Jatropha curcas (jatropha) is an important non-edible oilseed crop with potential as a raw material for biofuel production. Although J. curcas has 30–35% oil content in its seeds, it has low seed yield ( < 2 ton/ha) and thus cannot become an economically viable crop. However, jatropha has many related species and genera such as J. integerrima, J. multifida, J. podagrica and Ricinus communis that are suitable for interspecific and intergeneric hybridization. The desirable features that can be obtained from these species are high number of inflorescences from J.integerrima, large fruit size from J. multifida, high oil content from J. podagrica and raceme-type inflorescence from R. communis. We were initially successful in producing hybrids between J. curcas and these related species. Hybridity was confirmed using expressed sequence tag (EST)–simple sequence repeat markers developed from the J. curcas EST database.

Ziziphus mauritiana Lam. is an important fruit crop of the Thar Desert of India. About 330 accessions and cultivars collected from various parts of India are currently being maintained at a farm in the Central Institute for Arid Horticulture. Utilization of such a large collection of germplasm for breeding and crop improvement is difficult. Therefore, in the present study, using a heuristic approach based on phenotypic characters, we identified 52 accessions that represented a core collection, with a coverage of 100% and a coincidence rate of 98.1%. No significant difference was observed with respect to either the Shannon–Weaver or the Nei diversity index for qualitative traits, mean values and ranges for quantitative traits or clustering patterns between the core and whole collections. The core collection represents the entire range of diversity with minimum redundancy and should be useful for the conservation and utilization of Z. mauritiana germplasm.

A global survey was conducted among a wide range of stakeholders to gain insight into the state of on-farm management (OFM) as a strategy for enhancing the conservation and sustainable use of plant genetic resources for food and agriculture (PGRFA). The results show that OFM is not considered a priority in national PGRFA programmes (NPGRPs), and that OFM practitioners and their organizations are not always aware of, or involved in, NPGRPs. The survey also highlighted the lack of awareness, understanding and collaboration between OFM practitioners and the managers and policy-makers associated with NPGRPs. The outcome of the analysis supports a hypothesis that OFM is, to a large extent, supported by stakeholders who are not directly engaged in the conservation and use of PGRFA, and therefore not associated with NPGRPs. This should be taken into consideration when seeking to improve the performance and impact of national programmes, and their commitment to safeguard PGRFA and contribute to food security, poverty alleviation and sustainable agriculture.

Based on the sequences of Brassica rapa ssp. pekinensis, we carried out a single-nucleotide polymorphism (SNP) study for genes controlling disease resistance (clubroot, turnip mosaic virus and soft rot) and leaf traits in B. rapa leafy genotypes ‘VC40’ and ‘SR5’. In total, 7645 SNP markers were obtained based on the annotation of a B. rapa database for disease resistance. Among these 7645 SNP markers, 141 were related to 125 genes linked to leaf traits. From these 141 SNP markers, 63 were screened and High Resolution Melt (HRM) primers were designed for genomic studies. A total of 20 polymorphic SNP primers were finally obtained. Eventually, these markers will be further used for the detection of quantitative trait loci and mapping studies.

Annual wild soybean characterized by low 100-seed weight (100SW), high protein content (PRC) and low oil content (OIC) may have favourable exotic genes/alleles for broadening the genetic base of the cultivated soybean. To evaluate the wild alleles/segments, a chromosome segment substitution line population comprising 151 lines with N24852 (wild) as the donor and NN1138-2 (cultivated) as the recurrent parent was analysed using single-marker analysis, interval mapping, inclusive composite interval mapping and mixed linear composite interval mapping. On 14 segments of ten chromosomes, 17 quantitative trait loci (QTL) were identified, with two segments each containing two QTL for 100SW and OIC and one segment containing two QTL for PRC and OIC, respectively. All the seven wild alleles/segments for 100SW were associated with negative effects and three were associated with positive effects, but one was associated with a negative effect for PRC, and five were associated with negative effects, but one was associated with a positive effect for OIC. Except Satt216 and Sat_224 for 100SW, the identified QTL/segments have been reported from cultivated soybean mapping populations. The detected wild segments may provide materials for further characterization, cloning and pyramiding of the alleles conferring the seed-quality traits.

The Drake Passage arises as a likely route for gene flow into Antarctica, as it is the shortest path between this continent and the rest of the world. Despite this, long-distance dispersion into Antarctica could be particularly complex for terrestrial biota. To compare the levels of genetic diversity between Antarctic and South American populations of the Antarctic pearlwort, Colobanthus quitensis, we conducted the first estimation of genetic diversity in this species using amplified fragment length polymorphism. Four populations across the Drake Passage were selected and their genetic composition was characterized. Differences among the levels of genetic diversity were found between the populations analysed as well as between their allelic identities. However, interestingly, their spatial distribution across the Drake Passage suggests a north-to-south gradient of increasing genetic diversity.

