The deduced amino-acid sequences of 17 protein disulphide isomerase (PDI) and PDI-like cDNAs of wheat assigned to nine homoeologous groups were searched for conserved motives by comparison with characterized sequences in different protein databases. The wheat protein sequences encoded by genes of different homoelogous groups showed a high level of structural similarity with the corresponding protein sequences of other species clustering into the same phylogenetic group. The proteins of five groups (I–V) share two thioredoxin-like active domains and show structural similarities with the corresponding proteins of higher eukaryotes, whereas those of the remaining three groups (VI–VIII) contain a single thioredoxin-like active domain. The expression analysis of the nine non-homoeologous wheat genes, which was carried out by quantitative RT-PCR in developing caryopses and in seedlings subjected to temperature stresses, showed their constitutive although highly variable transcription rate. The comprehensive structural and transcriptional characterization of the PDI and PDI-like genes of wheat performed in this study represents a basis for future functional characterization of the PDI gene family in the hexaploid context of bread wheat.

Mungbean yellow mosaic virus (MYMV) disease is one of the most devastating biotic constraints of mungbean production in India. Dependable knowledge on the number and mode of action of genes controlling resistance to MYMV disease is one of the keys to develop resistant cultivars. The F1s of four crosses derived from four MYMV resistant genotypes × one highly susceptible genotype, their parents, F2s and F3s along with a susceptible check were screened for responses to MYMV disease following the infector-row technique under natural infection conditions. A good fit of F2 population segregation to the hypothesized ratio of 15 susceptible:1 resistant and that of F3 population segregation to the expected ratio of 55 susceptible:9 resistant at 55 days after planting confirmed the involvement of two recessive genes in imparting resistance to MYMV disease.

As a country of origin of coffee, Ethiopia is endowed with an immense diversity of the crop in its diverse coffee-growing agro-ecologies. Amaro Kelo is one of the major coffee production agro-ecologies in Ethiopia, where the genetic diversity of its landrace coffee germplasm was not properly characterized previously. The study aimed to characterize 64 Amaro Kelo local coffee accessions to understand the potential of the accessions for utilization in future coffee genetic improvement efforts. The experiment was laid out in an 8 × 8 simple lattice design with two replications at Awada Agricultural Research Sub-Center. Data were collected on 19 quantitative and 10 qualitative traits, and subjected to multivariate analyses, i.e. cluster and principal component analyses. The cluster analysis identified five clusters based on the quantitative characters, and the distances between most of the clusters were highly significant at P < 0.01. Principal component analysis revealed the first six principal components with Eigenvalues greater than one accounted for 77.7% of the total variation. The first two principal components with respective contributions of 23.32 and 18.85% cumulatively accounted for 42.2% of the total variation in the accessions. In addition, high values of Shannon-diversity index were found for the qualitative traits: branching habit, growth habit, fruit shape, overall appearance and stem habit. In general, the multivariate analyses confirmed the presence of high variation among the studied Amaro-Kelo coffee accessions that might serve as an important genetic resource for future coffee genetic improvement or conservation efforts.

Dongxiang wild rice (Oryza rufipogon Griff.) (DXWR) is the northernmost distributed wild rice found in the world. Similar to other populations of O. rufipogon, DXWR contains a large number of agronomically valuable genes, which makes it a natural gene pool for rice breeding. Molecular markers, especially simple repeat sequence (SSR) markers, play important roles in plant breeding. Although a large number of SSR markers have been developed, most of them are derived from the genome coding sequences, rarely from non-coding sequences. Meanwhile, long non-coding RNAs (lncRNAs), which are derived from the transcription of non-coding sequences, play vital roles in plant growth, development and stress responses. In our previous study, we obtained 1655 lncRNA transcripts from DXWR using strand-specific RNA sequencing. In this study, 1878 SSR loci were detected from the lncRNA sequences of DXWR, and 1258 lncRNA-derived-SSR markers were developed on the genome-wide scale. To verify the validity and applicability of these markers, 72 pairs of primers were randomly selected to test 44 rice accessions. The results showed that 42 (58.33%) pairs of primers have abundant polymorphism among these rice materials; the polymorphism information content values ranged from 0.04 to 0.87 with an average of 0.50; the genetic diversity index of SSR loci varied from 0.04 to 0.88 with an average of 0.56; and the number of alleles per marker ranged from 2 to 11 with an average of 4.36. Thus, we concluded that these lncRNA-derived-SSR markers are a very useful source for future basic and applied research.

