Advances in genomics have provided technologies for high throughput analysis of plant genomes with potential for use in gene discovery in germplasm collections. The establishment of DNA banks facilitates this screening by making DNA from large numbers of plant accessions widely available. DNA banks require the development of appropriate policies for access and benefit sharing. Tools for automating sample and data handling are essential. Standard molecular methods for fingerprinting DNA accessions for international comparisons need to be determined. New screening technologies are required to take advantage of the emerging availability of large DNA collections. The Australian Plant DNA Bank aims to collect DNA from all Australian plant species and to sample the diversity within each species. DNA from all individuals of the species is being stored for rare species. Domesticated or economically important species from all countries are also being collected and stored. International networking of DNA banks will be a key step in linking genomics tools to global plant diversity.

The endangered alpine plant Aconitum heterophyllum was conserved under ex situ conditions (greenhouse and open) of Palampur by overcoming seed dormancy and plant establishment through hot water treatment (40–60 °C for 30–120 s) of seeds. High seed germination (88 and 76%) was obtained when seeds were treated with hot water at 45 and 50 °C for 90 s. Correlation studies also revealed that treatment enhanced vegetative growth and reproductive yield of the plants. The total alkaloid content of the roots and rhizomes of the plants growing under ex situ conditions was lower than the ones collected from the natural habitat in the 1-year-old plants. However, in the 2-year-old plants, it was almost at par with the ones collected from nature. The life cycle of the plants growing under ex situ conditions also did not vary largely from the plants growing under in situ conditions. Therefore, the present study indicates the successful adaptation of A. heterophyllum plants in conditions other than their natural habitat and hence its potential for sustainable commercialization.

In Uruguay, onion (Allium cepa L.) germplasm is mainly derived from the genetic material introduced by several waves of European immigrants and subsequently multiplied by household farmers, resulting in a wealth of locally adapted populations. This study examined the genetic diversity in a collection of 27 local onion populations and two cultivars derived from them. A total of 843 onion plants were fingerprinted, and 83 inter-simple sequence repeat polymorphic bands were generated. Analysis of molecular variance showed high diversity within the populations (66% of the total variation). Some short-day populations from different geographical origins were grouped together by the unweighted pair-group method using arithmetic averages, principal coordinate analysis and cluster analysis, while the more extensively sampled long- and intermediate-day populations showed a widespread distribution, with no significant subgrouping among them. This weakly structured gene pool is probably the consequence of seed and bulb exchange between farmers and natural inter-pollination. Nevertheless, a Bayesian analysis allowed the distinction of four genetic backgrounds of alleles in the whole collection, and populations were predominately assigned to each genetic background. In addition, mitochondrial variants determining normal (N) pollen fertility or the sterile S or T types were analysed for the same set of plants using specific primers. Most accessions showed a proportion of male-sterile individuals. Cytoplasm type T was the most represented (26 out of 29 accessions), and cytoplasm type S was found in a low proportion of individuals in seven populations. Uruguayan onion germplasm maintains a low degree of genetic differentiation despite the small cultivated area and intense seed exchange, probably due in part to different market purposes based on the growing cycle.

Germplasm of common beans from the Mesoamerican gene pool races: Durango, Jalisco, Mesoamerica and Guatemala have highest genetic variation for the crop's improvement. The objective was to assign 50 common bean germplasm in Uganda into its gene pool races based on analyses of population structure. Secondly, to estimate heritability and effects of genotype × environment (GXE) interaction on common bean agronomic and yield traits in space and time. Sample genomic DNA was amplified in 2011 with 22 Simple sequence repeat markers (SSRs) and alleles separated using capillary electrophoresis. Field evaluations were conducted in 2010 and 2011 at NaCRRI and 2015 at CIAT – Kawanda. Multivariate analyses of SSRs data identified four subgroups within the germplasm: K4.1–K4.4, with corresponding Wrights fixation indices (FST) as 0.1829 for K4.1, 0.1585 for K4.4, 0.1579 for K4.2 and least for K4.3 at 0.0678. Gene pool race admixtures in the population (14%) were notable and attributed to gene flow. Four superior parents currently used in improving resistance to major diseases grouped as; Jalisco for MLB49-89A; Mesoamerica for MCM5001 and G2333; Durango for MEXICO 54. Heritability values for yield traits estimated using phenotypic data from above fixed parents, was above 0.81. Season and location had significant effect (P < 0.05) on numbers of: flower buds per inflorescence, pod formation and weight of 100 seeds. The findings will improve understanding of co-evolutionary relationships between bean hosts and pathogens for better disease management and will broaden the germplasm base for improving other tropical production constraints.

