Alternative oxidase (AOX) has been proposed as a promising functional marker candidate for multiple plant stress behaviour. The present paper describes natural polymorphism in AOX2b of Daucus carota L. (DcAOX2b). Exon-primed intron crossing-PCR (EPIC-PCR) revealed length variation (intron length polymorphisms, ILPs) in intron 1. Six fragment patterns were identified in 40 genotypes. However, no more than two fragments were found per genotype, suggesting the presence of two alleles. The ILPs were able to discriminate between single plant genotypes in cv. Rotin and to distinguish individual wild carrot plants. The repetitive pattern of intron 1 length variation allows the grouping of genotypes for functional analysis in future studies. Sequence analysis in intron 1 of polymorphic but also of obviously identical PCR-fragments revealed underlying high levels of sequence polymorphisms between alleles and genotypes. Variation was due to repetitive insertion/deletion (InDel) events and single-nucleotide polymorphisms (SNPs). The results suggest that high AOX2b gene diversity in D. carota may be a source of functional markers for agronomic traits related to environmental stress responses.

Changes in global biodiversity at the genetic level have proved difficult to determine for most organisms because of lack of standardized, repeated or historical data; this hampers the attempts to meet the convention on biological diversity (CBD) 2010 targets of reducing loss of genetic diversity, particularly of crop species. For rice, where germplasm and genetic data have been collected throughout South and Southeast Asia over many decades, contrary to popular opinion, we have been unable to detect a significant reduction of available genetic diversity in our study material. This absence of a decline may be viewed positively; over the 33-year timescale of our study, genetic diversity amongst landraces grown in traditional agricultural systems was still sufficiently abundant to be collected for ex situ conservation. However, if significant genetic erosion does take place in the future as a result of accelerating global warming and/or major changes in land use or agricultural practices, will it be catastrophic or gradual, and how will it be detected? We have shown a strong link between numbers of landraces collected (and therefore extant) and genetic diversity; hence, we have a clear indicator to detect loss of genetic diversity in the future. Our findings lend considerable support for ex situ conservation of germplasm; the more than substantial genetic resources already in genebanks are now safe. On the other hand, it is the germplasm growing in farmers' fields, continually adapting genetically to changing environmental conditions and evolving novel genetic forms, whose future has been much less certain but can now be effectively monitored using our criteria.

Drought is a major constraint to oil palm plantation in many regions relying on rainfall. One strategy to overcome this problem is to develop drought-tolerant cultivars through screening and selection. Drought tolerance assessment based on growth and physiological traits provides an alternative approach for rapid screening especially in tree crops. The aims of this study were to determine the contribution of some growth and physiological parameters to drought response variation in oil palm seedling and to use those parameters to evaluate relative drought stress tolerance in tenera oil palm progenies. Eight D × P progenies were grown under well-watered, moderate and severe stressed conditions for a total of 6 months. Data on growth traits, maximum quantum yield (Fv/Fm), SPAD value and proline content were recorded. Principal component analysis (PCA) on studied traits revealed that PC1 and PC2 explained 74.57 and 76.80% of total variance in moderate and severe drought treatments, respectively. Major contributions towards the variation of control and drought-treated plants were identified and appeared to be growth traits in moderate drought stress and growth trait plus proline content in severe drought stress. According to drought tolerance index, PCA analysis and ranking method using integrated PCA values, PSU-106 and PSU-206 were identified to be relatively high tolerant to severe drought stress, while PSU-106, PSU-128, PSU-206 and PSU-208 were tolerant to moderate drought stress. Field validation of D × P progenies selected as drought tolerance is recommended to establish this indirect selection approach in oil palm breeding programme.