Heterosis is a main force underlying the hybrid seed industry in maize. Our experimental approach consists of a correlation study between retrotransposon-related genetic distances between parental inbred lines and hybrid performance. The assumption is that, at least for certain traits, heterosis results from genome rearrangements, largely related to retrotransposon insertions and/or removals. Fifteen maize inbred lines and one F1 hybrid, representative of the genetic diversity among sweet corn and field corn lines were screened for polymorphism by retrotransposon microsatellite amplified polymorphism markers. DNA fingerprints served as row data for estimating genetic diversity of maize inbred lines and its correlation with the heterotic effect in their hybrids. A correlation between phenotypic and molecular distances was evident only at the level of individual inbred lines. Weak correlation between genetic distances and heterosis effect was observed for the average of all inbred lines. Phenotypic distances negatively correlated with heterosis for insertion height, diameter of the ear and number of kernel rows per ear. The relative contribution of each inbred line to heterosis in its derived hybrids was also estimated. Accordingly, we identified inbred lines with increased genetic distances that mostly add to the heterosis effect in their hybrids and that we recommend as prospective to be used in maize breeding programmes.

Based on the distribution, molecular similarity and use of Morinda citrifolia L., and occurrence of a wild Morinda species, Southeast Asia and Micronesia have been suggested to be the places where noni originated. The present article discusses the indices used by Vavilov and subsequent authorities on the origin of crop plants to argue that South Asia (Southeast India) has a greater probability of being the centre of domestication/origin for noni than Southeast Asia or Micronesia. The basic reasoning is that economically important plant cannot originate without richness in biodiversity and ingenuity of local people. India with rich floristic diversity, one of the centres of origin of crop plants with a natural distribution of Morinda species, including M. citrifolia L. and its immediate ancestors, has the oldest reference of occurrence, use and cultivation (Vedic literature); therefore, it appears to be the more probable centre of noni's origin. The ancient history of the expansion of Indian culture, religion and trade to Southeast Asian countries corroborate the possible role of Indians in the introduction of noni or knowledge regarding its value to Southeast Asia, from which it was carried to Micronesia and Polynesia, which provided a more favourable environmental niche for perpetuation and use.

Silene ciliata (Caryophyllaceae) is a key species to test evolutionary hypotheses in a global warming context. The recent advances in Next Generation Sequencing technologies can help in providing clues about climate-mediated local adaptation. In the present study, we analysed the full transcriptome of six individuals of S. ciliata from Central Spain, by aligning it with the transcriptome of S. latifolia. We aimed (a) to identify Single Nucleotide Polymorphisms (SNPs) in the transcriptome of the species, (b) to describe the biological function of the polymorphic genes expressed and (c) to identify loci that may be involved in local adaptation processes at optimal and marginal populations of the species. We identified a total of 147,118 SNPs distributed throughout 12,688 sequences. The number of polymorphic sequences annotated was 8023. One hundred thirty sequences containing polymorphisms strongly associated with optimal and marginal conditions were selected. Gene ontology searches were successful for 118, and many of these were related to responses to stress (n = 19) and abiotic stimulus (n = 16). Genomic data generated provide a starting point for further research on the identification of candidate genes related to local adaptation and other processes in the species.

A commentary on the highlights of the 2013 EUCARPIA (the European Associationc for Research on Plant Breeding) Plant Genetic Resources Section meeting at the Swedish University of Agricultural Sciences in Alnarp is presented here. The central theme of the meeting was the use of plant genetic resources in pre-breeding programmes, particularly in the context of incipient climate change and human population pressure.