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.

Triticum urartu, the A-genome donor of tetraploid and hexaploid wheats, is a potential source of novel alleles for crop improvement. A fertile amphiploid between T. urartu (2n = 2x = 14; AuAu) and durum wheat cv ‘Yavaros’ (Triticum turgidum ssp. durum; 2n = 4x = 28, AABB) was obtained as a first step to making the genetic variability of the wild ancestor available to durum wheat breeding. The amphiploid was backcrossed with ‘Yavaros’ and the offspring from this cross was selfed. A plant from this progeny (founder line) with 28 chromosomes and active x and y subunits of the Glu-A1 locus of T. urartu was selfed, which resulted in the obtaining of 98 pre-introgression lines (pre-ILs). In this work, a set of 78 wheat chromosome-specific microsatellite markers (simple sequence repeats, SSR), uniformly distributed over the A genome, was used for marker-assisted selection of T. urartu in a durum wheat background. A total of 57 SSRs allowed a clear discrimination between T. urartu and ‘Yavaros’. This set of markers was further used for characterizing the pre-ILs, identifying and defining the T. urartu introgressed regions. The applicability of these markers is discussed.

Sugarbeet cultivars are almost exclusively hybrids, which are produced using the sole source of cytoplasmic male sterility (CMS), the so-called Owen CMS. Several alternative sources of CMS have been described. One of these, I-12CMS(3), was derived from wild beets collected in Pakistan, and another CMS source, GCMS, has a cytoplasmic origin in wild sea beets from France. During the past decade, male sterility-associated mitochondrial genes have been identified in these three CMS systems. Moreover, the recent development of a variety of DNA markers has permitted the genetic mapping of nuclear restorer-of-fertility genes for both Owen and GCMS. This review focuses on the mechanism of CMS in beets.

Digitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis transcriptome. Thirty-seven primer pairs were randomly selected and tested for their ability to cross-amplify to related species. Clear amplification patterns were observed on 24 primer pairs. Of these, 71, 74 and 35% showed polymorphism in three species: D. exilis, D. longiflora and D. iburua. The transferability from D. exilis was 96% to D. longiflora and 71% to D. iburua. The new SSR markers confirmed the close genetic proximity of D. exilis with D. longiflora and its stronger genetic difference of D. exilis from D. iburua. These markers will be valuable for completing future knowledge on Digitaria evolutionary history, and for testing gene flows between related species.

North Africa enclosed original apricot genetic resources with the cohabitation of grafting and seed-propagated accessions. In this study, we assessed the genetic diversity and population structure of 183 apricot accessions using 24 microsatellite markers distributed evenly in the Prunus genome. A total of 192 alleles and a high level of gene diversity (0.593) were detected among the whole panel. Genetic structure analysis revealed the presence of four genetic clusters. We also found that both geographical origin and mode of propagation are important factors structuring genetic diversity in apricot species. Results confirmed the presence of gene exchange between the northern and southern countries of the Mediterranean Basin. Subsequently, a core collection of 98 accessions based on M (maximization) strategy showing 99.47% of allele retention ratio was constructed. No significant differences for Shannon's information index and Nei's diversity index were observed between the core and entire collections. Our results provide an effective aid for future germplasm preservation and conservation strategies as well as genetic association studies development in relation to phenotypic data.