Plant height is important for crop yield improvement. In this study, a dwarf mutant, Gmdwarf1, was screened from a γ-ray-treated soybean population. Compared with the wild type, the mutant exhibited later germination, smaller and darker green leaves, and less-elongated shoots. Genome-wide transcriptome detection through RNA-seq analysis revealed that not only gibberellin-related genes but many other genes involved in hormone biosynthetic pathways were also significantly influenced in the mutant. We presumed that Gmdwarf1 might play essential roles in the plant hormone pathways. Future functional analysis of this dwarf mutant would help us to understand the underlying mechanisms and be beneficial for improving soybean yield.

Genetic diversity and structure plays a key role in the selection of parents for crosses in plant breeding programmes. The aim of the present study was to analyse the genetic diversity and structure of Eritrean bread wheat accessions. We analysed 284 wheat accessions from Eritrea using 30 simple sequence repeat markers. A total of 539 alleles were detected. The allele number per locus ranged from 2 to 21, with a mean allele number of 9.2. The average genetic diversity index was 0.66, with values ranging from 0.01 to 0.89. Comparing the three genomes of wheat, the B genome had the highest genetic diversity (0.66) and the D genome the lowest diversity (0.61). A STRUCTURE analysis based on the Bayesian model-based cluster analysis followed by a graphical representation of the distances by non-parametric multidimensional scaling revealed a distinct partition of the Eritrean wheat accessions into two major groups. This is the first report of the genetic diversity and structure of Eritrean bread wheat.

In India, the registration and protection of new and notified/extant plant varieties are based on the criteria of distinctness, uniformity and stability (DUS) of morphological characteristics. However, these morphological traits have not been helpful in resolving closely related genotypes. The molecular markers can very well support the DUS testing in such cases. Therefore, in the present study, 20 accessions of bottle gourd were fingerprinted using 20 simple sequence repeat (SSR) primers. Of these, ten primers exhibited polymorphic profiles, while nine exhibited monomorphic patterns and one revealed a null allele. The number of alleles ranged from 2 to 4 with an average of 2.6 alleles per locus. Unique DNA profiles of all the accessions could be created using a set of five polymorphic primers. Therefore, SSR markers used in the present study could precisely distinguish all the 20 accessions from each other, and these SSR markers can be further used to differentiate the future genotypes from the existing ones. The dendrogram depicting the genetic relationships as revealed by NTSYS-pc 2.02 and the tree diagram generated using the DARwin 5.0 program classified the accessions into two main clusters. There is no strong association between the clustering pattern and geographical origin of these accessions. This SSR marker-based diversity would facilitate the implementation of marker-assisted breeding schemes for efficient introduction of the desired traits into bottle gourd.

More than 3200 new mutant varieties have been bred and used by millions of farmers, which has significantly contributed to world food security. A lot more mutants have also served as tools for gene discovery and functional analysis. Recent genomic approaches including TILLING (Targeting Induced Local Lesions In Genome) have enabled screening of mutations at the molecular level. This review describes the molecular nature of chemically and physically induced mutations and their repercussions. Analyses of TILLING reports indicate that chemically induced mutations are mostly nucleotide substitutions, but that mutation frequencies fluctuate among plant species ranging from one DNA lesion per 300 kbp in Arabidopsis to one DNA lesion per 30 kbp in bread wheat, which reciprocate with an increase in ploidy levels. The majority (>95%) of chemically induced DNA lesions are silent or missense mutations. Mutations induced by physical mutagens seem to be more diverse, including single-nucleotide substitutions, insertions, inversions and translocations, although short deletions ( < 15 bp) are relatively more predominant. The proportion of complex mutations (translocation, inversions, etc.) may increase with an increase in the linear energy transfer of radiations. In addition, the implications of these findings for the roles of induced mutants in breeding and gene function analysis are briefly discussed.

