Zingiber barbatum Wall. (family Zingiberaceae), is an underutilized medicinal plant and commonly known as ‘Meik tha-lin’ in Myanmar where it is used in the indigenous system of medicine. In the present study, 19 accessions of Z. barbatum from five provinces in Myanmar have been utilized to characterize and assess genetic diversity. Twenty-nine morphological characters were noted, including growth habit, leaf, pseudo-stem and rhizome characters. Fifteen primer sets of P450-based analogue (PBA) markers were used to reveal molecular characteristics. Of the 29 morphological characters, 22 showed a high degree of variation within wild ginger accessions, whereas 20 of these characters contributed significantly to morphological variation. Eleven amplified primer sets gave a total of 175 bands and exhibited 92.15% polymorphism across Z. barbatum accessions. Based on morphological characters and PBA markers, 19 accessions can be divided into two morphotype groups with comparatively higher genetic diversity. This information can be applied in future crop improvement, proper conservation and better use of this underutilized medicinal species.

The aim of this research was to use variance components to calculate total phenotypic variation for 12 vegetative and reproductive maize traits. A set of 59 accessions, belonging to nine Peruvian highland maize races, were grown at two consecutive planting seasons in 2 years at one inter-Andean site in northern Peru. The trial data provided a means for calculating the variance components using the restricted maximum-likelihood method. The variance components were assumed to be stable while the number of environments and replications varied to simulate phenotypic variation for each trait. The least number of environments and replications, which does not affect the precision of phenotyping, was selected for assessing each trait. Tabulated data provide the number of environments and replications that can be used as a reference for Peruvian highland trials to assess quantitative variation in plant and reproductive traits. The results suggest that fewer environments and replications are needed for reproductive than for plant traits because the former show higher heritability than vegetative traits.

Pigeonpea (Cajanus cajan (L.) Millsp.) seed harvested while it is immature is a nutritious vegetable and forms a substitute for green pea [Pisum sativum (L.)]. Using the characterization data of more than 12,000 accessions conserved at ICRISAT genebank, Patancheru, India, 105 accessions were selected for important traits of vegetable pigeonpea (mature pod length>6 cm, seeds per pod>5 and 100-seed weight>15 g) and evaluated for these traits during 2007–08. From the initial evaluation, 51 accessions were identified as vegetable type and further evaluated for traits of vegetable pigeonpea during 2008–09 to identify most promising accessions. ICP 13831 produced longest immature pods (10.3 cm), ICP 13828 had maximum number of seeds per pod (5.9) and ICP 12746 produced larger seeds (44.8 g/100 seeds). Highest percentage of total soluble sugars (9.7%) was recorded in immature seeds of ICP 13413. ICP 15143 followed by ICP 15186 recorded more dry pods per plant and seed yield per plant. Performance of ICP 12184, ICP 13413, ICP 14085 and ICP 15169 was better than that of the best control for pod length, seeds per pod, soluble sugars and protein content. Cluster analysis based on scores of first five principal components resulted in three clusters that differed significantly for days to 50% flowering, days to 75% maturity, shelling percentage and soluble sugars. Important traits of vegetable pigeonpea such as immature pod length, seeds per pod, seed soluble sugars and protein content had shown strong positive correlation. Caribbean and Eastern Africa were found as the best source regions for vegetable pigeonpea. Evaluation of selected accessions at potential locations in different countries was suggested to identify vegetable pigeonpeas suitable for different regions and for use in crop improvement programs.

Terminal-repeat retrotransposon in miniature (TRIM) elements are a miniature form of retrotransposons and play an important role in genome organization. The Cassandra TRIM family has been identified in over 50 plant species, including both monocots and dicots. Cassandra elements carry an independently transcribed 5S RNA sequence in their terminal repeat regions, which is unique compared with other TRIM families. Although the existence of Cassandra elements has been documented in many plants, much work remains to characterize Cassandra family members and elucidate their distribution. In this study, we comparatively analysed the Cassandra family members in the Brassica oleracea, B. rapa and Arabidopsis thaliana genomes. A total of 602, 451 and 173 members, of which 130, 60 and 9 were relatively intact, were identified from the B. oleracea, B. rapa and A. thaliana genomes, respectively. Most of the Cassandra elements (1120/1226) were found in intergenic spaces, but 106 elements were inserted in genic regions such as introns, exons and untranslated regions. Our comparative analysis of the Cassandra family members in A. thaliana, B. rapa and B. oleracea reveals that some Cassandra elements have been commonly retained during the last 20 million years in three species and some elements have been uniquely evolved in Brassica species. This study promotes our understanding of the role and utility of Cassandra elements in the evolution of the Brassicaceae family.

