Drought is the major abiotic constraint to the rice production in the rain-fed areas across Asia and sub-Saharan Africa. Wild species of Oryza offer a wide spectrum of adaptive traits and can serve as potential donors of biotic and abiotic stress tolerance. At the Punjab Agricultural University, we are maintaining an active collection of 1630 accessions of wild species germplasm (AA, CC, BBCC and CCDD) of rice. These accessions were screened to assess genetic variation for drought tolerance under field conditions. Severe water stress was imposed at the late vegetative stage by withholding water initially for 25 d and then extended further to 35 d during kharif season in the years 2013–14 and 2015–16. The tolerance score for drought stress was based on the extent of leaf rolling and leaf drying. Based on the 2 years’ data, seven accessions from Oryza rufipogon, four from Oryza longistaminata and one each from Oryza officinalis and Oryza latifolia were found tolerant to drought stress. These selected accessions were further phenotype for root morphology. The average root length among the selected accessions ranges between 36 and 80 cm and the number of primary roots vary from 30 to 87 cm. The O. rufipogon accession IRGC 106433, O. longistaminata accession IRGC 92656A, O. officinalis accession IRGC 101152 and O. latifolia accession IRGC 80769 showed approximately 2–2.5 times longer root length and number than the indica rice elite cultivar PR121. The results indicated potentiality of selected wild species germplasm for conferring drought tolerance to the elite cultivars.

Full potential of African tomato has not been tapped due to lack of information regarding its characterization. The aim of this work was to study the diversity of 17 African tomato landraces collected from Solanaceae gene bank – Tanzania. Evaluation was done using Complete Random Block Design. Morphological data collected were subjected to GenStat's and Darwin6 software. RNA was extracted from leaf samples, fruits at three ripening stages using modified Trizol method and sequencing done using Illumina sequencing platform. The raw reads were filtered and analysed using the Bioinformatics tools. Phenotypically, the landraces clustered into three clusters dendrogram representation. Clustering was attributed by phenotypic variation. Analysis of variance showed significant phenotypic variations among the landraces (P < 0.05). A total of 115,965 validated single nucleotide polymorphisms (SNPs) were mined from the 303,754,051 high-quality filtered reads. Molecular characterization showed significant variation within the landraces at fruit development stages. Unlike the phenotypic variation, phylogenetic tree representation grouped the 17 landraces according to their geographical location with some landraces from different countries grouping together. The findings of this study reveal significant morphological variation among African tomato contributed by plant height, leaf blade length, leaf blade width and fruit width. Positive correlation between fruit width and yield (r = 0.93, P < 0.01) was observed. Results of this study reveal that there is admixture of landraces from various geographical locations. Morphological characterization of African tomato can only lay a foundation but it does not reveal genetic diversity. The transcriptome SNP analysis revealed significant variation among the African tomato according to their geographical location.

Chinese jiaotou is an economically important crop that is widely cultivated in East Asia. The lack of simple sequence repeat (SSR) markers has been a major obstacle for genetic studies of this crop. In the present study, SSR markers were developed for Chinese jiaotou on a large scale, based on the crop's transcriptome assembled de novo by a previous study. A search for SSR loci in the transcriptome's expressed sequence tags (ESTs) revealed 2157 SSRs, of which primer pairs could be developed for 1494. Among these resulting SSRs, trinucleotide repeat motifs were the most abundant type, with GAA/TTC motifs occurring most frequently. Analysing the annotated function of SSR-containing ESTs revealed that they enriched into the GO categories involved in transcription regulation, oxidation–reduction, transport, etc. The quality and transferability of these markers were also assessed using 100 randomly selected EST–SSRs, and the result showed that these markers were of good quality and possessed high cross-species transferability. In addition, the developed SSR markers were used to analyse the genetic diversity of 19 cultivated and four wild accessions, resulting in three distinct groups, cluster I, II and III. Interestingly, all four wild accessions were assigned to cluster III, and two local varieties from northern Hunan, China, were closely related to the wild genotypes. These results provide new insights into the origin of Chinese jiaotou. The EST–SSRs developed herein represent the first large-scale development of SSR markers in Chinese jiaotou, and they can be widely used for genetic studies of the crop.

