastigiata Waldron, the vars. aequatoriana Krapov. & W.C. Gregory and vulgaris Harz contained a similar amount of oil in seeds (491 g/kg), not significantly different from other botanical varieties, but var. fastigiata contained a higher amount of oil (500 g/kg) than the var. peruviana Krapov. & W.C. Gregory (483 g/kg). In terms of the fatty acid composition, oil from seeds of var. hypogaea contained much more oleic acid than did var. hirsuta (491 vs. 377 g/kg, P < 0.05), but much less palmitic acid (97 vs. 138 g/kg, P < 0.05%) and linoleic acid (308 vs. 402 g/kg, P < 0.05). Oil from seeds of var. vulgaris contained much more oleic acid than did var. aequatoriana (437 vs. 402 g/kg, P < 0.05), but much less linoleic acid (346 vs. 380 g/kg, P < 0.05). Significant negative correlations of oleic with palmitic and linoleic acids were detected. The information on the oil content and fatty acid composition variability among botanical varieties would be useful for peanut breeders seeking germplasm containing both high oil content and proper fatty acid composition.

Drought tolerance (DT) is a very complex trait. For the purpose of developing DT rice cultivars, a research programme was initiated in 1997 in China, consisting of four coherent parts: the development of a DT field screen facility and evaluation standard; the collection, evaluation and enhancement of DT rice resources; DT gene/quantitative trait locus (QTL) discovery; and DT rice breeding. More than 2000 rice accessions, mostly from China, were collected and evaluated in a new DT screening facility with a powerful water management system. Eighty-six entries were selected to serve as a core DT collection. A set of 187 recombinant inbred lines was developed for the genetic mapping of DT and high yield-related QTL under drought conditions. Several DT rice cultivars adapted to southern and central China were released. DT rice CMS lines were developed and distributed to most parts of China to encourage the development of DT or water-saving hybrid rice.

To assess the genetic diversity of spinach germplasm, 250 individuals of 50 accessions collected from geographically diverse regions (West Asia, East Asia, Japan, Europe and the USA) were analysed using simple sequence repeat (SSR) markers. A total of 39 polymorphic alleles were identified, with an average of 6.5 alleles per locus for six loci. The overall gene diversity (0.62) in the entire set of individuals suggests that the germplasm has high genetic variability. The West Asian accessions showed the highest gene diversity, with a value of 0.57, followed by the East Asian accessions. These results help confirm the notion that spinach originated from West Asia. Hierarchical analysis of molecular variance revealed significant genetic differentiation among the geographical regions, which accounts for 26% of the total variation detected. Furthermore, pairwise Φst values indicate low genetic differentiation between the East Asian and Japanese germplasm accessions, both of which showed high genetic differentiation from the European accessions. The differentiation between the East Asian and European gene pools may be attributed to the founder effect associated with crop dissemination, as well as to the selection and genetic drift that occurred during the breeding process.

The recent introduction of Illumina single nucleotide polymorphism (SNP) arrays is an important step towards comprehensive genome-wide studies of genetic diversity in wheat. In this study, 90 cultivars of hexaploid spring wheat growing in Kazakhstan were genotyped using the high-density wheat 90 K Illumina SNP array. The analysis allowed the identification of 30,288 polymorphic SNPs. A subset of 3541 high-quality SNPs were used for a comparison of 690 wheat accessions representing landraces and varieties, including those from Asia, Australia, Canada, Europe, Kazakhstan, USA and other parts of the world. Phylogenetic analysis showed a clear separation of wheat cultivars according to their geographic origin. In the phylogenetic tree, accessions from Kazakhstan and the USA formed two neighbouring clusters with a common node, and they were distinct from accessions from other regions of the world, including Europe. The results provide important new insights into the genetic relationships between diverse wheat accessions.

Ethiopia is believed to be the centre of origin and domestication for sorghum, where sorghum remains one of the main staple crops. Loss of biodiversity is occurring at an alarming rate in Ethiopia and crops, including sorghum, have long been recognized as vulnerable to genetic erosion. A major collection of sorghum germplasm was made in 1973 by Gebrekidan and Ejeta from north-eastern Ethiopia. A new collection of landraces was made in 2003, and these were field evaluated at Sirinka in 2004 along with representative samples from the 1973 collection. Farmer surveys and soil and climate surveys were also performed. Preliminary analysis demonstrated that some important landraces have disappeared either locally or regionally in the past 30 years and many other landraces have become marginalized. Landraces which are less preferred in terms of agronomic value and end use, and introductions, have become increasingly important. Late maturing landraces were found to be particularly vulnerable, with a number disappearing altogether. Farmers have become more risk averse, and factors such as declining soil fertility, more frequent drought and unreliable rainfall, and increased pest infestation have contributed to a change in farmer landrace selection. Data are presented on the variability and unique characters of some of the Ethiopian landraces, and implications for conservation are discussed.

The purpose of the study was to support the selection process of the most valuable currant and gooseberry accessions cultivated in Northern Europe, in order to establish a decentralized core collection and, following the selection, to ensure sufficient genetic diversity in the selected collection. Molecular analyses of the material from nine project partners were run at seven different laboratories. The results were first analysed for each partner separately, and then combined to ensure sufficient genetic diversity in the core collection.