Sweet cherries can be grafted onto a wide range of rootstocks belonging to the genus Prunus. The identification of sweet cherry rootstocks using morphological traits is almost impossible particularly during the dormant season, yet it is very important for the grower to know exactly the rootstock as this has a major influence on cultivar performance and agricultural practices. However, DNA-based molecular analysis carried out on actively growing shoot tips, leaves or dormant buds provides a good opportunity to reliably distinguish the rootstocks. Herein, we have integrated high-resolution melting (HRM) analysis, coupled with five simple sequence repeat (SSR) markers, in order to facilitate the identification of the most popular sweet cherry rootstocks in Greece. The five SSR loci used were highly informative and generated a unique melting curve profile of microsatellites for each of the six sweet cherry rootstocks tested. In particular, one marker, BPPCT002, with six HRM profiles was sufficient to discriminate all the sweet cherry rootstocks studied, highlighting its potential use for rootstock identification. Hence, this assay provided a flexible, cost-effective and closed-tube microsatellite genotyping method well suited to sweet cherry rootstock identification.

Improved root architecture of cultivated barley can improve crop performance in drought-prone areas. In this study, seedlings of 315 wild barley (Hordeum vulgare subsp. spontaneum) accessions from the Wild Barley Diversity Collection (WBDC) were grown under hydroponic conditions for 8 d after germination and then root characteristics were analysed. Significant differences were observed among the accessions with regard to seminal root number (SRN), root length (RL), specific root length (SRL), root fresh weight and root dry weight (RDW). Principal component analysis explained about 81% of the total variation for ten traits. Principal component (PC) 1, PC2 and PC3 explained about 38, 30 and 13% of the total variation among the accessions. The two most prominent contributors in each PC were RL and SRL, RDW and SRN, and the longitude and latitude of the collection sites, respectively. Accessions WBDC266, WBDC302, WBDC286 and WBDC011 had the longest RL and the highest RDW, specific dry root weight and SRL, respectively. These accessions may be useful genetic resources for the improvement of these root traits in cultivated barley.

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

To evaluate the genetic diversity (GD) of wild and cultivated soybeans and determine the genetic relationships between them, in this study, 127 wild soybean accessions and 219 cultivated soybean accessions were genotyped using 74 simple sequence repeat (SSR) markers. The results of the study revealed that the GD of the wild soybeans exceeded that of the cultivated soybeans. In all, 924 alleles were detected in the 346 soybean accessions using 74 SSRs, with an average of 12.49 alleles per locus. In the 219 cultivated soybean accessions, 687 alleles were detected, with an average of 9.28 alleles per locus; in the 127 wild soybean accessions, 835 alleles were detected, with an average of 11.28 alleles per locus. We identified 237 wild-soybean-specific alleles and 89 cultivated-soybean-specific alleles in the 346 soybean accessions, and these alleles accounted for 35.28% of all the alleles in the sample. Principal coordinates analysis and phylogenetic analysis based on Nei's genetic distance indicated that all the accessions could be classified into two major clusters, corresponding to wild and cultivated soybeans. These results will increase our understanding of the genetic differences and relationships between wild and cultivated soybeans and provide information to develop future breeding strategies to improve soybean yield.

Despite widespread mungbean [Vigna radiata (L.) Wilczek] consumption in Indonesia, few molecular studies have been carried out on accessions and available data are minimal. In this study, we used 30 newly developed simple sequence repeat (SSR) markers designed from the mapped sequence scaffolds of the Korean Sunhwanokdu and Gyeonggijaerae 5 mungbean genomes. These markers were used to examine loci in 83 mungbean accessions collected from diverse geographical areas in Indonesia. A total of 107 alleles were detected among the accessions with 29 polymorphic markers. However, the mean of polymorphic information content (0.33) value and diversity index (0.38) value was indicative of low genetic diversity in this germplasm. The mungbean population structure was not clearly differentiated and the number of subpopulations was unclear. Neighbour-joining tree analysis revealed that the genetic cluster did not reflect the geographical origin of the accessions. Interestingly, the most agriculturally improved varieties were genetically similar to some landraces from one of the main mungbean-producing regions. These newly developed SSR markers could be useful for detecting genetic variability as a basis for establishing a conservation strategy for mungbean germplasm with the aim of enhancing Indonesian breeding programmes.

Fucosyltransferases are a group of enzymes that catalyse the transfer of l-fucose from a donor substrate to an acceptor molecule. Silybum marianum is also called ‘milk thistle’ due to its characteristic flower shape. It produces two major flavonoids: silymarin and silybin. The plant and its major secondary metabolites are used for treatment/recovery after chronic liver disease, liver rehabilitation after hepatitis and treatment of gallbladder disease. These compounds also act as antioxidants for scavenging free radicals and inhibiting lipid peroxidation. We identified two peptide motifs (YYEAYLSHADEK and TTPDPSCGR designated as motif 1 and motif 2, respectively) of a fucosyltransferase derived from S. marianum that are highly conserved in its counterparts across the plant species and sources. The nature and properties of the motifs are discussed in terms of their putative participation in catalysis and enzyme/active site conformation.