This study evaluates the agronomic and morphological traits, chemical composition and traits related to consumer perception of local tomato landraces mostly collected in the suburban area of Madrid. Results showed remarkable variability at all the studied levels in this small area – intra- and inter-accession variability, and in morphological, agronomical and quality traits – and was often dependent on the environmental conditions where the crop was grown. However, few morphotypes could be defined. Some morphological traits of the studied samples seemed to be associated. For instance, ribbed fruits ripened with green shoulder and dark flesh accumulated more soluble solids. Consumer appreciation and fruit morphology, i.e. traits related to fruit size and shape, seemed to be the main determinants of tomato-type definition, although nutrient content also played an important role. Consumers positively received heirloom tomatoes, especially when they were cultivated in the open-field near their area of selection where they express their full potential in the nutrient synthesis and sensory properties. Although total soluble solids content seems to be the main trait related to appreciation, some morphological traits could be determinant in consumers’ choice. Furthermore, some consumers were more interested in different tomato typologies and nutritional characters like acidity.

The present research was conducted to determine the reactions of 200 pure lines selected from bread wheat landraces collected from 18 provinces and seven regions of Turkey against bunt disease (Tilletia foetida) under field conditions for 3 years. Bunt disease reactions of pure lines were assessed based on the infected spike/total spike ratio. For visually assessed materials, the GGE-biplot method, where G = genotype effect and GE = genotype-by-environment effect, was used to group the reactions against bunt disease. Fifty-nine pure lines showed high resistance (with infection rates ranging from 0.1 to 10%); 24 in the moderate resistance (with infection rates ranging from 10.1 to 25%); 75 in the moderate susceptibility (with infection rates ranging from 25.1 to 45%); 38 in the susceptibility (with infection rates ranging from 45.1 to 70%) and finally four in the highly susceptibility (with infection rates of >70.1%). PC1 and PC2 of the GGE-biplot graph created over the years explained 76.49% of the total variation. The GGE-biplot graph provided efficient identification of resistant genotypes. The lowest PC1 values and PC2 values close to 0.0 explained the resistance of pure line to bunt disease best. The resistance of pure lines to bunt disease over the biplot decreased from the first section through the last section. Based on the results of present study, 19 pure lines (located within the first circle of the biplot graph) were selected for resistance breeding programmes against the diseases.

Jatropha curcas L. is a potential bioenergy crop but has a lack of improved cultivars with high yields and oil content. Therefore, increasing our understanding of J. curcas germplasm is important for designing breeding strategies. This study was performed to investigate the genetic diversity and population structure of Indonesian J. curcas populations from six different islands. To construct a reference, we de novo assembled the scaffolds (N50 = 355.5 kb) using 182 Gb Illumina HiSeq sequencing data from Thai J. curcas variety Chai Nat. Genetic diversity analysis among 52 Indonesian J. curcas accessions was conducted based on yield traits and single nucleotide polymorphism (SNP) markers detected by mapping genotyping-by-sequencing reads from Indonesian population to Chai Nat scaffolds. Strong variation in yield traits was detected among accessions. Using J. integerrima as an outgroup, 13,916 SNPs were detected. Among J. curcas accessions, including accessions from other countries (Thailand, the Philippines and China), 856 SNPs were detected, but only 297 SNPs were detected among Indonesian J. curcas populations, representing low genetic diversity. Through phylogenetic and structural analysis, the populations were clustered into two major groups. Group one consists of populations from Bangka and Sulawesi in the northern part of Indonesia, which are located at a distance of 1572.59 km. Group two contains populations from islands in the southern part: Java, Lombok-Sumbawa, Flores and Timor. These results indicate that introduction of diverse J. curcas germplasms is necessary for the improvement of the genetic variation in the Indonesian collections.

Tomato (Solanum lycopersicum) fruit quality and yield are highly dependent on adequate uptake of nutrients. Potassium, magnesium and calcium are essential elements that influence fruit quality traits such as colour, uniformity of ripening, hollow fruit, fruit shape, firmness and acidity. Sodium is not an essential element for tomato and can detrimentally compete with the absorption of potassium and calcium. Daily intakes of potassium, magnesium and calcium in human diets are typically below healthful levels, while sodium intake is often excessive. The objective of this study was to compare 52 diverse commercially important varieties of tomato for concentrations of potassium, magnesium, calcium and sodium in fruits. The tomatoes were produced in replicated plots in Geneva, NY in 2010 and 2011. Multiple fruits per plot were harvested vine-ripe, homogenized and assayed for cations. Analysis of variance showed significant differences among the 52 varieties for all four traits, i.e. cation concentrations (df = 51, P < 0.0001–0.0034) and no significant differences between years for any trait (df = 1, P = 0.3432–0.6770). Factor analysis showed a strong interrelationship between potassium and magnesium that was independent of calcium and sodium. Potassium and magnesium were highly significantly correlated with each other (r = 0.64, P < 0.0001). No other correlations between pairs of traits were observed. Results supported a genetic basis for potassium, magnesium, calcium and sodium concentrations that was consistent across environments (i.e. years). Results can contribute to the development of cultivars with favourable cation profiles in terms of human health and fruit quality.