Triticum monococcum ssp. monococcum has useful traits for bread wheat improvement. The synthesis of Triticum turgidum–T. monococcum amphiploids is an essential step for transferring genes from T. monococcum into bread wheat. In this study, 264 wide hybridization combinations were done by crossing 60 T. turgidum lines belonging to five subspecies with 83 T. monococcum accessions. Without embryo rescue and hormone treatment, from the 10,810 florets pollinated, 1983 seeds were obtained, with a mean crossability of 18.34% (range 0–89.29%). Many hybrid seeds (90.73%, 923/1017) could germinate and produce plants. A total of 56 new amphiploids (AABBAmAm) were produced by colchicine treatment of T. turgidum × T. monococcum F1 hybrids. The chromosome constitution of amphiploids was characterized by fluorescence in situ hybridization using oligonucleotides probes with different chromosome and sub-chromosome specificities. Sodium dodecyl sulphate polyacrylamide gel electrophoresis analysis indicated that the Glu-A1m-b, Glu-A1m-c, Glu-A1m-d and Glu-A1m-h proteins of T. monococcum were expressed in some amphiploids. Despite resistance reduction in several cases, 45 out of 56 amphiploids exhibited resistance to the current predominant Chinese stripe rust races at both the seedling and adult plant stage. These novel amphiploids provide new germplasm for the potential improvement of bread wheat quality and stripe rust resistance.

Root-knot nematodes (RKNs), Meloidogyne spp., are considered, worldwide, as one of the main pathogens of solanaceous crops, including pepper (Capsicum spp.). Restrictions on the use of standard nematicides have motivated the development and use of resistant cultivars and rootstocks. Three genes in pepper, called Me1, Me3 and N, confer resistance to the three main RKN species (Meloidogyne incognita, Meloidogyne javanica and Meloidogyne arenaria). However, their effectiveness seems to be limited because nematode populations that have overcome the resistance have been found, leading to a search for new sources of resistance and strategies to preserve their effectiveness. In two greenhouses and over a 7-month growing period, we evaluated the resistance to M. incognita and the agronomic behaviour as rootstocks of nine pepper (Capsicum annuum) accessions – HDA330 (Me1 carrier), Serrano Criollo de Morelos, (Me3 carrier), Yolo Wonder (partially resistant) and another six accessions of unknown resistance originating from cultivars well adapted to the local growing conditions. The resistance conferred by the Me1 gene was more robust than that conferred by Me3. Resistance to M. incognita was found in four new accessions: P13, CTL, CT5, and P14. In P13, the level of resistance was similar to that of HDA330. The resistant accessions showed better agronomic behaviour than the susceptible accessions, which was most noticeable towards the final of the growing period. Some accessions constitute a potential resource for use in the genetic breeding of RKN-resistant rootstocks.

Error-prone repair of radiation-induced DNA double-strand breaks (DSBs) results in DNA mutation that is essential for mutation breeding. Non-homologous end joining might be the principal DSB repair mechanism in eukaryotes, which is mediated and activated by Ku protein, a heterodimer of 70 and 80 kDa subunits. In this study, on the basis of complementary DNA (cDNA), the genomic sequences of TaKu70 and TaKu80 genes in all the three genomes of wheat were characterized. Only single-nucleotide substitutions and no insertions or deletions were detected in the exons of TaKu70 and TaKu80 genes. The size of the introns exhibited a slight variation between the sequences. Yeast two-hybrid analysis demonstrated that TaKu70 and TaKu80 formed a heterodimer, and electrophoretic mobility shift assays revealed that this heterodimer bound to double-stranded DNA, but not to single-stranded DNA. The quantitative polymerase chain reaction analysis revealed that the expression of TaKu70 and TaKu80 genes was up-regulated under γ-ray irradiation in a dose-dependent manner in the seedlings of wheat. These results suggest that TaKu70 and TaKu80 form a functional heterodimer and are associated with the repair of the induced DSBs in wheat.

Cocoa butterfat and cocoa powder are key economic products from the seeds of the cacao tree (Theobroma cacao L.). In this study, 323 accessions (comprised mainly of Upper Amazon Forasteros and Refractarios) from the International Cocoa Genebank, Trinidad were characterized for one biochemical and five morphological seed-derived traits. The data were analysed using non-parametric statistics including correlation analysis to identify promising parental candidates for future cacao breeding programmes. The Upper Amazon Forastero group had the greatest proportion of accessions with high butterfat content in cotyledons, whereas Refractario and Trinitario groups tended to contain more accessions with high butterfat content per fruit. The correlation of butterfat content of cotyledons with the dry mass of cotyledons was inconsistent in significance and direction. However, consistent significant positive correlations between butterfat content per fruit, cotyledon size and dry mass of cotyledons were found. The results suggested that butterfat content is a likely trait for independent selection but that selection for increased cotyledon size could lead to the selection of genotypes for high butterfat yield. Several promising accessions exhibited favourable levels of multiple traits and MATINA 1/7, CRU 51, AM 2/91 [POU], CRU 133, EET 58 [ECU] and POUND 18/A [POU] could be recommended as good choices for parental stock in breeding programmes for improving cacao butterfat content.