Chickpea (Cicer arietinum L.) is an important food legume crop grown mostly in Asia and Africa as well as in other parts of the world, and serves as an important source of protein in the diets of vegetarian people. Lot of variation in grain quality traits has been observed in cultivated chickpea in both desi and Kabuli types. It has often been observed that seeds with smaller size have more protein when compared with those with larger size. The joint dependence of these two traits on the same primary characteristics results in this negative relationship. This negative correlation coupled with breeding efforts aimed at increasing grain yield has hampered the progress of improving these two traits simultaneously. Therefore, a germplasm exhibiting wider variability for these quantitative traits is an important resource for the identification of novel alleles. Herein, we report the wide variation observed for five important quantitative traits including days to flowering, days to maturity, plant height, 100-seed weight and protein content, and also report the significant positive correlation observed between 100-seed weight and protein content in a diverse collection of chickpea germplasm comprising both desi and Kabuli types.

In this study, maize landraces, previously collected from different regions of Turkey through a national maize breeding project, were screened for kernel oil content and oil quality. After a seed reproduction in 2017, the screening trial was conducted in 2018, using an Augmented Experimental Design with 192 local maize populations along with seven check hybrids. Data were collected on oil, oleic acid, linoleic acid, monounsaturated (MUFA), polyunsaturated and saturated fatty acids, total carotenoid and total tocopherol contents. The results showed that there was a considerable amount of genetic variation among the Turkish maize landraces for almost all the traits investigated in this study. Some of the evaluated landraces are available that could be considered as high oil variety or special genotypes in terms of certain oil quality traits. Landraces had significantly higher values than checks for oil content, oleic acid, MUFA and tocopherol contents. Genetic analyses suggest that the kernel quality traits could be successfully manipulated using the investigated plant material. Heritability values were found high for all the traits of interest, except for saturated fatty acid and total carotenoid content. The promising landraces detected in this study could be exploited in future breeding programmes upon further evaluations at the population level.

In order to investigate further the interest of using the Chilean gene pool in potato breeding programmes, the genetic diversity and population structure of a collection of Solanum tuberosum L. genotypes including 350 worldwide varieties or breeders' lines (referred to as the modern group) and 30 Chiloé Island landraces were examined using simple sequence repeat markers. The close genetic proximity of the Chiloé Island landraces to the modern group was confirmed using several structure analysis methods: principal coordinate analysis; hierarchical clustering analysis; analysis of molecular variance; Bayesian model-based clustering analysis. The latter analysis, in particular, revealed no clear genetic structure between the modern group and the Chiloé Island landraces. The Chiloé Island germplasm appears to represent an interesting gene pool that could be exploited in potato breeding programmes using an association mapping approach.

Microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) is an important component of the plant innate immunity response to invading pathogens. Although several MTI responses can be measured in different plant species, their magnitude is probably plant species specific and even cultivar specific. In this study, a genome-wide transcriptome analysis of two soybean parental lines and two progeny lines treated for 30 min with the MAMPs flg22 and chitin was carried out. This analysis revealed a clear variation in gene expression, under both untreated and flg22+chitin-treated conditions. In addition, genes with potential additive and non-additive effects were identified in the two progeny lines, with several of these genes having a potential function in the control of innate immunity. The data presented herein represent the basis for further functional analysis that can lead to a better understanding of the soybean innate immunity response.

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.