The overexpression of wheat Bx7 subunit (Bx7OE) encoded by the Glu-B1al allele is originated from a duplication event of the Bx7 gene, and has a positive effect on gluten strength. Thus, it is an important genetic resource for wheat quality improvement. In this study, the Bx7OE subunit from a large number of bread wheat and related species was characterized by sodium dodecyl sulphate–polyacrylamide gel electrophoresis, reversed-phase high-performance liquid chromatography (RP-HPLC) and Sequence-Tagged sites (STS) markers. Only 31 bread wheat varieties were found to carry Bx7OE. RP-HPLC quantification analysis revealed that the mean proportion of the Bx7OE subunit to the total amount of high-molecular-weight glutenin subunits among the 31 bread wheat varieties was 41.8%, which is much higher than that of varieties with the normal Bx7 subunit (generally at 30%). Flour quality analysis of seven representative varieties with Bx7OE and three with the normal Bx7 subunit showed that the varieties with Bx7OE generally displayed better gluten strength than those with the normal Bx7 subunit. STS markers demonstrated that, in addition to the 31 bread wheat varieties with Bx7OE, no PCR products were obtained from the related Triticum and Aegilops species. This suggests that the retroelement-mediated recombination event at the Glu-B1 locus could have occurred more recently, later than the formation of hexaploid wheat. The Bx7OE subunit is mainly distributed in some bread wheat varieties from American countries with a low frequency, which is of particular importance for the quality improvement of wheat gluten.

Bioprospecting is the search for valuable products from natural sources. Given that most species are poorly known, a key question is where to search. Ethnodirected bioprospecting approaches use traditional knowledge in the process of selecting plants to screen for desired properties. A complementary approach is to utilize phylogenetic analyses based on traditional uses or known chemistry to identify lineages in which desired properties are most likely to be found. Novel discoveries of plant bioactivity from these approaches can aid the development of treatments for diseases with unmet medical needs. For example, neurological disorders are a growing concern, and psychoactive plants used in traditional medicine may provide botanical sources for bioactivity relevant for treating diseases related to the brain and nervous system. However, no systematic study has explored the diversity and phylogenetic distribution of psychoactive plants. We compiled a database of 501 psychoactive plant species and their properties from published sources. We mapped these plant attributes on a phylogenetic tree of all land plant genera and showed that psychoactive properties are not randomly distributed on the phylogeny of land plants; instead certain plant lineages show overabundance of psychoactive properties. Furthermore, employing a ‘hot nodes’ approach to identify these lineages, we can narrow down our search for novel psychoactive plants to 8.5% of all plant genera for psychoactivity in general and 1–4% for specific categories of psychoactivity investigated. Our results showcase the potential of using a phylogenetic approach to bioprospect plants for psychoactivity and can serve as foundation for future investigations.

Iron (Fe) and zinc (Zn) contents in hexaploid wheat are very low and are further reduced because of the removal of micronutrient-rich bran of wheat grains during milling and processing. Therefore, hexaploid wheat, its wild species and wheat–Aegilops kotschyi substitution lines were evaluated to identify the genome(s) carrying gene(s) for high Fe and Zn concentrations in bran and endosperm fractions of grains. It is reflected from the results that Triticum monococcum (acc. W463) may serve as a promising donor for biofortification of Fe, and Aegilops speltoides (acc. 3804) may serve as a promising donor for biofortification of Zn in the endosperm of cultivated wheat. Further, among the three wheat–Ae. kotschyi substitution lines, the higher concentration of Fe and Zn in endosperm fraction was observed in BC2F4 63-2-13-1. The work on precise transfer of useful gene(s) from 7Uk chromosome of this line is in progress to reduce linkage drag.