Woad (Isatis tinctoria L.) was the most important source of natural blue indigo, a pigment used mainly for dyestuff until the beginning of the 20th century, when the increased use of synthetic dyes by the industry lead to a decrease in the interest of natural dyes and to the abandonment of dye crops. The aim of this study was to characterize, according to morphological and agronomical traits, 11 woad accessions from different countries and to quantify the indigo precursor content by high-performance liquid chromatograph-diode array detection (HPLC-DAD). Qualitative traits revealed a low variability and a great variation was observed in quantitative traits. Principal component analysis (PCA) diagrams divided the accessions into four groups, primarily according to their geographic origin. The first three components of the PCA accounted for 76.8% of the total variation. Reciprocal interactions between indigo precursors and fresh leaf weight were compared through genetic diversity, with significant differences in isatan B (0.5–5.1 g/kg), indoxyl (0.3–2.0 g/kg) and residual indigo (0.3–0.5 g/kg). This information, together with genetic data, can be used to assist local farmers to re-introduce Isatis species in the European agricultural system, not only indicating the higher indigo yielding genotypes, but also the most suitable harvest time.

Germination tests are performed on a routine basis to determine the viability of genebank accessions. The results determine which accessions have to be rejuvenated. The reliability of the germination test results used by the Centre for Genetic Resources, the Netherlands was determined by the retesting of 641 random samples anonymously, in the same year and by the same testing agency as the original tests. Results showed alarmingly low reliabilities, with error levels much higher than expected based on sampling effects. The result of a germination test of a random sample with a germination of 80% was shown to have a 95% confidence interval from 63 to 97%. The errors differed strongly over crops and testing years, and were larger for crop wild relatives than for crop species.

Hybrid breeding relies on selection of genetically unrelated and complementary parents for key traits. The objective of this study was to examine genetic variation and identify unique sorghum genotypes using phenotypic and simple sequence repeat (SSR) markers and to determine their relationships with combining ability and heterosis for grain yield. A total of 32 landraces and four cytoplasmic male sterile (CMS) lines were phenotyped using 25 agro-morphological traits and genotyped with 30 polymorphic SSR markers. The landraces were crossed with four CMS lines using a line × tester mating design. The 128 hybrids, 36 parentals and four check varieties were field-evaluated using a 12 × 14 alpha lattice design with three replications. General combining ability (GCA), specific combining ability (SCA) and heterosis for grain yield were determined. Genetic distance estimates ranged from 0.39 to 0.60 and 0.50 to 0.79, based on phenotypic and SSR markers, respectively. Landraces 72572, 75454, 200654, 239175, 239208, 244735A and 242039B and CMS lines ICSA 743 and ICSA 756 displayed positive and significant GCA effects for grain yield. Based on the SCA effects of yield, lines were classified into three heterotic groups aligned to the different cytoplasmic systems of testers. Lines with high GCA effects rendered hybrids with highly significant SCA effects with high mid-parent heterosis (MPH) for grain yield. Both marker systems were effective in demarcating sorghum genotypes that provided desirable cross-combinations with high combining ability effects and MPH for grain yield. The selected genotypes are recommended as potential parents for sorghum hybrid breeding in moisture stress environments.