Hybrid rice development, a major advance in rice breeding, has demonstrated its immense potential in enhancing the rice productivity. In the three line system of hybrid rice, the restoration of fertility of the widely used wild-abortive type of cytoplasmic male sterility is controlled by Rf3 and Rf4, two fertility restoration genes. Exploration for restorers in diverse genetic backgrounds is a critical step in hybrid rice breeding. As genetic resources constitute the major source of new genes/alleles, an attempt was made to assess the distribution of these two restorer genes in the native populations collected from the geographic regions known to be the primary and secondary centres of origin of rice. In addition, assays were performed on the populations of Oryza rufipogon and Oryza nivara, the wild progenitors of rice. The results suggest that the Rf genes are well distributed in the wild forms at a higher frequency, more in O. rufipogon, while in cultivated forms, their frequency is low, particularly for the Rf3 gene. The genes and the alleles identified in the genetically divergent, low-performing land races and wild relatives can be successfully employed for the development of new hybrid rice cultivars.

In the present study, inter- and intrapopulation diversity of five named rice landraces from parts of Odisha state of India representing static and dynamic management was examined using 14 sequence-tagged microsatellite site primer pairs. A total of 64 alleles were detected in ten populations of the five named landraces. The number of alleles ranged from 2 to 7, with an average of 4.57 alleles per locus. Of the 64 alleles, 60 were common and four were rare. Moderate-to-low diversity was observed in the landrace populations, with the number of alleles per population ranging from 16 to 25 and the percentage of polymorphism ranging from 14.29 to 64.29, respectively. The analysis of molecular variance indicated a highest variation of 75.7% among populations within groups (static vs. dynamic). The pairwise estimates of FST revealed very high significant population differentiation, which ranged from 0.68 to 0.89, indicating that the populations share limited genetic diversity among them. However, not many variations were observed in the phenotypes of populations representing static and dynamic management. This shows that adaptations of a population apparently persist over generations, but the underlying genotypes change and new alleles or combinations may arise and increase in frequency at the expense of other alleles that have disappeared. The importance of population biology research for in situ conservation requires both descriptive and hypothesis testing to guide technical improvement and management of landrace populations.

In an effort to control anthracnose disease, one of the major problems that has been faced by farmers, 14 chilli hybrids and their parents were screened phenotypically using the fruit inoculation method under laboratory conditions. Genotypic screening of 14 chilli hybrids and their parents was done by the identified polymorphic markers, HpmsE 051 and HpmsE 082. Based on the phenotypic and genotypic data, chilli hybrids, H1, H2, H3, H4, H6, H7, H8, H9, H11 and H12 were identified as resistant chilli hybrids against anthracnose disease caused by the C. truncatum. Molecular markers, HpmsE 051 and HpmsE 082 could be utilized as polymorphic markers to isolate resistant genotypes against C. truncatum.

To maximize heterosis, it is important to understand the genetic diversity of germplasm and associate useful phenotypic traits such as fertility restoration for hybrid rice breeding. The objectives of the present study were to characterize genetic diversity within a set of rice germplasm groups using coefficient of parentage (COP) values and 58 simple sequence repeat (SSR) markers for 124 genotypes having different attributes such as resistance/tolerance to various biotic and abiotic stresses. These lines were also used for identifying prospective restorers and maintainers for wild abortive-cytoplasmic male sterile (CMS) line. The mean COP value for all the lines was 0.11, indicating that the genotypes do not share common ancestry. The SSR analysis generated a total of 268 alleles with an average of 4.62 alleles per locus. The mean polymorphism information content value was 0.53, indicating that the markers selected were highly polymorphic. Grouping based on COP analysis revealed three major clusters pertaining to the indica, tropical japonica and japonica lines. A similar grouping pattern with some variation was also observed for the SSR markers. Fertility restoration phenotype based on the test cross of the 124 genotypes with a CMS line helped identify 23 maintainers, 58 restorers and 43 genotypes as either partial maintainers or partial restorers. This study demonstrates that COP analysis along with molecular marker analysis might encourage better organization of germplasm diversity and its use in hybrid rice breeding. Potential restorers identified in the study can be used for breeding high-yielding stress-tolerant medium-duration rice hybrids, while maintainers would prove useful for developing new rice CMS lines.

