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.

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.

Pigeonpea is an important grain legume. It contributes to the improvement of soil fertility through biological nitrogen (N) fixation. However, the symbiotic efficiency of pigeonpea with native soil rhizobia has not been determined adequately. This study was designed to determine the variation in the N fixation ability of pigeonpea inoculated with the native rhizobia. Forty soil samples were collected from diverse locations across South Africa and used for inoculating pigeonpea seed. Each pigeonpea genotype was inoculated separately with each soil sample and raised in a nitrogen-depleted growth medium in the greenhouse. A split-plot experimental design was used in the study. Several N fixation variables of pigeonpea were measured. There was >40.0% difference in the number of nodules between genotypes ‘Ex-PP-MD-321’ and ‘Mpuma-B-Spot’ but the nodule dry weight between the two genotypes was >80.0%. In contrast, the heaviest dry shoots (0.4513 g), weighed 52.0% heavier than those that were observed for ‘Mpuma-B-Spot’. Pigeonpea showed differential N fixation ability with the nodules, suggesting that there was potential to select for optimum host × rhizobial isolate combinations for the process and to expand the production area of the crop.

Iron walnut, Juglans sigillata Dode, restricted to southwestern China, has its centre of distribution in Yunnan Province which has a varied climate, geography and rich plant diversity. Yunnan contains abundant J. sigillata germplasm. In this study, a provincial-scale set of walnut germplasm resources (14 populations comprising 1122 individuals) was evaluated for genetic diversity based on 20 simple sequence repeat (SSR) loci. The number of SSR alleles per locus ranged from 7 to 27, with an average of 17.55. Mean allelic richness and mean private allelic richness ranged from 3.40 to 4.62 and 0.11 to 0.36, with average of 3.93 and 0.30, respectively. Expected heterozygosity (He) varied from 0.26 to 0.78, with an average of 0.57. Polymorphism information content ranged from 0.22 to 0.79, with an average of 0.57. Genetic differentiation (FST) was 0.05, indicating that only 5% of total genetic variability was inter-populational, a finding supported by an analysis of molecular variance and STRUCTURE analysis. Relatively high gene flow (Nm = 6.70) was observed between populations. A unweighted pair-group method with arithmetic analysis classified the 14 populations into two major groups. Mantel testing uncovered a significant correlation between geographic distance and genetic distance (r = 0.33, P = 0.04). Overall, the research revealed a moderately high level of genetic diversity in the germplasm and low genetic differentiation among populations, which showed great potential for further development and exploitation of this resource.

In order to highlight the genetic status and origin of Moroccan apricot populations, trees were collected from ten oasis agroecosystems and analysed with AFLP markers. A total of 87 accessions and 12 cultivars grown in Moroccan orchards, including ‘Canino’ and ‘Del Patriarca’ cultivars, were surveyed and compared with in situ Tunisian and ex situ Montfavet (France) collections. Our results highlighted a narrow genetic diversity in the Maghreb region (Tunisia and Morocco) associated with a strong differentiation from the other groups, which supports a bottleneck effect. A similar model was illustrated at a finer geographical scale, i.e. the Draa Valley in Morocco. Genetic structure appeared as two major clusters subdivided into six sub-clusters in which Moroccan germplasm constituted specific groups in comparison with other Mediterranean apricots. Moroccan germplasm was classified into three sub-clusters, two of which were formed by genotypes related to ‘Del Patriarca’ and ‘Canino’, respectively. The present study highlights the wide Moroccan apricot's diversity in traditional agroecosystems, and also suggests a substantial gene flow occurring from recently introduced cultivars (‘Canino’ and ‘Del Patriarca’) to local apricot populations, thus leading to local germplasm diversification through seedling propagation. If we consider its geographical position, the historical diffusion of the species and farming practices, Morocco could be viewed as an additional centre of secondary diversification for apricot. Understanding the origin and specificity of local apricot populations is crucial for managing local collections in regard to adaptive traits for arid and Saharan conditions as well as for introducing local genetic resources into current breeding programmes.

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.

