The rising need for crop diversification to mitigate the impacts of climate change on food security urges the exploration of crop wild relatives (CWR) as potential genetic resources for crop improvement. This study aimed at assessing the diversity of CWR of the Indian Ocean islands of Mauritius and Rodrigues and proposing cost-effective conservation measures for their sustainable use. A comprehensive list of the native species was collated from The Mauritius Herbarium and published literature. Each species was assessed for the economic value of its related crop, utilization potential for crop improvement, relative distribution, occurrence status and Red List conservation status, using a standard scoring method for prioritization. The occurrence data of the priority species were collected, verified, geo-referenced and mapped. A total of 43 crop-related species were identified for both islands and 21 species were prioritized for active conservation. The CWR diversity hotspots in Mauritius included Mondrain, followed by Florin and Le Pouce Mountain. Although a wide diversity of CWR has been recorded on both islands, most do not relate to major economic crops in use, therefore only a few species may be gene donors to economic crops at the regional and global level. For example, coffee, a major global beverage crop, has three wild relatives on Mauritius, which could potentially be of interest for future predictive characterization.

Hydrangea and Schizophragma are popular horticultural and ornamental plants. This study was designed to identify unknown accessions of Hydrangeaceae that have leaf morphological characters different from Hydrangea anomala subsp. petiolaris and Schizophragma hydrangeoides in Jeju, Korea. A total of 29 accessions of Hydrangea and Schizophragma from the wild were collected and analyzed using randomly amplified polymorphic DNA (RAPD) and single nucleotide polymorphisms (SNPs) from the ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene. Morphological characteristics of leaves and shoot apices of several accessions were also examined. Based on the RAPD markers, SNPs of the (rbcL) gene and morphological characteristics of apical buds, the unknown accessions were identified as H. anomala var. petiolaris.

The aim of the study was to develop the system of polymerase chain reaction (PCR)-based markers for the assessment of genetic diversity and population genetic studies of Gentiana lutea L. as well as to determine the utility of two indices of marker informativeness. The informativeness was determined for 40 PCR primers of different types (random amplified polymorphic DNA, inter simple sequence repeat, inter-retrotransposon amplified polymorphism, resistance gene analog polymorphism and conserved DNA-derived polymorphism markers) by evaluating discriminating power (DL) and resolving power (Rp) in a sample of 30 plants from two populations. Analysis of correlation between the index value and the number of differentiated pairs of genotypes in the given sample revealed that DL is more efficient than Rp; therefore, we selected primers based on the DL value. In total, 12 primers with the largest values of DL were chosen. Analysis of genetic relationship among 86 plants from six populations showed that the number of bands produced by the three of selected primers was sufficient to give average bootstrap support across six key nodes in the dendrogram higher than 85%, while using six of the primers resulted in average bootstrap value exceeding 99%. Thus, a minimal set of three to six selected primers are sufficient for a quick assessment of genetic diversity of G. lutea populations, depending on the sample size and degree of differentiation between populations, while the rest of the primers with DL values above 0.8 may be used for ecogenetic surveys. Preliminary results obtained with selected primers indicate the moderate level of genetic variation within the species and significant differentiation among individual populations.

Potato (Solanum tuberosum L.) has been cultivated in Latvia since the 17th century, and formal breeding programmes have been established since the start of the 20th century. The Latvian potato genetic resource collection consists of 83 accessions of Latvian origin, including landraces, old cultivars released starting from the 1930's, modern cultivars and breeding material. These are maintained in field and in vitro collections. Pedigree information about the potato cultivars is often limited, and the use of hybrids of local cultivars as parents is common in the Latvian potato breeding programme. Ninety-four Latvian potato varieties and breeding lines and some commonly used foreign accessions were genotyped with the potato DNA diversity array technology. Analysis of the Latvian potato genetic resources collection revealed that the amount of genetic diversity has increased in the modern cultivars in comparison with the old cultivars.