Crop wild relatives (CWR) can provide one solution to future challenges on food security, sustainable agriculture and adaptation to climate change. Diversity found in CWR can be essential for adapting crops to these new demands. Since the need to improve in situ conservation of CWR has been recognized by the Convention on Biological Diversity (CBD) (2010) and the Global Strategy for Plant Conservation (2011–2020), it is important to develop ways to safeguard these important genetic resources. The Nordic flora includes many species related to food, forage and other crop groups, but little has been done to systematically secure these important wild resources. A Nordic regional approach to CWR conservation planning provided opportunities to network, find synergies, share knowledge, plan the conservation and give policy inputs on a regional level. A comprehensive CWR checklist for the Nordic region was generated and then prioritized by socio-economic value and utilization potential. Nordic CWR checklist was formed of 2553 taxa related to crop plants. Out of these, 114 taxa including 83 species were prioritized representing vegetable, cereal, fruit, berry, nut and forage crop groups. The in situ conservation planning of the priority CWR included ecogeographic and complementarity analyses to identify a potential network of genetic reserve sites in the region. Altogether 971,633 occurrence records of the priority species were analysed. A minimum number of sites within and outside existing conservation areas were identified that had the potential to support a maximum number of target species of maximum intraspecific diversity.

Cytological understanding is an important parameter to understand the genetic architecture of yam bean. The ploidy level and genome size of two cultivated species of yam bean (Pachyrhizus erosus and P. tuberosus) were estimated using flow cytometric analysis of young leaf tissue, with propidium iodide as a fluorescent dye. Six genotypes of P. erosus and three genotypes of P. tuberosus were analysed. Rice (Oryza sativa cv. Nipponbare) and Mung bean (Vigna radiata cv Berken) were used as internal reference standards. Variation of 2C nuclear DNA content among the six P. erousus lines was 4.18%, ranging from 1.17 to 1.22 pg, whereas only 1.8% variation was observed among the three P. tuberosus lines, which ranged from 1.07 to 1.09 pg. Moreover, it was found that the nuclear DNA content of P. tuberosus was lower than that of P. erosus. The result of the flow cytometric analysis showed that all the species were diploid (2n = 2x) and coefficient of variation (CV%) of all the accessions of the two species was less than 3.5%. This is the first report of ploidy analysis and genome size estimation of the leguminous underutilized tuber crop yam bean using flow cytometry. This result will be helpful for yam bean genome sequencing and crop improvement programmes.

Overexploitation in search of its valuable non-wood fragrance product has put pressure on the survival of the endangered Aquilaria trees in the wild. In this study, the pattern of genetic variation among wild populations was measured to aid in designing useful strategies for in situ conservation. We sequenced the internal transcribed spacer (ITS) of the nuclear region of 19 wild Aquilaria malaccensis populations from different states in Peninsular Malaysia, and compared the sequence with the same species residing outside of Malaysia, mainly from the Assam region in India and Sumatra in Indonesia. This widely distributed species is found in the Indomalesian region and is a major source of agarwood. In addition, we included five wild Aquilaria hirta populations for semblance purposes. Intraspecific variations were not found within A. malaccensis and A. hirta populations in Peninsular Malaysia. Interestingly, Single Nucleotide polymorphisms (SNPs) were identified when comparing A. malaccensis from three geographical regions, with a total of 25 SNPs detected. We imply that geographical segregation is a contributing factor toward genetic variation in A. malaccensis. This is the first report on utilizing the ITS region for analysing genetic variation in A. malaccensis of various geographical regions. The molecular information obtained in this study will serve as a useful reference in designing in situ programmes for this endangered species.

Mineral nutrient deficiencies are a worldwide problem that is directly correlated with poverty and food insecurity. The most common of these is iron deficiency; more than one-third of the world's population suffer from iron deficiency-induced anaemia, 80% of which are in developing countries. The consequences of iron deficiency include increased mortality and morbidity rates, diminished cognitive abilities in children and reduced labour productivity, which in turn stagnates national development. The developed world has made tremendous success in alleviating nutrient deficiencies through dietary diversification, food product fortification, improved public health care and supplementation. In developing countries, these strategies are often expensive and difficult to sustain, especially in rural areas. The rural poor typically consume what they grow and are dependent upon a small number of staple crops for the vast majority of their nutrition. Therefore, genetic improvement of staple crops (biofortification) is the most cost-effective and sustainable solution to this global health problem. In this study, we describe a strategy to enhance iron nutritional quality in maize using a human cell culture (Caco-2)-based bioassay as a phenotyping tool to guide genetic analysis of the trait. We also report validation of this approach using an animal feeding study.