Direct sowing of rice in a flooded paddy field is a beneficial cultivation practice for water use and labour efficiency, compared to the transplanted cultivation. However, a drastic reduction in seedling emergence under flooded paddy fields is a serious constraint especially when the seeds fell at deeper soil layers. Suitable rice germplasm for the direct sowing in flooded paddy fields could ensure the success of this cultivation practice. Instead of laborious field-based screening systems, a pot-based screening method was adopted for simplicity and efficient evaluation of seedling emergence of a subset of world rice germplasm (n = 75) at different sowing depths. As a result, two rice genotypes, ‘Vary Futsi’ (landrace from Madagascar, non-glutinous, subspecies Indica) and ‘Dahonggu’ (landrace from China, non-glutinous, subspecies Indica), with consistently better seedling emergence were identified from a wide range of rice germplasm. These genotypes could serve as excellent parents for the breeding program in developing new rice cultivars with the improved seedling emergence in flooded paddy fields. There were no significant differences in the seedling emergence rate in flooded paddy conditions among the groups from various agro-geographical regions.

Drought stress ‘particularly at seedling stage’ causes morpho-physiological differences in wheat which are crucial for its survival and adaptability. In the present study, 209 recombinant inbred lines (RILs) from synthetic wheat (W7984)× ‘Opata’ (also known as SynOpRIL) population were investigated under well-watered and water-limited conditions to identify quantitative trait loci (QTL) for morphological traits at seedling stage. Analysis of variance revealed significant differences (P < 0.01) among RILs, and water treatments for all traits with moderate to high broad sense heritability. Pearson's coefficient of correlation revealed positive correlation among all traits except dry root weight that showed poor correlation with fresh shoot weight (FSW) under water-limited conditions. A high-density linkage map was constructed with 2639 genotyping-by-sequencing markers and covering 5047 cM with an average marker density of 2 markers/cM. Composite interval mapping identified 16 QTL distributed over nine chromosomes, of which six were identified under well-watered and 10 in water-limited conditions. These QTL explained from 4 to 59% of the phenotypic variance. Six QTL were identified on chromosome 7B; three for shoot length under water-limited conditions (QSL.nust-7B) at 64, 104 and 221 cM, two for fresh root weight (QFRW.nust-7B) at 124 and 128 cM, and one for root length (QRL.nust-7B) at 122 cM positions. QFSW.nust-7B appeared to be the most significant QTL explaining 59% of the phenotypic variance and also associated with FSW at well-watered conditions. These QTL could serve as target regions for candidate gene discovery and marker-assisted selection in wheat breeding.

ICAR-Directorate of Cashew Research is the nodal agency for conducting cashew research and manages the largest field gene bank in India. Cashew is a perennial tree and needs more land and other resources to maintain accessions. Conservation through seeds is not feasible because of cross-pollination. Tissue culture efforts to regenerate plants from mature explants are not successful. Therefore, efficient management of the filed gene bank particularly utilization requires designation of the core collection representing the spectrum of diversity present in the entire collection. In this study, a relatively new technique, the advanced M strategy with heuristic approach was deployed to develop the core collection. Sixty-eight morphometric characters of 478 accessions were subjected to analysis resulting in the core collection of 49 accessions. Further, another core collection of same number was constituted by K-Means clustering to compare the efficiency of two approaches. The validation parameters like mean difference, variance difference, coincidence rate, variable rate and class coverage among others were employed for comparative analysis. The results of these parameters revealed that the core collection designated by heuristic approach was better able to efficiently represent and retain the diversity of the entire collection compared with the core identified by clustering approach. Future conservation and breeding efforts will be focused on establishing a separate block in the field gene bank having 49 accessions of cashew core collection.