Fusarium head blight (FHB) and stem rust (SR) threaten the sustainability of wheat production worldwide. Fhb1 and Sr2 confer partial durable resistance to FHB and SR, respectively. Despite resistant alleles of both genes are linked in repulsion, lines with Fhb1-Sr2 in coupling were developed at the University of Minnesota, USA. Marker-assisted backcrossing was used to incorporate the coupled Fhb1-Sr2 into four elite INIA-Uruguay spring wheat varieties lacking both genes and expressing different levels of FHB and SR resistance. In each case, the initial cross between the donor line and recurrent parent was backcrossed three times. Genotypes carrying Fhb1-Sr2 were selected using the molecular marker UMN10. In BC3F3 families, retention of Fhb1-Sr2 was further confirmed with the markers SNP3BS-8 and Sr2-ger9 for Fhb1 and Sr2, respectively. BC3F3 homozygous lines contrasting at UMN10, SNP3BS-8 and Sr2-ger9 were obtained to quantify the effect of Fhb1-Sr2 on the resistance to FHB under controlled conditions and to SR under field conditions. After 26 months period, successful introgression of Fhb1-Sr2 into the four cultivars was achieved, representing novel wheat genetic resources. Lines homozygous for the resistant alleles of Fhb1 were significantly more resistant to FHB as reflected by an 18% reduction of average FHB area under the disease progress curve. A significant effect of Sr2 on SR field resistance was observed in lines derived from the most susceptible cultivar ‘Génesis 2375’. The most resistant lines to both diseases are expected to be valuable genetic resources in breeding for durable resistance to FHB and SR.

Common bean (Phaseolus vulgaris L.) is an important crop of family Fabaceae used as a potential source of proteins, fibres and minerals. Thus, characterization of existing germplasm is useful for improvement and conservation. The Indian Himalayan Region harbours plentiful varieties of common bean, but it is nearly unexplored till date. In the present study, physical and genetic diversity of common bean was examined. Fifteen newly designed chloroplast microsatellite (cpSSR) markers were used to assess genetic diversity and population structure in 119 common bean individuals from 20 diverse accessions gathered from Uttarakhand, India. Significantly, positive (p< 0.05) relationship of seed weight was found with seed length (r = 0.813), seed width (r = 0.692) and seed length- width ratio (r = 0.694) using Pearson correlation analysis. A total of 20 alleles were identified using eight cpSSR markers. Mean number of alleles per locus (Na = 1.55), effective allele number (Ne = 1.370), expected heterozygosity (He = 0.213), average polymorphic loci (10.9) and Shannon information index (I = 0.313) were estimated based on cpSSR data. Maximum genetic diversity (He) was recorded in the AKJ/KK/DP/Jhalla/23 accession and minimum in the AKJ/YB/PS/Supi/43 accession. Bayesian-based STRUCTURE evaluation using cpSSR-based information partitioned 20 accessions into two distinct clusters which were also supported by neighbor-joining cluster analysis. These cpSSR markers also demonstrated transferability among other members like Vigna radiata, Macrotyloma uniflorum, Glycine max, Vigna mungo of Fabaceae family, therefore can be used to monitor their genetic heterogeneity. The findings from the study might be valuable to identify elite common bean accessions for production, conservation and future breeding programmes.

