The International Crops Research Institute for the semi-Arid Tropics Genebank at Patancheru, India holds the world's largest collection of 22,211 pearl millet germplasm accessions from 50 countries including 4488 landraces from 16 East and Southern African (ESA) countries. Gap analysis using FloraMap software and 3750 georeferenced pearl millet germplasm accessions from ESA countries revealed 34 districts located in 18 provinces of four East African countries and 76 districts located in 34 provinces of seven Southern African countries as geographical gaps. Analysis of characterization data using DIVA-GIS software showed 11 districts of seven provinces in Sudan and Uganda and 58 districts of 20 provinces of seven countries in Southern Africa as gaps in diversity for important morphoagronomic traits. The following districts were identified as gaps common to geographic area and diversity for some or the other traits: Amuria district in Soroti province of Uganda; Mpwapwa in Dodoma province of Tanzania; Mahalapye in Centre province and Kgatleng in Kgatleng province of Botswana; Lalomo in Southern province of Zambia; and Motoko, Mudzi and Wedza in the province of Mashonaland East; Makoni in Manikaland; Gutu and Chivi in Masvingo; Gwanda and Bulalimamangwe in Metabeland south; Hwange and Nkayi in Metabeland north; and Kwe Kwe in Midlands of Zimbabwe. For a successful germplasm collection mission to fill the gaps identified, planning should be made in advance of collaboration and consultation with National Agricultural Systems, local government officials and extension officers. It is suggested to collect the complete passport data including georeference information while collecting the germplasm.

Sugar and acidity levels are the main criteria of general fruit quality and for citrus juices pulp, in particular. The constituents of the acidity (organic acids) and the sweetness (glucose, fructose and sucrose) and the genes involved in their regulation have seldom been used to explore Citrus genetic diversity. We evaluated the juice composition of primary metabolic components for 87 varieties belonging to the eight major Citrus species grown under the same environmental and cultivation conditions by HPLC. We investigated the sequence polymorphism of nine candidate genes encoding for key enzymes of sugars and organic acids metabolic pathways by single strand conformation polymorphism (SSCP). Whatever the biochemical or molecular analyses, the observed structure of Citrus diversity was organized around three groups corresponding to the ancestral species (mandarin, pummelo and citron). As expected, the secondary species were closely related to their putative ancestors except for Citrus aurantium. Biochemical diversity was strongly correlated to molecular SSCP diversity at the genus level but not at the intraspecific level. Compared with other molecular marker types, higher diversity has been observed with SSCP technology, which makes it suitable for future quantitative trait loci mapping approach on gene polymorphism in citrus pulp acidity and sweetness regulation.

To facilitate the updating of in situ and ex situ conservation strategies for wild taxa of the genus Hordeum L., a combined ecogeographic survey and gap analysis was undertaken. The analysis was based on the Global Inventory of Barley Plant Genetic Resources held by ICARDA plus additional datasets, resulting in a database containing 17,131 wild Hordeum accessions. The analysis concluded that a genetic reserve should be established in the Mendoza Province of Argentina, as this is the most species-rich area globally for Hordeum. A network of reserves should also be set up across the Fertile Crescent in Israel, Palestine, Syria, Jordan, Lebanon and Turkey to provide effective conservation within the centres of diversity for gene pools 1B (Hordeum vulgare subsp. spontaneum (C. Koch) Thell.) and 2 (Hordeum bulbosum L.). The majority of the species were deemed under-collected, so further collecting missions are required worldwide where possible. Although ex situ and in situ conservation strategies have been developed, there needs to be further investigation into the ecological environments that Hordeum species occupy to ensure that any adaptive traits expressed are fully conserved. Additionally, studies are required to characterize existing collections and test the viability of rare species accessions held in genebanks to determine whether further ex situ collections are required alongside the proposed in situ conservation.

The capitate glandular trichomes of wild sunflowers (Helianthus spp.) are considered to be effective defence components that act against some herbivorous insects, but cultivated sunflowers are reportedly deficient in glandular trichomes. To investigate whether glandular trichomes have a role in the protection of cultivated sunflowers against insects, in the present study, Helianthus annuus L. accessions were grown to quantify glandular trichome density in wild and cultivated germplasm types and assess potential anti-insect effects of terpenoids in the glandular trichomes of cultivated sunflowers. Evaluation revealed that capitate glandular trichomes are often abundant in cultivated sunflowers; relative to wild H. annuus, inbred maintainer (HA) lines have similar numbers of glandular trichomes per floret, while commercial hybrids have only ≈ 20% fewer trichomes when compared with wild sunflowers. In the laboratory assay, it was found that glandular trichome extracts increased the mortality rates of sunflower moth, Homoeosoma electellum (Hulst), larvae exposed from the neonatal stage to 9 d. In the surviving larvae, the extracts significantly reduced larval mass and head capsule width. Though there are limitations to the value of glandular trichomes for host plant resistance, the feeding deterrent or toxic effects of sesquiterpene lactones and diterpenes in sunflower glandular trichomes are not limited to sunflower moth larvae, suggesting a potential for resistance to other sunflower insect pests. Additional research is required to understand the inheritance and value of glandular trichomes in commercial sunflower germplasm and how the composition of terpenoids in the glandular trichomes of wild H. annuus may differ from that in cultivated material.