Crop wild relatives are important components of agro-ecosystems as potential gene contributors for crop improvement programmes. Cajanus scarabaeoides (L.) Thou., a pigeonpea wild relative is crossable with cultivated pigeonpea and possesses several beneficial traits. Hundred accessions conserved at the ICRISAT genebank were characterized for 13 quantitative and ten qualitative traits to assess the diversity in the collection. Highly significant genotypic variance for leaflet length, days to 5% maturity, seeds per pod, 100-seed weight, seed protein content and trichome density and length was observed. All C. scarabaeoides accessions used in the present study are the best sources for extra early ( < 80 d to 50% flowering) and early maturity (80–100 d to 50% flowering). Eight accessions (ICP 15692, ICP 15696, ICP 15698, ICP 15699, ICP 15712, ICP 15719, ICP 15732 and ICP 15758) and the control ICP 15695 have produced more than 92% healthy pods per plant and higher number of seed per pod (4–6 seeds). Accessions in cluster 2, 3 and 4 with low mean values for days to 50% flowering were found as the best sources for early flowering and maturity. Accessions in cluster 2 and 3 for seeds per pod and cluster 2 for healthy pods per plant were found as promising sources for use in crop improvement. Mean diversity over all clusters was highest (H= 0.57 ± 0.01) for seeds per pod and lowest for days to 50% flowering (0.48 ± 0.02). Significant negative correlation between pods per raceme and healthy pods per plant ( − 0.213) indicated high pod damage in racemes having more pods. Trichome length had highly significant negative association with healthy pods per plant ( − 0.293). The probability map generated using FloraMap, a GIS tool, revealed the occurrence of C. scarabaeoides quite close to the origin and dispersal of pigeonpea. The probability (>75%) map identified a total of 118 provinces covering 790 districts in Bangladesh, Cambodia, India, Indonesia, Laos, Malaysia, Myanmar, Nepal, Papua New Guinea, Philippines, Thailand and Vietnam as geographical gaps in the collection. Complete passport data including location coordinates should be collected while collecting the germplasm to analyze the spatial aspects of species distribution.

Faba bean (Vicia faba L.) was used as the rootstock for lentil scions to test the feasibility of using in vivo inter-generic grafting techniques as a substitute for root induction and as a tool in lentil genetic improvement. An accession of each of the six wild Lens species was used as the scion in grafts to faba bean breeding line FB50-9 rootstock. Successful grafts were obtained for all species with survival of grafts to seed maturity between 70.7 and 87.7% except for Lens orientalis PI 72735 with 55.3% survival. Days to flower remained the same after grafting, except for scions of L. nigricans PI 72560 and L. orientalis PI 72735 which had a lag phase of 9 and 7 d, respectively. For all six wild species, seed diameter and seed weight were not significantly different between non-grafted controls and scions grafted onto faba bean rootstocks. This simple approach opens the possibility of using in vivo grafting techniques to rescue inter-specific hybrids of lentil. The technique has potential as a useful tool in lentil breeding, as a means of improving seed multiplication rate of rare genetic resources of wild lentil and as a way to reduce the costs of germplasm multiplication of wild lentil species.

The Germplasm Enhancement of Maize (GEM) Project is a cooperative effort between the USDA-ARS, private industry and public researchers to broaden and enhance the germplasm base of maize. In this program, selected accessions from the Latin American Maize Project, and seven tropical hybrids donated by DeKalb to the GEM Project, were crossed to elite proprietary inbred lines contributed by commercial plant breeding programs. In most cases, the resulting hybrids were crossed to a second commercial inbred line and the resulting 25% exotic hybrids were used as breeding populations for further development. To identify GEM germplasm with value to protein quality breeding programs, we developed a process for evaluating the content of the essential amino acids methionine, lysine and tryptophan in the grain of GEM germplasm that balances the need for multiple-year evaluations with the constantly changing entry list of this germplasm screening program. This process involves annual field trials with common checks. Weak entries are dropped from the trial each year to make room for new entries, while strong entries are retained. Methionine exhibited the most significant variation, followed by lysine and then tryptophan. A number of GEM lines had methionine or lysine levels that were significantly better than Corn Belt checks and some were competitive with high-amino acid checks.

Sinapis alba L. is a major specialty crop grown as a condiment in western Canada, but little is known about its genetic diversity. The objective of this study was to assess the level and pattern of genetic diversity in a collection of 127 S. alba accessions held at Plant Gene Resources of Canada using amplified fragment length polymorphism (AFLP) markers. Five AFLP primer pairs were applied, and 134 polymorphic bands were scored for each accession. These scored bands had frequencies of occurrence ranging from 0.02 to 0.99 with an average of 0.69. More AFLP variation was found within single (79.1%) than between (20.9%) S. alba accessions. A small degree of AFLP difference (1.7%) was observed among the accessions of various regions, while relatively large variation (9.2%) existed among the accessions of various countries. A large AFLP difference (15.6%) also existed between the yellow- and brown-seeded accessions, but only 6.2% difference was observed between the cultivar and landrace accessions. Two distinct groups of S. alba germplasm were identified on the basis of the seed colour (yellow or brown), although a few mixtures also existed. No apparent ‘duplicated’ accessions were observed. The most diverse accessions were from Italy, Spain, France and Greece. Among the most genetically distinct accessions were SA97 from Portugal, SA89 and SA88 from France, SA83 from Russia and SA57 from Italy. These findings are significant not only for managing S. alba germplasm, but also for identifying diverse germplasm that can be used by plant breeders to improve S. alba seed yield and quality parameters.

