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.

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.

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.

Introduction of clones from genetic groups that are underrepresented in the pedigree of commercial cacao varieties in West Africa represents an important aspect of cacao improvement strategy of broadening the genetic base to overcome current yield stagnation of the crop. The objective of the present study was to determine the combining abilities of more recently introduced cacao clones for yield and cropping efficiency in the early bearing years. Seven recently introduced clones were crossed as males to five clones commonly used in the seed gardens in Ghana using a North Carolina II design. The 35 F1 varieties and one commercial variety were evaluated in the field from June 2010 to March 2015 for four traits: increase in trunk cross-sectional area in the juvenile, and in the pod-bearing phases, bean yield and cropping efficiency. Though both GCA and SCA variances were significant for all traits, the ratios of GCA:SCA were much smaller than unity, indicating the importance of non-additive effects in the control of the traits. Among the set of clones therefore, prediction of F1 variety performance cannot be based on the GCA or per se (average) performance of the clones. Six varieties were more precocious, and eight had higher cropping efficiencies than the standard variety. Bean yields ranged from 0.74 to 1.05 t/ha/year in the fourth and fifth years after planting among the top six varieties. The study provides evidence of the large potential for productivity increase through the use of cacao clones beyond Pound's early introductions into West Africa.

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.

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.

Genetic structure of five populations of a locally common rice (Oryza sativa L.) landrace Jaulia from parts of Uttarakhand state of India was studied using sequence tagged microsatellite site (STMS) markers. Of these, four populations were on-farm managed, assembled from different niche environments, and one population was conserved ex situ and represented static conservation. The 16 STMS primer pairs fully differentiated the inter- and intrapopulation diversity. A total of 72 alleles were recorded with a mean of 4.5 alleles per locus. Population wise, the total number of alleles ranged from 21 to 41, with maximum number of alleles for population IC 548358 and minimum number of alleles for population IC 100051 representing static conservation. A greater number of alleles specific to populations under farmer management could be recorded. Changes in yield parameters also seemed to be affected under farmer management besides other environmental adaptations for qualitative morphological characters. The marker diversity using STMS primer pairs indicates the genetic differentiation among populations resulting from joint effects of several evolutionary forces operating within the historical and biological context of the crop landrace. The variations in adaptations, on the other hand, indicate the degree to which populations are adapted to their environments and their potential for continued performance or as donors of characters in plant breeding. Both biotic and abiotic aspects of the environment are involved.

Soybean is an important crop in Indonesia and its consumption has consistently surpassed local production in recent times. As the average yield is relatively low, a more efficient breeding programme that utilizes the latest technological developments in DNA analysis is required. To provide a genomic data resource for future breeding programmes, in this study, whole-genome sequencing was performed for five Indonesian soybean varieties, with an average sequencing depth of 34 reads. Comparison of these sequences with the Williams 82 reference sequence revealed 3,150,869 DNA variations, which averages to one variation in every 308 bases. Comparison of these variations with known single-nucleotide polymorphisms (SNPs) in the SoyKB database revealed that approximately 29% of them were novel SNPs unique to the Indonesian cultivars. Variations found within exons totalled 95,154. Of these, 57,171 were capable of causing mutations that would modify the amino-acid composition of the encoded proteins (nonsynonymous mutations). Phylogenetic analysis using a subset of these SNP data indicated that the cultivars had genetic similarities to landraces from China and Japan, which could provide clues to the origin of soybeans that were introduced into Indonesia.

Ultra-dry storage, storing orthodox seeds at ambient temperatures with moisture contents below 5%, can maintain seed viability for long periods with low input. Optimum moisture contents for ultra-dry storage exist and vary substantially among different seed lots due to their differences in desiccation tolerance, which is associated with the accumulation of protective compounds. To study the relationship between moisture contents of ultra-dry stored species, seed composition and the free-radical scavenging activity (FRSA). Eleven seed lots of maize, wheat, pepper, peanut, Chinese cabbage, and cucumber were chosen and multiple stepwise regression analysis was applied. In general, analysis of the seed lots revealed that optimum moisture contents for highest seed viability are below equilibrium moisture at 13% relative humidity and 20°C. Nevertheless, seed composition differed significantly among species. Lipids, flavonoids and the FRSA were significantly negatively correlated with the optimum moisture content of ultra-dry stored whole seeds and accounted for 97.7% of the total variation in the optimum moisture content. Lipids had the highest effect (90.0%) on the optimum moisture content of ultra-dry storage, which is consistent with the previous results. The FRSA and flavonoids accounted for 4.8 and 2.9% of total variation of optimum moisture content of ultra-dry stored whole seeds, respectively. The FRSA and flavonoids were also significantly negatively correlated with the optimum moisture content for non-lipid fraction of ultra-dry stored seeds, and accounted for 74.1 and 15.3% of the total variation in the optimum moisture content, respectively.