Genetic diversity identified in the Capsicum genepool has been utilized extensively to improve pepper disease resistance, fruit quality and varied yield attributes. Little attention has been dedicated to evaluating the breadth of potential diversity within Capsicum for fresh-cut attributes and genetic enhancement of fresh-cut fruit quality. We evaluated fresh-cut attributes in pepper accessions with diverse fruit phenotype selected from available cultivars and the USDA, ARS Capsicum genebank. Subjective assessment of product quality and objective measurement of package atmospheric composition, tissue juice leakage and membrane electrolyte leakage after 7, 10 and 14 d of storage identified significant differences for fresh-cut attributes among as well as within sweet bell, large elongate, jalapeno and serrano germplasm. Sweet bell and large elongate fruited accessions generally exhibited increasing electrolyte leakage over days of storage, whereas jalapeno and serrano accessions maintained stable electrolyte leakage levels. Jalapeno and serrano fruit classes were typified by faster decline in package headspace O2 and accumulation in CO2 partial pressures in comparison to sweet bell and large elongated fruit classes. Regression analysis demonstrated a relationship between overall visual quality and electrolyte leakage after 14 d of storage for sweet bell and large elongated fruit classes. The results demonstrate extensive variation in Capsicum germplasm to improve pepper for fresh-cut applications and facilitate research to better understand physiological and heritable determinants of fresh-cut product quality.

Jackfruit (Artocarpus heterophyllus Lam.) is a nutritious crop from the Moraceae family. The current study was undertaken to evaluate the phenotypic diversity of fruit characteristics using a set of 27 standardized fruit descriptors to describe 28 jackfruit genotypes. These data were used to identify the superior jackfruit genotype that could be used for commercial cultivation. The data revealed a wide range of differences among the genotypes for all the traits studied. Cluster analysis classified the genotypes into four major groups that confirmed the wide diversity among them. Principal component analysis (PCA) also revealed that 80.22% of the variability among the jackfruit genotypes was explained by the first five principal components (PCs). Based on the overall results, the Indian Council of Agricultural Research, Research Complex for Eastern Region (ICAR-RCER) JS 6/3 and 10/3 genotypes were found to be the most promising for table purposes (medium fruit size, pulp percentage >50 and total soluble solid (TSS) >20°Brix), whereas the ICAR-RCER JS 7/7 genotype with large fruit size, pulp percentage >50 and TSS >20°Brix was found to be suitable for processing. The coefficient of variation was the least for traits such as TSS (12.56%) and average seed length (13.56%). Hence, priority may also be given to the TSS and seed size when exploring promising genotypes and operating a selection procedure for crop improvement in jackfruit. The information generated under the study forms a potential baseline for fruit breeders to use in selecting genotypes with superior fruit qualities for jackfruit crop improvement programmes in the future.

This paper examines the fate of alleles and changes of genetic diversity in old (ca 1930s) versus more modern (ca 1990s) UK bread wheat varieties using 14 mapped DNA microsatellite (simple sequence repeat, SSR) loci and morphological markers. The allelic constitution of varieties belonging to three time periods (early, intermediate, late) was determined. While at certain loci one or more SSR alleles were gained between early and late periods, at others the allelic representation remained constant, although a shift in allelic frequencies could sometimes be detected. No locus showed a clear, net loss in the total number of alleles over the time period. In a further group of loci, there was neither clear gain nor loss, but rather a dynamic flux of alleles. A comparison of the allelic constitution of the UK variety set with a larger genetic pool (non-UK varieties) showed that some loci were rather similar in allelic constitution, while others possessed additional diversity. Certain SSR alleles appeared to be associated with old or modern varieties, possibly indicating associations with chromosome regions under selection pressure. The same exercise was conducted on the basis of 14 of the morphological characteristics recorded in the course of distinctness, uniformity and stability testing of varieties. Overall, this analysis generated a similar picture of changes in diversity to that obtained from the microsatellite data.