Genebanks explore new partnerships with farmers and other user groups to provide smallholder farmers in Africa better access to crop diversity for improved nutrition, climate change adaptation and agricultural diversification. This paper shows how the World Vegetable Center (WorldVeg) genebank of traditional African vegetables and its partners distributed over 42,000 seed kits containing over 183,000 vegetable seed samples from 2013 to 2017 to smallholder farmers in Tanzania, Kenya and Uganda. The seed kits contained seed samples of promising accessions and open-pollinated breeding lines of traditional African vegetables, and to a lower degree of tomato, Capsicum pepper and soybean, usually enough to plant in a home garden. We identified four research questions to better understand the role of vegetable seed kits in strengthening local seed systems, impact on local vegetable diversity, improving human nutrition and supporting climate-resilient agriculture. As formal seed systems expand their reach, the genebank's role to supply vegetable diversity to public and private breeding programmes becomes more important. To optimize supply of vegetable diversity, the WorldVeg genebank of traditional African vegetables continues working with partners in both formal and local seed systems.

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.

With increasing interest in natural products of plant origin for medicinal and health care benefits there is added emphasis on the quality of the source raw material. In most cases the vegetative tissues and organs are the source of the required raw material. However, such tissues/organs may become infested/susceptible to many diseases causing deterioration of the quality of the desired economic product and loss of genetic resources. Considerable progress has been made with respect to the identification of disease causing organisms, and their pathogenic impact at organ, cellular and biochemical level. This review focuses on various diseases caused by bacteria, fungi, nematodes, viruses and phytoplasmas threatening the yield, biomass, bioactive potential of medicinal and aromatic plants of the sub-tropics. Several studies suggest that management of diseases through biological measures is more effective to check multiple diseases. Necessary management strategies for efficient disease management to realize quality raw material and enhanced metabolite productive potential have been outlined.

Among domesticated traits, pre-harvest sprouting (PHS) caused by the early breakage of dormancy leads to severe economic losses. Therefore, regulating PHS is important for cereal crop improvement against changes in climate. In this study, we surveyed naturally occurring variations in seed germination in diverse rice germplasm for the available resources of this trait, and investigated the changes of abscisic acid (ABA) levels during grain development by the distinguished PHS-resistant groups. We discovered wide variations in germination among the 205 rice accessions examined and found that 90 accessions are resistant (germination <20%) to PHS. Tropical and subtropical accessions, which are subjected to long wet periods, are more resistant to PHS than the other accessions. We detected an increase in germination of detached seeds from the panicle compared with intact seeds in panicle at harvesting time. This might be attributed to a weakening of the mechanical barrier that prevents water imbibition and radical emergence. ABA levels were maximal at 10 d after flowering and decreased thereafter. Interestingly, PHS-susceptible accessions maintained higher or similar ABA levels compared with PHS-resistant accessions, suggesting that the key factors for seed dormancy and its breakage are ABA perception and signal transduction rather than total ABA content. The diversity of germination ability detected in this study could be sustainably used for crop improvement and to help unveil the genetic and physiological basis of this quantitative trait.

Association mapping (AM), an alternative method of quantitative trait loci (QTL) discovery, exploits historic linkage disequilibrium (LD) present in natural populations. AM is effective in self-pollinated crops such as Dolichos bean as LD extends over longer genomic distance driven-by low rate of recombination and thereby requiring fewer markers for exploring marker-traits associations. A core set of Dolichos bean germplasm consisting of 64 accessions was evaluated for nine quantitative traits (QTs) during 2014 and 2015 rainy seasons and genotyped using 234 simple sequence repeats (SSR) markers. Substantial diversity was observed among the core set accessions at loci controlling QTs and 95 of the 234 SSR markers were found polymorphic. The structure analysis and low magnitude of fixation indices suggested weak population structure, which in-turn indicated the low possibility of false discovery rates in the marker-QTs association. The marker allele's scores were regressed onto phenotypes at nine QTs following general linear model and mixed linear model for exploring marker-QTs associations. Significantly higher number of SSR markers was found associated with genomic regions controlling nine QTs. A few of the markers such as KT Dolichos (KTD) 200 for days to 50% flowering, KTD 273 for fresh pod yield per plant and KTD 130 for fresh pods per plant explained ≥10% of the trait variations. The study could also identify a few SSR markers such as KTD 273, KTD 271 and KTD 130 linked to multiple traits. These linked SSR markers are suggested for validation for their use in marker-assisted Dolichos bean improvement programmes.