A useful biological interpretation of diploid heterozygotes is in terms of the dose of the common allele (0, 1 or 2 copies). We have developed a PERL script that converts FASTA files into coded spreadsheets suitable for principal component analysis. In combination with R and R Commander, two- and three-dimensional plots can be generated for visualizing genetic relationships. Such plots are useful for characterizing plant genetic resources. This method nicely illustrated the spectrum of genetic diversity in tomato landraces and the varieties categorized according to human-mediated dispersal.

Among grain legumes, faba bean is reputed to be relatively sensitive to drought stress. Epicuticular wax (ECW) quantity is considered as an important drought adaptation strategy in plant species. This study aimed to define variation in leaf ECW concentration as a drought-adaptive trait in 197 faba bean accessions under well-watered conditions. The relationship between ECW and stomatal characteristics was also investigated. Highly significant differences were found in the ECW concentration, which ranged from 0.680 to 2.104 mg/dm2. No relationships were found between ECW and any measure of stomatal morphology and function. This study provides evidence of the wide variation in ECW in faba bean germplasm, which is independent of stomatal characteristics and leaf water content. This variation may allow the genetic improvement of ECW as a drought-adaptive character in faba bean breeding programs aiming at the economical use of water.

Common lilac is a popular landscape plant with nearly 2000 cultivars. In the present study, nine novel polymorphic microsatellite markers were developed for common lilac using genome screening with inter-simple sequence repeat primers. Each of the nine markers revealed two to five alleles. The markers were used for genotyping of 75 common lilac shrubs, including 17 accessions that represented named cultivars. A dendrogram, based on the allele profiles of the shrubs, was generally in agreement with the grouping made on the basis of morphological traits, as well as with the pedigree information available. The novel markers appear valuable for differentiation between common lilac cultivars.

Sorghum halepense grows in a vast range of ecological regions of Iran. In this study, inter-retrotransposon amplified polymorphism (IRAP) markers were used to assess the genetic diversity of 38 accessions of S. halepense and two accessions of Sorghum bicolor (used as out groups) collected from different regions of Iran. In total, 180 DNA fragments were amplified from eight combinations of IRAP primers, from which 178 (98.9%) were polymorphic. The IRAP-based trees and two-dimensional plot of principal coordinate analysis demonstrated six different groups corresponding to their geographical origin in Iranian germplasm of S. halepense: (1) in the south-west region; (2) in the west along the Zagros Mountains; (3) in the north-west of the country; (4) in the centre of the country; (5) and (6) in the northern region along the eastern and western coast of Caspian Sea. The most variable populations were found in the centre and the west of Iran. The results showed high gene flow among different regions, although the south-western accessions were well differentiated from those growing in other regions. The accessions collected from western coast of Caspian Sea were differentiated from neighbouring regions in both morphological characters and IRAP data. The measured genetic distances were independent of geographical distances. This survey demonstrates high genetic dynamism in Iranian germplasm of S. halepense and indicates that the present germplasm is of great value in terms of sampling for new alleles for crop improvement.