Kenya lies within sorghum centre of diversity. However, information on the relative extent of diversity patterns within and among genetically defined groups of distinct ecosystems is lacking. The objective was to assess the structure and phenotypic diversity of wild sorghum populations across a range of geographical and ecological conditions in the country. Sixty-two wild sorghum populations (30 individuals per population) sampled from four distinct sorghum growing regions of Kenya and covering different agroecologies were characterized for ten qualitative traits. Plant height, number of tillers, panicle sizes and flag leaf dimensions were also recorded. Frequencies of the phenotypic classes of each character were calculated. The Shannon diversity index (H′) was used to estimate the magnitude of diversity. Principal component analysis was used to differentiate populations within and between regions. Wild sorghum is widely distributed in Kenya, occurring in sympatric ranges with cultivated sorghum, and both have overlapping flowering windows. All characters considered displayed great phenotypic diversity. Pooled over characters within regions, the mean H′ ranged between 0.60 and 0.93 in Western and Coast regions, respectively. Wild sorghum was found to show a weak regional differentiation, probably reflecting the importance of seed-mediated gene flow in shaping the wild sorghum population structure. Trait distribution was variable among regions, but there was no conspicuous distribution of the traits studied in any given region. Spontaneous hybridization and introgression of genes from cultivated to wild sorghum seems to be likely, and may already have occurred for a long time, although undocumented. Implications for in situ and ex situ genetic resources conservation are discussed.

The range-wide genetic structure of the highly productive and valuable timber species Sequoia sempervirens (D. Don) Endl. is still insufficiently studied, although published data based on different genetic markers (nuclear and chloroplast microsatellites, AFLP, RFLP and isozymes) demonstrated relatively low population structure. However, more genetic markers are needed to increase the efficiency of population genetic studies in coast redwood. Therefore, we developed seven nuclear and five chloroplast microsatellite or simple sequence repeat (SSR) markers based on expressed sequence tags (ESTs) and the complete chloroplast genome sequence, respectively. All selected markers were tested in a range-wide sample representing trees from 16 locations. They are highly polymorphic microsatellite loci with the number of alleles ranging from 3 to 17, and the number of effective alleles from 1.1 to 2.48. Coast redwood is a hexaploid species, and its chloroplasts are paternally inherited. Therefore, the chloroplast SSR markers are especially useful for this species, because their genotyping is not affected by nuclear genome ploidy. Moreover, they showed high gene diversity for each locus within and across all populations and can be used to study range-wide population genetic structure, pollen-based gene flow and long-distance gene transfer. Coast redwood can propagate clonally, and nuclear polymorphic EST-SSRs can be used for clonal identification. They are linked with expressed genes and their variation can reflect variation in genes under selection, including those that could be potentially important for local adaptation of coast redwood considering the threat of climate change.

Theobroma cacao L. (cacao) is an important tropical crop used to produce chocolate. Evolutionary relationships between cultivated and wild cacao genotypes and their genetic diversity are poorly understood. Exploring phylogenetic diversity and spatial patterns of both cultivated and crop wild relatives can improve the knowledge of the evolutionary history of a crop, giving insights into its cultivation, breeding programmes and conservation. This study identifies biodiversity priority areas in Colombia by calculating phylogenetic diversity indices using a set of 87 single nucleotide polymorphism markers. These were sourced from 279 genotypes conserved in the Corporación Colombiana de Investigación Agropecuaria (Agrosavia) germplasm collection. The Caribbean and North Andes areas exhibited the highest phylogenetic diversity and significantly high relative phylogenetic diversity. We propose that those regions where wild cacao occurs should be prioritized as conservation areas. Besides, cacao lineages that have recently diverged and are present in Arauca, Huila and Nariño areas, with significantly low relative phylogenetic diversity, should be prioritized for breeding programmes. The Amazonia genotypes were closer to the root of the phylogenetic tree, suggesting an older origin than those found in the Andes region. Our study highlights the importance of using T. cacao germplasm from the Amazonia region as a priority to recover relict diversity in breeding programmes and broaden the gene pool of modern cultivated cacao.