Improving plant resistance against Fusarium wilt (FW) is key to sustaining chickpea production worldwide. Given this, the current study tested a set of 75 FW-responsive chickpea breeding lines including checks in a wilt-sick plot for two consecutive years (2016 and 2017). Genetic diversity analysis using 75 simple sequence repeats (SSRs) revealed a total of 267 alleles with an average of 3.56 alleles per marker. The entire set was divided into two major classes based on clustering method and factorial analysis. Similarly, STRUCTURE analysis placed the 75 genotypes into three distinct sub-groups (K = 3). Marker-trait association (MTA) analysis using the generalized linear model approach revealed nine and eight significant MTAs for FW resistance in the years 2016 and 2017, respectively. Three significant MTAs were obtained for FW resistance following the mixed linear model approach for both years. The SSR markers CESSR433, NCPGR21 and ICCM0284 could be potentially employed for targeted and accelerated improvement of FW resistance in chickpea. To the best of our knowledge, this is the first report on association mapping of the genomic loci controlling FW (Foc2) resistance in chickpea.

Numerous factors influence the chemical quality of medicinal plants from crop establishment to extraction of raw material. The most important ones are described using the example of Hypericum perforatum. Optimization of these factors contributes to the objective of producing a high-quality drug, and a method consisting of three scientific approaches (technological, agronomical, plant breeding) is presented. All data concerning the plant (biology, physiology and environmental impacts) and the active components and by-products (pathway, localization and stability) are useful to adapt and to develop management sequences. Although plant breeding appears to be the principal way of improvement, and gives good results in terms of resistance to pathogens, active component content and yield; the agronomical and the technological approaches are also very important. The technological approach after harvesting is especially important to avoid degradation of the active components and to induce, in some cases, the transformation of by-products to those molecules sought. This integrated method (plant breeding and agronomical and chemical approaches) requires research on different levels of organization from molecule to field, and includes all processing systems from farmers to chemists.

Extensive research has been conducted on the characterization of hundreds of date palm (Phoenix dactylifera L.) cultivars worldwide. However, the population genetics of date palms has never been studied. In this study, we collected 200 individuals from 19 populations of different geographical locations in Sudan. The collection sites were grouped according to the type of dates (date palm fruits) that dominates in the area. Ten microsatellite markers were used to investigate the genetic diversity within and among populations and the correlation between the genetic and geographical distances. The tested microsatellite markers showed a high level of polymorphism. A total of 261 alleles were detected at the ten loci. The overall mean value of fixation indices equalled − 0.163, which shows the presence of excess heterozygosity. However, the χ2 tests conducted for every locus in each population indicated no significant deviation from the Hardy–Weinberg equilibrium. The analyses of molecular variance exhibited that about 95% of the total genetic variation existed within populations, while significant differentiation within the type groups could be detected. Although significant isolation by distance (r2 = 0.552, P < 0.05) was detected by a Mantel test, it seems that the spatial effect has become complicated as a result from the exchange and introduction of different kinds of plant materials by date palm growers and traders, as well as seed dispersal. This complexity was clearly apparent in the weak clustering relationships among most of the tested populations.

Graminaceous plants including staple cereals secrete certain phytosiderophores (PS) in calcareous soils with lower iron and zinc availability to enhance their uptake and translocation to the leaves and grains. A few Triticum aestivum cultivars and accessions of six Aegilops species were investigated for release of PS in vitro under iron- and zinc-sufficient and -deficient conditions, and for root and shoot iron and zinc concentrations. All the Aegilops species had three to four times higher release of PS than the wheat cultivars under both nutrient-sufficient and -deficient conditions. The maximum rate of increase of PS was observed on days 11 and 14 under iron- and zinc-deficient conditions, respectively, which levelled off rapidly among the wheat cultivars and continued to be high among Aegilops species till the end of the experiment. The absolute amount of iron and zinc expressed on dry weight basis after 18 d under iron- and zinc-deficient conditions showed nearly three times higher concentration in both roots and shoots of Aegilops species than that of the wheat cultivars. A significantly high correlation between concentrations of iron (r = 0.94) and zinc (r = 0.91) in roots and the PS released was found. The higher grain iron and zinc contents in the Aegilops species reported earlier may be attributed to their diverse and efficient mechanism(s) for PS-mediated micronutrient uptake and translocation system, which could be exploited for biofortification of wheat.