Rosa x odorata (sect. Chinenses, Rosaceae) is an important species distributed only in Yunnan Province, China. There is an abundance of wild variation within the species. Using 22 germplasm resources collected from the wild, as well as R. chinensis var. spontanea, R. chinensis ‘Old Blush’ and R. lucidissima, this study involved morphological variation analysis, inter-trait correlation analysis, principal component analysis and clustering analysis based on 16 morphological traits. This study identified a high degree of morphological diversity in R. x odorata germplasm resources and the variation coefficients had a distribution range from 18.00 to 184.04%. The flower colour had the highest degree of variation, while leaflet length/width had the lowest degree of variation. Inter-trait correlation analysis revealed that there was an extremely significant positive correlation between leaflet length and leaflet width. There was also a significant positive correlation between the number of petals and duration of blooming, and the L* and a* values of flower colour were significantly negatively correlated. Principal component analysis screened five principal components with the highest cumulative contribution rate (81.679%) to population variance. Among the 16 morphological traits, style length, sepal width, flower diameter, flower colour, leaflet length and leaflet width were important indices that influenced the morphology of R. x odorata. This study offers guidance for the further development and utilization of R. x odorata germplasm resources.

Ocimum gratissimum L. is a well-known medicinal plant with several therapeutic properties, but molecular studies on this species are lacking. Therefore, we have sequenced the whole transcriptome from the leaves of O. gratissimum and assembled 121,651 transcripts. The transcriptome of O. gratissimum was closely related to Sesamum indicum and Erythranthe guttata in congruence with the molecular phylogenetic relationships among these species. Further, 62,194 transcripts were annotated and classified according to the GO terms concerning the biological process, cellular component and metabolic function. In the KEGG pathway analysis, 34,876 transcripts were mapped to 149 pathways and 1410 of them were involved in the biosynthesis of secondary metabolites. In the phenylpropanoid pathway, 101 transcripts were associated with the biosynthesis of eugenol, the principal constituent of the essential oil of O. gratissimum. In the caffeine metabolism pathway, none of the transcripts was related to caffeine biosynthesis, supportive of the caffeine-free nature of Ocimum. Transcripts coding for the metallothionein were abundant in the leaves, supporting the observation that O. gratissimum is an accumulator of heavy metals. We also identified the 930 transcripts coding for 59 transcription factors families with myeloblastosis transcription factors being the most predominant. About 6500 simple sequence repeats were identified, which will be useful in DNA marker-based applications. This is the first report of the leaf transcriptome of O. gratissimum, which will serve as an essential resource for further molecular studies in this important medicinal species.

Rice blast disease, caused by Magnaporthe oryzae, is one of the most damaging diseases of rice worldwide. Cultivation of rice varieties carrying resistance genes is the most economic and successful strategy to control the disease. In this study, 451 rice varieties from around the world including 363 Thai landrace rice varieties, 21 Thai improved rice varieties, 43 Japanese rice varieties and 24 worldwide rice varieties were screened by PCR technique using gene-specific markers for 10 rice blast resistance genes: Pi9, Piz-t, Pi50, Pigm(t), Pid2, Pid3, Pia, Pik, Pi54 and Pita. The results showed that 382 (99.48%) Thai rice varieties have at least one resistance gene and two rice varieties, ‘Hom’ and ‘Bak muay’, contained eight out of ten screened rice blast resistance genes. 320 rice varieties (83.33%) contained three or more rice blast resistance genes. The frequency of the rice blast resistance gene ranges from 87.76–9.64 per cent, of which the Pid3 gene has the highest frequency and the Pi54 gene has the lowest frequency. Two major resistance genes, found in Japanese rice varieties, are the Pik gene (76.74%) and the Pi9 gene (72.09%). While two major resistance genes, found in the international rice varieties are the Pi9 gene (66.67%) and the Pi54 gene (62.50%). The disease resistance gene profile of each rice variety obtained from this study will benefit the rice blast resistant breeding programme in the future.

This study discusses some of the important aspects of laws/regulations formulated for the protection of plant varieties in Union for the Protection of New Varieties of Plants (UPOV) member states, European Community countries and India. The study also provides an insight into some of the unique features of Indian sui generis system for the protection of plant varieties. During this study, the registration of crop notified in India and in some selected UPOV member countries has been examined. Since India is not an UPOV member state, the system of plant variety protection (PVP) is independent of international scenario but aims for similar standards. The study provides useful information in order to analyse the implementation of PVP laws in UPOV member states and India. Some important features were selected for carrying out a comparative analysis. These include Intellectual Property Rights protection (patent/breeder's right), types of varieties protected, methods of testing, criteria for protection, duration of protection, exemptions (researcher/farmer's exemption), infringement and penalty and compulsory license.