A drought-related gene belonging to the Dehydration Responsive Element Binding protein (DREB) family has been reported and characterized in durum wheat. Unlike other DREB-homologous genes, it consists of four exons and three introns and produces three transcripts by an alternative splicing mechanism. The gene sequence was analysed in a number of varieties/lines/accessions of durum wheat, triticale and in wheat genome donors, Aegilops speltoides, A. tauschii and Triticum urartu, in order to evaluate the variability and to detect other interesting molecular features. Herewith, some results are presented. In the exon 1, a single sequence repeat codifying for a stretch of alanine residues variable in length (from 3 to 7), was identified. A novel non-autonomous transposon was identified, encompassing the intron1–intron3 region and this was characterized in detail. Part of the exon 4, containing the APetala2 (AP2) domain, responsible for DNA recognition and binding, was isolated and sequenced in a collection of Aegilops species and A. speltoides accessions from the Fertile Crescent, a region characterized by a high wheat biodiversity. Although the 338 bp-long analysed sequences did not reveal substantial differences in the polymorphic patterns, using a geographic subdivision with three clusters (east, centre and west), they completely separated Aegilops from the A. speltoides genus.

Allele composition at the major growth habit (Ppd-D1, Vrn-1, Rht-1 and Rht8) loci was determined in 52 Bulgarian bread wheat cultivars and landraces, using recently developed diagnostic molecular markers. The study showed that Bulgarian wheat germplasm varies for photoperiod, vernalization and height-reducing genes. The photoperiod-sensitive allele (Ppd-D1b) was the most frequent one in the old cultivars and landraces (90.9%), while the photoperiod-insensitive allele (Ppd-D1a) showed the highest frequency in the modern cultivars (96.71%). The alleles conferring winter growth habit (vrn-A1, vrn-B1 and vrn-D1) were more common in both the old (72.7%) and the modern (93.3%) wheat genotypes. The spring allele Vrn-A1c was not detected in Bulgarian germplasm, while the spring allele Vrn-B1 was found only in the old genotypes (13.6%). The semi-dwarfing allele Rht-B1b was observed in several modern cultivars. Seven allele variants were found in the microsatellite locus Xgwm261, closely located to the Rht8 gene. Among them, alleles of 164, 212 and 216 bp length were specific for the old genotypes studied, while alleles of 192 and 202 bp length were specific for the modern ones. The allele combination Rht-B1b//192 or 202 bp allele (Xgwm261 locus)//Ppd-D1a//vrn-A1/vrn–B1/vrn-D1 was detected in most of the early-heading modern cultivars. Our study emphasizes on the plasticity of the adaptive response of bread wheat cultivars sown in Bulgaria, as well as on the effect of variation for major growth habit on some yield and reproductive characteristics.

Drought remains the most important factor that affects rice productivity, especially in rainfed areas, worldwide. Upland rice is one of the crop choices of farmers in the rainfed environment. Although upland rice varieties require less water than lowland rice varieties, yields often remain limited by drought, particularly in the period of early growth. The aims of this study were to identify the traits related to early drought tolerance in upland rice varieties, and to identify the potential sources of germplasm for early drought tolerance. A total of sixty upland rice varieties were planted in a factorial experiment with a randomized complete block design with 3 replications in the rainy seasons of 2011 and 2012, under greenhouse conditions. Based on the drought tolerance index (DTI), the test germplasm sources were classified into three groups: (i) susceptible; (ii) moderately tolerant; (iii) tolerant to drought stress. Grain yield (GY) showed significant negative correlations with the leaf rolling score (r= − 0.623, P< 0.01), the leaf death score (LDS) (r= − 0.673, P< 0.01) and the recovery score (r= − 0.746, P< 0.01), while leaf dry matter (r= 0.698, P< 0.01) and leaf water potential (r= 0.618, P< 0.01) had significant positive correlations with GY. These findings indicate the suitability of the DTI as the selection criteria for early drought tolerance in a breeding programme. In addition, the upland rice germplasm accessions KKU-ULR011, KKU-ULR012, KKU-ULR125, KKU-ULR199 and KKU-ULR292 were identified as having high levels of stability for drought tolerance in both the 2011 and 2012 experiments, suggesting their potential for further use for rice variety improvement for drought tolerance.