Characterization and genotype identification are essential for rational conservation, management and genetic diversity evaluation. In this work, simple sequence repeat (SSR) markers were used to identify 57 accessions of sweet potato kept at the ‘in vitro’ Gene Bank of INTA, Argentina. This collection includes primitive materials from primary zones of dispersion, commercial varieties, breeding clones and foreign materials from different parts of the world (Africa, Asia and USA). Average similarity between the materials evaluated was 0.367. Grouping analysis revealed six clusters and a strong association with skin colour of storage roots. The set of selected SSR markers allowed us to verify identity, detect duplicates and estimate the genetic similarity of the materials analysed. This characterization complements morphological data and provides tools to estimate the variation of diversity between local and foreign germplasm groups.

The development of modern approaches to the genetic improvement of the tree crops Ilex paraguariensis (‘yerba mate’) and Ilex dumosa (‘yerba señorita’) is halted by the scarcity of basic genetic information. In this study, we characterized the implementation of low-cost methodologies such as representational difference analysis (RDA), single-strand conformation polymorphisms (SSCP), and reverse and direct dot-blot filter hybridization assays coupled with thorough bioinformatic characterization of sequence data for both species. Also, we estimated the genome size of each species using flow cytometry. This study contributes to the better understanding of the genetic differences between two cultivated species, by generating new quantitative and qualitative genome-level data. Using the RDA technique, we isolated a group of non-coding repetitive sequences, tentatively considered as Ilex-specific, which were 1.21- to 39.62-fold more abundant in the genome of I. paraguariensis. Another group of repetitive DNA sequences involved retrotransposons, which appeared 1.41- to 35.77-fold more abundantly in the genome of I. dumosa. The genomic DNA of each species showed different performances in filter hybridizations: while I. paraguariensis showed a high intraspecific affinity, I. dumosa exhibited a higher affinity for the genome of the former species (i.e. interspecific). These differences could be attributed to the occurrence of homologous but slightly divergent repetitive DNA sequences, highly amplified in the genome of I. paraguariensis but not in the genome of I. dumosa. Additionally, our hybridization outcomes suggest that the genomes of both species have less than 80% similarity. Moreover, for the first time, we report herein a genome size estimate of 1670 Mbp for I. paraguariensis and that of 1848 Mbp for I. dumosa.

Climate change-induced events are causing salinization of many rice-growing areas, requiring the identification of new sources of genetic variation for salt tolerance in plant genetic resources since commonly grown cultivars are sensitive to salt. To identify the level of salt tolerance across a wide range of genotypes, we used a multivariate screening method using multiple growth and physiological traits simultaneously. For this purpose, four indica, two japonica and two wild rice genotypes were grown hydroponically under 40 and 80 mM NaCl stresses; fourteen different growth, qualitative and physiological traits, e.g. plant height, biomass, root and shoot elongation rates, and tissue ion accumulation, were recorded. In general, indica varieties performed better than both japonica and wild species. Our approach identified the existence of qualitatively different mechanisms of salt tolerance across the genotypes. For example, Pokkali, a salt-tolerant indica variety, displayed both ‘Na exclusion’ and ‘ion balance’ mechanisms, whereas PSBRc50 and IR58 showed only ‘Na exclusion’, and the Japonica genotypes Banikat and Nipponbare showed only ‘ion balance’. The results demonstrated that the tolerance is dependent on the level of stress and that this varies between genotypes; Nipponbare is moderately tolerant to 40 mM NaCl but not to 80 mM. We also suggest that the use of multivariate analyses can simplify the complex salinity tolerance picture and can effectively reveal the salinity tolerant genotype from a wide range of germplasm. The results reported here identify different physiological mechanism of tolerance across the genotypes and provide a sound basis for future studies examining their underlying molecular mechanisms.