White Guinea yam (Dioscorea rotundata Poir.) is indigenous to West Africa, a region that harbours the crop's tremendous landrace diversity. The knowledge and understanding of local cultivars’ genetic diversity are essential for properly managing genetic resources, conservation, sustainable use and their improvement through breeding. This study aimed to dissect phenotypic and molecular diversity of white yam cultivars from Benin using agro-morphological and single nucleotide polymorphism (SNP) markers. Eighty-eight Beninese white Guinea yam cultivars collected through a countrywide ethnobotanical survey were phenotyped with 53 traits and genotyped with 9725 DArT-SNP. Multivariate analysis using phenotypic traits revealed 30 traits as most discriminative and explained up to 80.78% of cultivars’ phenotypic variation. Assessment of diversity indices such as Shannon–Wiener (H′), inverse Shannon (H.B.), Simpson's (λ) index and Pilou evenness (J) based molecular and phenotypic data depicted a moderate genetic diversity in Beninese white Guinea yam cultivars. Genetic differentiation of cultivars among country production zones was low due to the high exchange of planting materials among farmers of different regions. However, there was high genetic diversity within regions. Hierarchical clusters (HCs) on phenotypic data revealed the presence of two groups while HCs based on the SNP markers and the combined analysis identified three genetic groups. Our result provided valuable insights into the Beninese white Guinea yam diversity for its proper conservation and improvement through breeding.

The wheat landraces collected by Dr Hitoshi Kihara et al. from Afghanistan, the place of secondary origin of wheat, are an untapped genetic resource for mining novel alleles. In this study, approximately 400 landraces were collected from seven agroecological zones and characterized using diversity array technology and single-nucleotide polymorphism markers, as well as diagnostic molecular markers at important loci controlling vernalization (Vrn), photoperiod response (Ppd), grain colour (R), leaf rust (Lr), yellow rust (Yr), stem rust (Sr) and Fusarium head blight (Fhb). A genome-wide marker array revealed a large amount of genetic diversity among the landraces, 53% of which were winter types, 43% were either spring types or facultative and 4% were either unknown or had Vrn-A1c – a rare spring allele that needs to be confirmed with additional genotyping and phenotyping. At Ppd, 97% of the lines carried a photosensitive allele. In the case of grain colour, classification based on dominant or recessive allelic combinations revealed that approximately 39% of the population is characterized by white grain. Four gene-specific markers that were targeted to identify loci for rust and Fhb resistance enabled us to identify 17 unique landraces with known resistance genes.

The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) genebank in India holds the world's largest collection of 21,594 pearl millet germplasm accessions including 18,447 landraces from 50 countries. West and Central Africa (WCA) region, which is considered as the centre of diversity for pearl millet, is also an important pearl millet germplasm source for resistance to biotic and abiotic stresses. A total of 7372 landraces were assembled from WCA countries. Out of which, 6434 landraces have the georeference data. The geographic origins of these landraces were analyzed using geographic information system tools to identify gaps in the collection. Geographical distribution of existing collections, type of vegetation, land cover and the high probability (>70%) for the occurrence of pearl millet estimated using the FloraMap software in different countries show that 62 districts in 13 provinces of Nigeria, 50 districts in 16 provinces of Burkina Faso, 9 districts in 6 provinces each of Mali and Mauritania, 8 districts in 8 provinces of Chad and 7 districts in 3 provinces of Ghana as the major geographical gaps in the pearl millet collection at the ICRISAT genebank. In view of this, we suggest that the final areas for exploration in these districts should be decided prior to the launch of the collection missions in consultation with local government officials and extension officers, who have the knowledge of pearl millet cultivation in the districts identified.