Cassava brown streak disease (CBSD) remains a major threat to cassava production in Mozambique. Breeding for CBSD resistant varieties that are also preferred by farmers is an integral part of managing the disease. The main objective of the study was to determine the genetic relationship between farmer-preferred varieties from Mozambique with those from Tanzania whose resistance to CBSD is known and some of which are being used as parents in quantitative trait loci (QTL) detection studies. To achieve this, 103 genotypes collected from farmers’ field in three provinces of Mozambique were genotyped together with five varieties from Tanzania whose CBSD response is well known. Thirty-five single nucleotide polymorphism (SNP) markers with a high minor allele frequency in East African landraces were used. Results indicated that seven Mozambican genotypes were genetically similar to either one of the four Tanzanian CBSD resistant genotypes while Xino Nn'gole was genetically identical to Namikonga a CBSD resistant variety, based on the SNPs used here. Little genetic differentiation was observed in cassava between provinces, with the majority of genetic variation distributed within individual genotypes (98%) rather than among provinces (2%). Both observed (Ho) and expected (He) heterozygosity in three provinces were generally high (Ho = 0.496) and (He = 0.455). There is a high likelihood that the eight genotypes similar/identical to those from Tanzania may share the same QTL associated with CBSD resistance thus should be further evaluated for agronomic traits as well as response to CBSD.

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.

Significant genetic diversity for sucrose and fibre percentages exists in the species that served as the foundation of present day sugarcane cultivars. However, information is lacking worldwide on the recent contributions of sugarcane crop wild relatives (mainly Saccharum, Erianthus and Miscanthus wild species) in developing new varieties. There is renewed interest in using those relatives for creating new varieties to use as a dedicated bioenergy crop with higher fibre. This study focuses on past data analysis of sugarcane breeding in Mauritius with the objective to assess the efficiency in exploiting sugarcane wild relatives since 1970s to date. Pedigree analyses helped retrace the parentages of elite inter-specific hybrids reaching the final stages of selection. The studies confirmed the high prevalence of a few ‘wonder canes’ (successful hybrids with wild canes produced in the beginning of last century) among the ancestors of Mauritian varieties. Among the wild relatives, eight Saccharum spontaneum, two S. robustum, and one Erianthus clones were involved in generating elite genotypes worth evaluating at the advanced variety trial stages. A few early generation hybrids were released in the past for industrial exploitation, the latest one being M 1002/02 in 2016, with sugar as the primary output. Recent studies on the biomass potential and fibre yield of inter-specific hybrids are giving promising results, which expands the horizon in the use of sugarcane wild relatives for the generation of novel type of sugarcane varieties for multiple end-uses.

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.

The current study focused on characterization of the underlying genetic divergence in inbred lines developed from local landraces of North Eastern Hill Region of India – a designated Asiatic maize diversity centre – following six generations of inbreeding. Substantial genetic differentiation was indicated based on very high to moderate Fst values for 22 of the 38 simple sequence repeat markers studied. STRUCTURE analysis partitioned the subset into two distinct and one admixture subgroup (Populations I, II and III respectively) accompanied by a significant reduction in heterozygosity. Population II was further subdivided into subpopulations Pop-M9 and Pop-T9. Nei's pairwise genetic distance and population Fst values indicated that Populations I and II were more divergent with neighbour joining clustering analysis clearly defining landraces originating from the states of Tripura (Population II) and Sikkim (Population I) as most divergent. Principal coordinates analysis could explain 31.26% of the variation present in the subgroups wherein Population I was more variable. Analysis of molecular variance and Fst coefficients (P < 0.001) indicated 17% population structuring with 55% variation detected for individuals within populations. These results combined with the presence of phenotypic variability in the subgroups for yield traits supported by results of a preliminary partial diallel analysis strongly suggest the existence of distinct heterotic groups. Divergence studies are crucial for exploiting heterosis, and the current study would go a long way to help establish a germplasm base for developing varieties with improved agronomic performance and surer commercial prospects no reports of which are available thus far.

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.

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.

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.

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.

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.

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.

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.

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.

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.