Knowledge on genetic diversity is necessary to determine the relationships among the genotypes, which allow the selection of individual accessions for crop breeding programmes. The present study aimed at assessing the extent and pattern of genetic diversity within a set of 251 sorghum genotypes using SSR markers. A total of 393 alleles were detected from the 251 genotypes, with the number of alleles ranging from 2 (Xcup11) to 24 (Sb5-206) and an average of 10.07 alleles per primer pair. Pairwise Wright's FST statistic and Nei's genetic distance estimates revealed that the race and geographical origin were responsible for the pattern of diversity and structure in the genetic materials. In addition, the analysis also revealed high genetic differentiation between the rainy and post-rainy sorghum groups. Narrow diversity was observed among the different working groups in the rainy (restorers and varieties) and post-rainy (varieties and advanced breeding lines) sorghum groups. Neighbour-joining and STRUCTURE analysis also classified 44 elite lines broadly into two distinct groups (rainy and post-rainy). However, limited diversity within the rainy and post-rainy sorghum groups warranted an urgent need for the utilization of diverse germplasm accessions for broadening the genetic base of the Indian breeding programme. The diverse germplasm accessions identified from the mini-core accessions for utilization in breeding programmes are discussed.

Efficiently distinguishing various Syzygium cumini L. Skeels (jamun) accessions holds practical significance for selection purposes. This study concentrated on 15 superior genotypes of jamun from the North Western Indian Himalayas, selected for their pivotal horticultural traits. Drawn from a pool of 82 collected genotypes and assessed across two consecutive years (2019 and 2020), these genotypes underwent morphological evaluations utilizing a randomized block design replicated thrice. Concurrently, random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers were employed for molecular analysis. Substantial variations surfaced among genotypes, both in morphological traits and fruit biochemistry. Notably, tree 43 exhibited promise across multiple horticultural facets, encompassing fruit weight, length, pulp weight, pulp-to-seed ratio and pulp percentage. Conversely, tree 49 excelled in elevated levels of total soluble solids, total sugar and reducing sugar. While principal component analysis and cluster analysis unveiled modest genetic variability, RAPD and ISSR markers unveiled pronounced molecular-level polymorphism. Agglomerative hierarchical clustering delineated the genotypes into five distinct clusters. Cluster I encompassed two genotypes, cluster II embraced five while the largest group, cluster III, included six genotypes. Clusters IV and V highlighted individual genotypes, trees 43 and 54 respectively. In the molecular analysis, UPGMA clustering yielded two primary clusters, spotlighting the noteworthy similarity between genotypes trees 49 and 52 whereas, trees 40, 43, 44 and 48 stood distinct. The observed genetic diversity stands as a valuable resource with substantial potential to enrich diverse breeding initiatives. These salient genetic variations underscore the richness within the studied population, offering a valuable asset for focused future pursuits.

Blackberry is a fruiting berry species with very high nutrient contents. With the recent increasing consumer demand for blackberries, new sources of germplasm and breeding techniques are required to improve blackberry production. This study was carried out to evaluate the genetic diversity (GD) and relationship among 55 blackberry (Rubus fruticosus) mutants derived from γ-ray treatment (52 lines) and N-methyl-N′-nitrosourea (MNU) treatment (three lines) using an inter-simple sequence repeat marker. A total of 18 bands were amplified with an average of 3.6 bands per primer. Among them, eight bands were identified to be polymorphic with a rate of 44.4%. In addition, the GD information content values were highest in the 60 Gy treatment population and the GD values were higher in the γ-ray treatment populations than in the MNU treatment population. According to a cluster analysis, all the mutant lines can be classified into five categories, and the genetic distance was greatest between the 80 Gy-irradiated population and other populations. These results indicate that mutant lines have high GD and can be effectively utilized for improving blackberry breeding.