Colombia, situated at the northern end of the Andes mountains of South America and in proximity to Central America, is an important centre of diversity for common bean (Phaseolus vulgaris L.) that has a mix of cultivated germplasm from both major gene pools (Andean and Mesoamerican) for the species. Microsatellites are a useful marker system for analyzing genetic diversity of this crop and can be analyzed with manual (silver-stain) or automated (ABI) detection systems and using unlabelled or fluorescently labelled markers, respectively. The objectives of this research were to evaluate the genetic diversity of 92 Colombian landraces and gene pool controls with 36 fluorescent and 30 non-fluorescent microsatellite markers and to determine the extent of introgression between the Andean and Mesoamerican gene pools for this germplasm. A comparison of fluorescent versus non-fluorescent marker systems was performed with 14 loci, which were evaluated with both methods; the fluorescent markers were found to be more precise than the non-fluorescent markers in determining population structure. A combined analysis of 52 microsatellites using the 36 fluorescent markers and 16 non-overlapping, silver-stained markers produced an accurate population structure for the Andean gene pool that separated race Nueva Granada and race Peru genotypes and clearly identified introgression between these races and the gene pools. The results of this research are important for the application of microsatellite markers to diversity analysis in common bean and for the conservation of landraces in Colombia and neighbouring countries of Latin America, where similar germplasm exists and where gene pool or race mixtures also occur.

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.

More than 3200 new mutant varieties have been bred and used by millions of farmers, which has significantly contributed to world food security. A lot more mutants have also served as tools for gene discovery and functional analysis. Recent genomic approaches including TILLING (Targeting Induced Local Lesions In Genome) have enabled screening of mutations at the molecular level. This review describes the molecular nature of chemically and physically induced mutations and their repercussions. Analyses of TILLING reports indicate that chemically induced mutations are mostly nucleotide substitutions, but that mutation frequencies fluctuate among plant species ranging from one DNA lesion per 300 kbp in Arabidopsis to one DNA lesion per 30 kbp in bread wheat, which reciprocate with an increase in ploidy levels. The majority (>95%) of chemically induced DNA lesions are silent or missense mutations. Mutations induced by physical mutagens seem to be more diverse, including single-nucleotide substitutions, insertions, inversions and translocations, although short deletions ( < 15 bp) are relatively more predominant. The proportion of complex mutations (translocation, inversions, etc.) may increase with an increase in the linear energy transfer of radiations. In addition, the implications of these findings for the roles of induced mutants in breeding and gene function analysis are briefly discussed.

Eighty-six chickpea (Cicer arietinum L.) genotypes, including 44 Kabuli type and 42 Desi type, were evaluated for their phenological, physicochemical and cooking quality traits. There were significant differences among the genotypes for days to 50% flowering (34–81 d), days to maturity (85–122 d), number of pods per plant (13–66), number of seeds per plant (15–85), 100-seed weight (10.5–58.6 g), seed yield (561–1852 kg/ha), hydration capacity (0.11–0.68 g water/seed), hydration index (0.80–1.21), swelling capacity (0.11–0.7 ml/seed), seed volume (0.1–0.52 ml/seed) and cooking time (38–125 min). The Desi and Kabuli types of chickpea differed significantly from each other for all the traits except for hydration index, swelling index and cooking time. High heritability coupled with high genetic advance was recorded for 100-seed weight, hydration capacity, swelling capacity and seed volume in both Desi and Kabuli genotypes. Seed size (100-seed weight and seed volume) showed significant positive correlations with hydration capacity and swelling capacity. Cooking time did not show any significant positive or negative correlation with any of the traits studied, including seed size, indicating that other additional factors may be involved in controlling cooking time. The results of this study indicate that it is possible to develop cultivars with faster cooking time in both Kabuli and Desi types and in all seed size categories.

Characterization of plant germplasm using molecular techniques is playing an increasingly important role in the management and utilization of plant genetic resources, but has its limitations in the screening of large numbers of accessions held in seed genebanks worldwide. Bulking individual plants from one accession or group to form a representative sample is a promising approach to widening the scope of a characterization, but it is not without technical problems in detecting genetic variation. This review was conducted to assess the technical pitfalls of bulking, and to evaluate the effectiveness of various bulking methods in the assessment of genetic variation and genetic relationships, and in the identification of plant germplasm. Clearly, some alleles, particularly those occurring at low frequency, may go undetected in a bulked sample, depending on the bulking methods and the molecular techniques used. As a result, genetic diversity estimates and genetic relationship inferences can be significantly biased. Germplasm identification may not be always reliable. Thus, it is imperative that the detection limit imposed by bulking be assessed for a newly initiated molecular germplasm characterization and bias be considered in interpretation of the resulting characterization data. Equally imperative is the need for continuous efforts of exploring efficient bulking procedures for the screening of large germplasm collections, particularly by the newly developed marker systems.

Niche modelling software can be used to assess the probability of detecting a population of a plant species at a certain location. In this study, we used the distribution of the wild relatives of lettuce (Lactuca spp.) to investigate the applicability of Maxent species distribution models for collecting missions. Geographic origin data of genebank and herbarium specimens and climatic data of the origin locations were used as input. For Lactuca saligna, we varied the input data by omitting the specimens from different parts of the known distribution area to assess the robustness of the predicted distributions. Furthermore, we examined the accuracy of the modelling by comparing the predicted probabilities of population presence against recent expedition data for the endemic Lactuca georgica and the cosmopolitan Lactuca serriola. We found Maxent to be quite robust in its predictions, although its usefulness was higher for endemic taxa than for more widespread species. The exclusion of occurrence data from the perceived range margins of the species can result in important information about local adaptation to distinct climatic conditions. We discuss the potential for enhanced use of Maxent in germplasm collecting planning.