In India, Protection of Plant Varieties and Farmer's Rights Act (PPV&FRA, 2001) requires the registration and protection of new and notified/extant plant varieties based on the criteria of distinctness, uniformity and stability (DUS) of morphological characteristics. However, these morphological traits have not been able to resolve closely related genotypes. The molecular markers can very well support the DUS testing in such cases. In the present study, therefore, 14 varieties of rice cultivated in Punjab state of India were fingerprinted using 75 simple sequence repeat (SSR) primers. Out of these, 58 primers produced polymorphic profiles, while 13 were monomorphic, 2 revealed null allele and the remaining 2 amplified only from super basmati. In a screen of 7 cultivars, 16 SSR loci produced 17 rare/unique alleles, which provided an opportunity for their unambiguous identification. Cluster analysis based on SSR data clearly distinguished the cultivars into two dist inct groups: comprising non-basmati (group I) and basmati (group II). The cluster pattern was consistent with the pedigree and breeding history of the cultivars.

Genealogical data have been used very widely to construct indices with which to examine the contribution of plant breeding programmes to the maintenance and enhancement of genetic resources. In this paper we use such indices to examine changes in the genetic diversity of the winter wheat crop in England and Wales between 1923 and 1995. We find that, except for one period characterized by the dominance of imported varieties, the genetic diversity of the winter wheat crop has been remarkably stable. This agrees with many studies of plant breeding programmes elsewhere. However, underlying the stability of the winter wheat crop is accelerating varietal turnover without any significant diversification of the genetic resources used. Moreover, the changes we observe are more directly attributable to changes in the varietal shares of the area under winter wheat than to the genealogical relationship between the varieties sown. We argue, therefore, that while genealogical indices reflect how well plant breeders have retained and exploited the resources with which they started, these indices suffer from a critical limitation. They do not reflect the proportion of the available range of genetic resources which has been effectively utilized in the breeding programme: complex crosses of a given set of varieties can yield high indices, and yet disguise the loss (or non-utilization) of a large proportion of the available genetic diversity.

Karnal bunt (KB) of wheat, caused by Tilletia indica (Mitra) Mundkur, adversely affects international wheat trading and the movement of germplasm between countries due to quarantine restrictions. Breeding for host plant resistance requires the identification of KB resistance sources. Accessions of the D genome progenitor of bread wheat, Aegilops tauschii, were screened in a specially designed screen-house, where the optimum environmental conditions conducive for KB development were simulated by controlling temperature, humidity, fogging and shading. The 183 accessions were subjected to artificial inoculation with a mixture of nine KB isolates, and seven proved highly resistant and four moderately resistant over three rounds of screening over 3 years.

Scientific research has always been concerned with aspects of human health. There are several systems of medicines besides the globally accepted allopathy, which are based on compounds originating from natural products. Recent research has been centred around validation of the traditional knowledge on medicinal products. The traditional systems in India, China and forklore medicines in other parts of the world have indicated the potential of natural products consist of various chemical compounds that could be used as drugs. The search for drugs against five major dreadful diseases namely, cancer, AIDS, heart disease, diabetes and pulmonary disorders that attack the present day human from natural products has been in progress for some time. Microbes, plants and animals are the sources of natural products. In the past five decades, the research on bioactive chemicals from marine algae has been incited and several compounds with biological activity were isolated from algae. Generally, these are secondary metabolites produced for chemical defence against the biotic pressure of predators, consumers and epibionts. These potential drugs are now attracting considerable attention from the pharmaceutical industries due to the necessity of identifying substances that could be utilized for novel therapeutic purposes. Several compounds such as alginate, carrageenans, sulphated and halogenated polysachcharise and other derivatives have been shown to provide drugs that could be antiviral, anticancer and antimicrobial. The present account is on the potential of marine macro-algae for medicinally important products.

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.

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.

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.

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.

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.

The complete chloroplast (cp) genome sequences of three Amaranthus species (Amaranthus hypochondriacus, A. cruentus and A. caudatus) were determined by next-generation sequencing. The cp genome sequences of A. hypochondriacus, A. cruentus and A. caudatus were 150,523, 150,757 and 150,523 bp in length, respectively, each containing 84 genes with identical contents and orders. Expansion or contraction of the inverted repeat region was not observed among the three Amaranthus species. The coding regions were highly conserved with 99.3% homology in nucleotide and amino acid sequences. Five genes – matK, accD, ndhJ, ccsA and ndhF – showed relatively high non-synonymous/synonymous values (Ka/Ks > 0.1). Sequence comparison identified two insertion/deletion (InDels) greater than 40 bp in length, and polymerase chain reaction markers that could amplify these InDel regions were applied to diverse Korean Genbank accessions, which could discriminate the three Amaranthus species. Phylogenetic analyses based on 62 protein-coding genes showed that the core Caryophyllales were monophyletic and Amaranthoideae formed a sister group with the Betoideae and Chenopodioideae clade. Comparing each homologous locus among the three Amaranthus species, identified eight regions with high Pi values (>0.03). Seven of these loci, except for rps19-trnH (GUG), were considered to be useful molecular markers for further phylogenetic studies.