The grain of modern wheat cultivars has a significantly lower mineral content, including the content of copper, iron, magnesium, manganese, phosphorous, selenium and zinc. For this reason cereal breeders, are constantly searching for new genetic sources of minerals that are essential in human nutrition. Triticum polonicum, which is grown on a small scale in Spain, southern Italy, Algeria, Ethiopia and warm regions of Asia, deserves special attention in this context. The micronutrient and macronutrient content of T. polonicum versus T. durum and T. aestivum was compared in this study. Polish wheat grain was characterized by the significantly highest content of phosphorus (4.55 g/kg), sulphur (1.82 g/kg), magnesium (1.42 g/kg), zinc (49.5 mg/kg), iron (39.1 mg/kg) and boron (0.56 mg/kg) as well as a low content of aluminium (only 1.04 mg/kg). The macronutrient profile of most T. polonicum lines differed completely from that of common wheat and durum wheat. The principal component analysis supported discrimination of seven Polish wheat lines with a particularly beneficial micronutrient profile (P2, P3, P5, P7, P9, P22 and P25). These lines were characterized by the highest content of copper, iron and zinc, as well as the lowest concentrations of strontium, aluminium and barium which are undesirable in food products. The above lines can be potentially applied as source materials for breeding new wheat varieties. The results of this study indicate that Polish wheat could be used in genetic biofortification of durum wheat and common wheat.

Molecular variability of vanilla (Vanilla planifolia) and three wild species was assessed to explore the possible sources of variation that can be used for crop improvement. A total of 154 ISSR loci were analysed by the UPGMA, assignment tests of individuals (STRUCTURE) and indices of genetic diversity. The assignment tests were done at two levels: first considering the four species and then only the accessions of V. planifolia. The molecular analysis indicated 99.3% polymorphism among all species and 70.45% within V. planifolia. The UPGMA showed the separation of these four species into three groups and grouped V. planifolia accessions into three subgroups. The more genetically differentiated accessions were of the Rayada morphotype and a wild accession was from Oaxaca, followed by a wild accession from Quintana Roo; all the commercial accessions of V. planifolia (Mansa morphotype) were grouped together. The STRUCTURE analysis differentiated between V. planifolia and the three wild species, and among the accessions of the Mansa and Rayada morphotypes and the wild accessions. The STRUCTURE analysis also indicated the presence of mixed individuals. These results are of great importance since the accessions of V. planifolia that are genetically more differentiated are the most threatened due to the scarcity of these individuals, the destruction of habitat and replacement by the commercial morphotype. These individuals should be salvaged and used to expand the genetic background of vanilla.

Sets of microsatellites extracted from both a genomic library (gSSRs) and from expressed sequence tag sequence (eSSRs), and single nucleotide polymorphisms (SNPs) were applied to assess the levels of genetic diversity in a sample of 70 barley accessions, originating from 28 countries in Asia, Africa, the Middle East and Europe. The eSSR assays detected a mean of 9.5 alleles per locus, and the gSSRs only 5.7 alleles per locus, but the polymorphism information content values for the two assay types were indistinguishable. Strong and statistically significant correlations were observed between the eSSR and gSSR (r = 0.86, P < 0.05), the eSSR and SNP (r = 0.74, P < 0.05) and the gSSR and SNP genotypes (r = 0.67, P < 0.05). Accessions originating from the Middle East and Asia had the highest levels of genetic diversity. Pairwise genetic similarity ranged from 0.16 to 0.87 (mean 0.43), indicating that the sample was genetically diverse. When clustered on the basis of genotype, Asian and African accessions tended to be grouped together, but those originating from the Middle East were not concentrated in any particular cluster.