Faba bean (Vicia faba L.) is one of the most important legumes in the world. Little is known about the genetic resources of faba bean in Southern Tunisia. In the present study, genetic diversity within Tunisian faba bean germplasms was investigated using 16 simple sequence repeat markers. In total, 50 alleles were detected. The number of alleles per marker ranged from 2 to 6, with an average of 3. Genetic diversity and polymorphism information content values averaged, respectively, 0.43 (range 0.34–0.51) and 0.36 (range 0.28–0.43). The mean heterozygosity value was 0.27. A model-based structure analysis based on neighbour-joining tree and factorial correspondence analysis revealed the presence of two subpopulations, consistent with the clustering based on genetic distance (GD). The overall Fis value was 0.36, indicating the importance of selfing in these populations. Analysis of molecular variance revealed that the within-population genetic variance component was much higher than the between-population or between-subpopulation variance component. The genetic relationships based on Nei's GD revealed that AGD (Aguadulce) and SAG (Super Aguadulce) and TF1 and TF2 (Tafartassa-Gafsa) were the most closely related populations. Assessment of genetic variation within faba bean populations will be informative for the conservation of germplasms and the implementation of effective breeding programmes in Tunisia.

The Triticeae tribe (Poaceae) includes several important cereal crops, cultivated forages, annual and perennial grass weeds and ecologically diverse native North American grasses. Elymus L. is the largest and most complex genus in the Triticeae tribe with approximately 150 polyploid perennial grass species occurring worldwide. The genomic constitutions of approximately 40% of the Elymus species are unknown. Molecular markers are needed to facilitate genetic analysis of diversity and functional traits in these species. We have developed simple sequence repeat (SSR) markers for use in Elymus based on Elymus expressed sequence tag sequences. To test the polymorphic content and transferability of these SSRs, 100 SSR primer pairs were tested on 84 plants representing seven North American Elymus, Pseudoroegneria and Pascopyrum species. The number of bands produced from each of the SSRs ranged from 1 to 11 with an average of 4.3 bands/SSR. A subset of the 23 most polymorphic SSRs produced 142 bands, an average of 6.2 bands/SSR. Binary data from the 100 SSRs successfully separated all individuals into their respective accessions in a neighbour-joining phylogram with a 100% confidence interval. Analysis of molecular variance showed that 29.9% of the total variation was within and 70.1% was among the accessions. These SSRs will be a useful tool for investigating genetic diversity, genome constitutions and molecular mapping in Elymus and other Triticeae grasses.

Pine wilt disease, caused by the pinewood nematode Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle, is originating severe infections in pine trees. The disease is detected when external symptoms appear (e.g. needle chlorosis), but trees could remain asymptomatic for long periods and serve as a long-term host. The primary goal of this study was to assess the effect of inoculation with an avirulent isolate of B. xylophilus (C14-5) on different Pinus spp. seedlings (P. sylvestris, P. nigra, P. pinea and P. pinaster). At the same time, seedlings were also inoculated with a virulent strain, HF, in order to compare the phenotypic and genomic results of the two types of inoculations. The effect of inoculation was determined in terms of expression of various Pinus genes potentially involved in the response to the disease.The results suggest that P. pinea and P. nigra are more resistant to infection by the nematode than P. sylvestris and P. pinaster. The phenotypic and genetic differences were more marked among P. pinea and P. pinaster.

Microsatellites or simple sequence repeats (SSRs) are useful molecular markers allowing for efficient conservation and sustainable use of genetic resources of plant species. Development of SSR marker system for new species is a very expensive task and time consuming. Cross-species amplification of microsatellite loci is considered as a cost-effective approach for developing microsatellite markers for new species. The aim of this work was to examine the transferability of some SSR markers of two Arecaceae species (Astrocaryum aculeatum and Elaeis oleifera), in Acrocomia aculeata. Out of the total markers analysed 44% of the markers successfully amplified the genomic DNA in A. aculeata, of which 26% were polymorphic detecting a range of three to eight alleles with an average of 4.5 per locus. High average percentage of polymorphic loci (P= 71.2%) per provenance was obtained within a range of 57–100% detecting genetic variation in A. aculeata germplasm collections. The polymorphic markers detected a positive inbreeding coefficient (F>0) per locus revealing heterozygote deficiency in the accessions that were analysed. As the cross-amplification was at family level, in which the taxonomic distance is relatively wider between the sources (A. aculeatum and E. oleifera) and the target (A. aculeata) species, the amplification success was relatively low. However, the results are promising and implicated that high cross-amplification success could be achieved at species or genus level in A. aculeata. The markers will contribute towards the domestication of the potential macaw palm through realizing various studies such as population genetics, germplasm characterization, genetic improvement and conservation.