The goal of most rice improvement programs is the enhancement of farmers’ yield using less land and limited water. This study evaluated 77 upland rice genotypes under optimal upland growing conditions in the field and ranked the genotypes using base indices. Subsequently, eighteen cultivars selected from the field trial were screened under drought in rainout-shelter conditions. The traits evaluated for index selection were yield, days to flowering, plant height, number of panicles and filled grains. Under field conditions, based on the sum of economic weight assigned to five traits used to compute the selection index, IR 68704-145-1-1-B and IR 63380-16 were the best genotypes. In the rainout-shelter experiment, Ofada 2 (508 gm−2) had the highest grain yield under non-stress conditions while ITA 117 (152.38 gm−2) had the highest grain yield under drought stress. The base index was efficient for selecting superior genotypes with the best combination for all the traits considered. Susceptibility to drought stress of the landraces leads to poor grain yield.

Dongxiang wild rice (Oryza rufipogon, DXWR) exhibits valuable agronomic traits and represents a precious germplasm resource for rice breeding. The use of genetic markers can greatly speed up the breeding process and facilitate research on genetics and genomics. In our previous study, we identified insertion–deletion polymorphisms between DXWR and cultivated rice Nipponbare (Oryza sativa ssp. japonica), using whole-genome sequencing in DXWR. In this study, to further explore the genetic variations and enrich the available genetic markers of DXWR, we identified 1,089,478 single-nucleotide polymorphisms (SNPs) (corresponding to one SNP per 0.33 kb of the genome) by genomic comparison between DXWR and Nipponbare, using the genome sequencing data and bioinformatics approaches. Furthermore, the accuracy of the identified SNPs was also validated by polymerase chain reaction amplification and Sanger sequencing. This genome-wide SNPs identification greatly increases the number of genetic markers available for DXWR and provides new opportunities to exploit this valuable and endangered germplasm resource.

The red algal genus Porphyra is sister to the genus Pyropia, the single most valuable marine crop in the Orient. We developed microsatellite loci for the red alga Porphyra umbilicalis, a widespread species in the Northern Atlantic. Enriched DNA libraries were constructed and 68 loci were screened for amplification and polymorphism. Seven polymorphic microsatellite markers were isolated using 44 individuals collected from four natural populations. The number of alleles per locus ranged from two to 12. Null alleles were detected in three loci. Among the markers reported, we tested also cross-amplification with two other Porphyra spp. These polymorphic microsatellite markers should be useful for investigating population genetic structure of P. umbilicalis in the North East Atlantic.

Paphiopedilum hirsutissimum (Lindl. ex Hook. f.) Stein (Orchidaceae) is a valuable but endangered ornamental plant. In the present study, the microsatellites characteristics were analysed and 14 polymorphic simple sequence repeat (SSR) markers were developed based on the de novo transcriptome sequencing for P. hirsutissimum using Illumina pair-end sequencing technology. A total of 7406 SSRs were detected in 56,688 unigenes, with the occurrence frequency of 13.06% and an average density of one SSR per 5.42 kb; and 150 primer pairs randomly selected from 2090 pairs except mononucleotide repeats were synthesized for verification. These loci were validated in 32 individuals from the concentrated distribution centre, and were successfully amplified using 14 primer sets showing a high level of polymorphism. These SSR markers will be useful in future studies of genetic diversity, the population structure of P. hirsutissimum and make effective conservation strategy.

Pearl millet is an important cereal crop for smallholder farmers’ food security in Africa and India. However, its production has stagnated due to several factors such as downy mildew (DM). Thus, a study was conducted to identify new sources of resistance from pearl millet inbred lines derived from a collection of landraces originated from West and Central African countries. A set of 101 lines, including 99 inbred lines from West and Central Africa along with a 7042S and SOSAT C 88 as susceptible and resistant checks, respectively, were evaluated under field conditions with infector rows in Bambey and Nioro research stations during the rainy season of 2016. Data on DM incidence and severity, plant height, flowering time, panicle length and productive tillers were recorded. The results showed highly significant differences among lines for all observed traits. Among the tested lines, 55 including SOSAT C 88 were resistant, 16 moderately resistant and 30 including 7042S were susceptible to the disease. Out of the 55 resistant lines, 20 were disease free. Hierarchical ascendant cluster analysis grouped the lines into three clusters with the DM parameters and plant height as the most discriminant factors. Cluster II contains the susceptible lines, while cluster III comprises the moderately resistant lines. The lines which belongs to cluster I were characterized by their resistance to the disease. Further use of these available new sources of resistance will be very useful for improvement of pearl millet for DM resistance and other agronomic traits.