The Ethiopian core collection of the USDA-Agriculture Research Service, National Plant Germplasm System (NPGS) includes 376 accessions and a genomic characterization that revealed 151,210 single nucleotide polymorphisms. This collection, however, lacks phenotypic characterization for several important agriculture traits. A total of 330 accessions from this NPGS Ethiopian core set were evaluated for grain mould resistance response across four tropical environments. Most of the accessions in the NPGS Ethiopian collection showed susceptibility to grain mould based on the low emergence rate and high seed deterioration observed in the seeds. The population structure of the collection was not related to grain mould resistance response suggesting this germplasm originated in regions with low disease pressure. The analysis identified two accessions with high emergence (PI 457867 and PI 454221) and three (PI 455036, PI 455213 and PI 330821) with low seed degradation. Genome-wide association analysis found genomic regions in chromosome 1, 3 and 8 associated with the observed grain mould resistance variation. Candidate gene analysis within these three loci identified diseases resistance genes involved in pathogen recognition and signalling cascades of the plant immunity system. These five NPGS Ethiopian accessions are candidates for use in a pre-breeding germplasm programme to develop improved germplasm with grain mould resistance.

A total of 32 sweet potato genotypes were evaluated to assess the genetic diversity based on quantitative traits and molecular markers, as well as stability for yield and related traits. Wider variability was observed for the traits like vine length (181.2–501.3 cm), number of leaves/plant (103.0–414.0 cm), internodal length (3.20–14.80 cm), petiole length (6.5–21.3 cm), leaf length (8.50–14.5 cm), leaf breadth (8.20–15.30 cm), leaf area (42.50–115.62 cm2), tuber length (7.77–18.07 cm), tuber diameter (2.67–6.90 cm), tuber weight (65.60–192.09 g), tuber yield (7.77–28.87 t ha−1), dry matter (27.34–36.41%), total sugar (4.50–5.70%) and starch (18.50–29.92%) content. Desirable traits such as tuber yield, dry matter and starch content have shown high heritability (>60%) with moderate to high genetic advance. Under molecular analysis, a total of 232 alleles were observed from all 32 microsatellite markers, which ranged from 4 to 14 with an average of 7.77 alleles per locus. In the population, the average observed heterozygosity (0.51) was higher than the expected heterozygosity (0.49). The contribution of genotype, genotype by environment interaction to the total variations was found to be significant. Based on the multi-trait stability index (tuber length, tuber diameter, tuber weight and tuber yield), genotypes X-24, MLSPC-3, MLSPC-5, ARSPC-1 and TSP-12-12 were found to be most stable. Among them, the high-yielding and stable genotypes TSP-12-10 (26.0 t ha−1) and MLSPC-3 (23.9 t ha−1) can be promoted for commercial production or used as parental material in future crop improvement programmes.

The wild species of tomato Solanum pennellii (Lpa) is more tolerant to salt-induced oxidative stress than the cultivated species Solanum lycopersicum (Lem), due to the increase of several antioxidative metabolites and enzymes in this species under stress. The increase of reduced glutathione (GSH), one of these metabolites, in NaCl-treated Lpa, is due at least partly to the elevation of γ-glutamylcysteine synthetase (γ-ECS). Introgression line IL 8–3, which was found to include the Lpa orthologue of the γ-ECS gene (Lpa γ-ECS) in Lem's genetic background, was used to assign this gene to chromosome 8 and to assess its relative contribution to the effective antioxidative response of Lpa to stress. The growth of IL 8–3 and Lem plants responded similarly to NaCl and cadmium (Cd) stresses. In both genotypes, GSH and H2O2 levels responded also similarly to NaCl stress. NaCl and Cd stresses affected similarly the transcription of the γ-ECS gene in leaves of both IL 8–3 and Lpa plants. The effect of buthionine sulfoximine (BSO), a competitive inhibitor of the γ-ECS enzyme, on γ-ECS transcription was also similar in these two genotypes. Taken together, these results suggest that γ-ECS orthologues differ mainly in the regulation of their transcription and not at the post-transcriptional or translational levels. The mutation(s) led to these differences in the response of the two orthologues to the salinity and heavy metal stresses are expected to occur in a cis-regulatory element(s) located relatively close to γ-ECS.