Cassava germplasm collection is important for the preservation of genetic variability, allowing the development of improved cultivars with desirable traits such as drought and disease tolerance, better starch quality and yield. Therefore, the assessment of diversity in cassava germplasm maintained by farmers is important for maintaining biodiversity and crop improvement. Herein, we report genetic diversity relationships of 52 farmer-preferred cassava landraces from the eastern zone of Tanzania based on morphological descriptors and single nucleotide polymorphisms (SNPs). Cluster analysis was performed for both morphological traits (genetic distance 1.18–0.15) and SNPs (genetic distance 0.078–0.002). The analysis revealed that there were a total of 17,393 variant positions, and that several of the SNPs were distributed across all the chromosomes. The abundance of SNP varied remarkably among the 18 cassava chromosomes, with chromosome 2 having the highest number of SNPs (1335) and chromosome 18 having the lowest number of SNPs (734). The power of SNPs in distinguishing morphologically similar landraces was shown. Both analyses did not group landraces according to geographical locations, suggesting that farmers were moving cassava germplasm to different areas. Their diversity was mainly due to adaptation and preferential selection by farmers. This further implied that within a geographical location, the cultivars were more diverse and there was no misnaming of cassava cultivars by farmers. The collection revealed a wide range of genetic diversity, and represented a valuable resource for trait improvement, allowing the capture of farmer-preferred traits in future cassava breeding programmes.

A global survey was conducted among a wide range of stakeholders to gain insight into the state of on-farm management (OFM) as a strategy for enhancing the conservation and sustainable use of plant genetic resources for food and agriculture (PGRFA). The results show that OFM is not considered a priority in national PGRFA programmes (NPGRPs), and that OFM practitioners and their organizations are not always aware of, or involved in, NPGRPs. The survey also highlighted the lack of awareness, understanding and collaboration between OFM practitioners and the managers and policy-makers associated with NPGRPs. The outcome of the analysis supports a hypothesis that OFM is, to a large extent, supported by stakeholders who are not directly engaged in the conservation and use of PGRFA, and therefore not associated with NPGRPs. This should be taken into consideration when seeking to improve the performance and impact of national programmes, and their commitment to safeguard PGRFA and contribute to food security, poverty alleviation and sustainable agriculture.

Drought tolerance is a highly complex trait and one of the important components of yield stability in wheat. An experiment was therefore conducted to study the drought tolerance status of 14 high-yielding wheat varieties based on morphological characteristics under a randomized complete block design following factorial arrangement with three replications. Variety × Treatment × Year interactions of wheat genotypes were studied for various morphological traits under normal and drought stress conditions for 2 years in plants grown in pots. Significant differences were observed among the 14 varieties of wheat. Sutlej-86 was found to be highly affected by drought, with maximum reductions in plant height, spike length and number of spikelets/spike. The variety with the maximum tolerance to drought was Bahawalpur-97; this variety also had the lowest reductions in the number of fertile tillers/plant, the number of spikelets/spike, spike weight, the number of grains/spike, 1000-grain weight, grain yield/spike, total biomass and stress susceptibility and tolerance indices. Stronger correlations among the studied attributes under drought stress over normal conditions further highlighted drought stress adversities. The studied traits are thus recognized as drought tolerance indicators for varietal selection, and varieties showing less reduction under drought could be used as a standard check in breeding programmes to identify lineages with drought tolerance and could be recommended for drought-stressed areas.