Seed coat colour is an important quality trait, domestication trait and morphological marker, and is closely associated with flavonoid and anthocyanin metabolism pathways. The seed coat colour of adzuki bean, an important legume crop, influences the processing quality of its paste, the commodity and its nutritional quality. In this study, the genetic relationships of seed coat colour were analysed using 12 hybridized combinations of F2 individuals and four F3 families derived from hybridized combinations between the accessions of eight seed coat colours. The loci of the colour traits were analysed based on phenotypes and using the chi-square test. Ivory colour is recessive to red and is controlled by a single R locus. Black, black mottle on grey, black mottle on red, light brown, golden and brown are all dominant to red. The phenotypes of black mottle on red, light brown, golden and brown are all controlled by a single genetic locus. Black mottle on grey is controlled by two loci. Black is controlled with two loci, and the black locus shows dominant epistasis to another locus. A genetic model of these seed coat colours was predicted. Our results will be important for gene mapping and cloning of seed coat colour characters and for providing further insight into the regulatory network of seed coat colour.

The genetic diversity of 39 Iranian black cumin (Nigella sativa L.) landraces was analysed using 14 polymorphic Start Codon Targeted (SCoT) markers. A total of 106 bands ranging from 3 (for SCoT70) to 13 (for SCoT23) were observed. Of them, 33 (31%) bands were polymorphic with a mean of 1.65 bands per primer. Polymorphism information content (PIC) per primer ranged from 0.035 (for SCoT12) to 0.133 (for SCoT70), with an average of 0.078. Besides PIC, Simpson's diversity (D) index was also calculated for each SCoT marker as an indication of discrimination power across population. The D index was used to adjust the PIC of the SCoT markers. As the adjusted PIC (PICD= PIC × D) was calculated based on both the PIC and the rate of band dispersion, this reflected the informativeness of a dominant marker more precisely than PIC. Genetic relationships were estimated using Jaccard's similarity coefficient-generated values between different pairs of genotypes that varied from 80 to 97% with an average of 88%. These coefficients were applied to construct a dendrogram using the UPGMA algorithm. A high genetic similarity was observed that might be due to the fact that N. sativa is a self-pollinated plant not originated from Iran and might have been imported from the Mediterranean regions.

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major biotic constraint of rice production in all the major irrigated/lowland rice growing regions of Asia, including Punjab and its adjoining states in India. None of the individual BB resistant Xa/xa genes is effective against Punjab pathotypes. In the present study, we have screened 1176 accessions, comprising 1007 accessions of A genome species Oryza glaberrima, O. barthii, O. nivara, O. rufipogon, O. longistaminata, O. meridionalis, O. glumaepatula and 169 accessions from ten other wild species having CC, FF, EE, BBCC and CCDD genomes against two most recently evolved Xoo pathotypes viz. PbXo-10 and PbXo-8 in Punjab state of India, for two constitutive years 2014 and 2015. Based on 2 years of data, four accessions of O. glaberrima (IRGC102206, IRGC1022445, IRGC102512 and IRGC102520) and two of the O. longistaminata accessions (IRGC92624 and IRGC101754) were identified with immune reaction against PbXo-8. For PbXo-10, O. longistaminata showed large number of accessions with complete to partial resistance followed by O. rufipogon (8), O. nivara (2), O. punctata (2) and O. officinalis (1). Two of the O. longistaminata accessions IRGC92624 and IRGC92644 from Mali were found to have resistance against both the Xoo pathotypes indicating presence of BB resistance gene other than Xa21. These can be transferred to elite cultivars of O. sativa for better management of BB.

The north-western Himalaya is one of the rich repositories of wheat genetic resources because of the preponderance of locally developed traditional crop varieties owing to high agro-climatic heterogeneity and local socio-cultural diversity. In the present study, 100 wheat landraces of this diversity rich region were evaluated for variability in physical parameters of seed to understand the basis of resistance against rice weevil, Sitophilus oryzae. The evaluation was based on the parameter of growth index (GI) of S. oryzae in different landraces. GI was correlated with different quantitative physical seed parameters, viz. hardness, length, width, length × width, test weight and qualitative parameter seed colour were studied to work out if these were related to resistance/susceptibility. Based on the parameter of GI, the six landraces viz. IC266831, IC266872, IC393109, IC392578, IC444217 and IC589276 were identified as resistant. Correlation coefficients between GI of S. oryzae and physical parameters of wheat landraces indicated that GI had significant positive relation with length × width (r = +0.573) and test weight (r = +0.549) indicated that small seeds confer resistance to S. oryzae. Also significant negative relation (r = −0.457) with GI of S. oryzae and seed hardness, indicated that hard seeds were relatively more resistant to S. oryzae.