The morphological characterisation and data analysis of germplasm accessions of wild Portuguese Lavandula luisieri (Rozeira) Rivas-Martínez from the southern Beira Interior region of central eastern Portugal are described. The study, based on seeds and cultivated plants, was conducted in 2005, 2006 and 2008 among populations selected from four sites (I, II, III and IV). Quantitative and qualitative phenotypic data relating to a set of 35 morphological traits were analysed using canonical discriminant analysis. Genetic similarity among accessions was assessed using amplified fragment length polymorphism molecular markers. The traits contributing most to the variability among studied populations were related to plant density, leaf colour, seed weight and various spike and flower characteristics. Plant populations from each of the four test sites were statistically distinct, exhibiting unique characteristics when compared with one another; however, populations from Sites II, III and IV showed greater genetic similarity and differed substantially from the population of Site I. Altitude and temperature were found to be the most significant environmental variables influencing plant traits, yet the morphological variability of L. luisieri was also influenced by soil pH levels, suggesting that the expressed variability is not only a result of genetic characteristics but also of existing ecological conditions.

This research attempts to systematically establish shape descriptor states through elliptic Fourier analysis (EFA) using pili (Canarium ovatum Engl.) kernel as a model. Kernel images of 53 pili accessions from the National Plant Genetic Resources Laboratory (NPGRL), University of the Philippines Los Baños were acquired using VideometerLab 3. Shape features, such as roundness, compactness and elongation, were extracted from the images. Shapes outlines were characterized using elliptic Fourier coefficients calculated from SHAPE version 1.3 software. Principal component analysis and cluster analysis were used to elucidate clusters representing the shape descriptor states. The first principal component accounts for the variation in length to width ratio; whereas, the second and third principal components explain the variation in the location of the widest portion and the truncation of the apex and base of the kernel, respectively. Cluster analysis separated the different accessions into six distinct clusters at 0.04 Euclidian distance. Six descriptor states, narrowly elliptic, elliptic, widely elliptic, ovate, obovate and lance-ovate, were characterized from the shape outlines and visualized through R's shape on r package. The discrimination between clusters was validated through MANOVA and LDA with 95% correct classification. The Fourier coefficients were also able to represent the variation observed from the physical properties of shape. The method may be used in establishing shape descriptors of all plant parts of all crop species.

Landraces (LRs) are important as a source of novel alleles for crop improvement, and their conservation is therefore necessary for food security. These genetic resources have suffered continuous erosion, especially in more accessible areas. We assess the loss of Nepali rice LRs and identify the factors influencing the probability of cultivating the most dominant LR via a logistic regression model. The majority of farmers cultivate LRs and modern varieties simultaneously. However, there has been a decrease in varietal diversity and a loss of some LRs over recent years, mainly because of their low yield, their sensitivity to diseases and pests, and their late maturity. The opportunity cost of maintaining the Satha landrace is higher on irrigated farms and for those farmers specializing in niche products. On the other hand, Satha is more likely to be cultivated by large-scale farmers and by those having a religious and/or a cultural attachment to this LR. Market-based incentives are less costly than publicly funded conservation programmes, and the superior taste of some LRs may allow them to be developed as niche products. However, to achieve this, public investment is needed to generate the necessary support infrastructure. In the more accessible Terai region, there is a particular need to introduce a flexible incentive mechanism to maintain LRs and to offset the negative effect of development intervention.

Rice blast caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases in rice production worldwide. Information on rice varieties with the blast disease resistance gene is important for rice cultivar development. This study identified rice blast resistant genes in 226 rice cultivars including 203 Thai landrace rice cultivars (19 upland rice cultivars from the North, 99 lowland rice cultivars from the Northeast, 45 floating rice cultivars from the Northeast and 40 cultivars from the South), 21 recommended rice varieties and two susceptible varieties ‘KDML105’ and ‘Nipponbare’ by using gene-specific markers for the blast resistant genes Pid3, Pi54 and Pigm. Results showed that 159 cultivars have at least one resistant gene and four cultivars have all three resistant genes. These results indicate that Thai landrace rice is a valuable source of rice blast resistant genes for rice breeding programmes.