Genetic resources form the basis of the new era of global food security. The food crises in many developing countries, reflected by food riots correlated with food prices, have been termed the Silent Tsunami. Plant genetic resources are clearly essential to food security for the future. Fortunately, genetic resources are generally considered a public good and shared internationally. Wild relatives of crop species and their derivatives represent the reservoir of genetic diversity that will help to meet the food demands of nine billion people by 2050. New technologies from genomics bolster conventional plant breeding for enhancing traits to meet these food demands. Genetic diversity is the lifeblood of traditional and modern plant breeding. The dramatic increase in the number of biotech crops reveals the value of new genetic resources. Genetic resources will provide a gateway to a new era of global food security. Although 7.4 million plant accessions are stored in 1750 germplasm banks around the world, only a small portion of the accessions has been used so far to produce commercial varieties. Our challenge is to find better ways to make more efficient use of gene bank materials for meeting food demands in the future.

The re-sequencing of the genomes of wild crop relatives is a rapid method to determine the likely utility of the germplasm in crop improvement. The conservation of genetic resources both in situ and ex situ can be guided by information on the novelty of specific populations at the whole-genome and specific allele levels. The analysis of Australian wild relatives of rice, coffee, Macadamia and Eucalypts is being used to support crop improvement and enhance food and energy security. Rice populations that are novel sources of diversity in the A genome of rice have been characterized at the whole-genome level. This has demonstrated the novelty of these species and will support taxonomic revisions of the Oryza species. Variation in the genomes of plants from diverse environments defines strategies that might be employed to develop climate-resilient crop varieties. Eucalypt sequencing aims to support the selection of species and genotypes for use as new energy crops.

Lutein has significant nutritional benefits for human health. Therefore, enhancing soybean lutein concentrations is an important breeding objective. However, selection for soybeans with high and environmentally stable lutein concentrations has been limited. The objectives of this study were to select soybeans with high seed lutein concentrations and to determine the stability of lutein concentrations across environments. A total of 314 genotypes were screened and 18 genotypes with high lutein concentrations and five genotypes with low lutein concentrations were selected for further examination. These 23 genotypes and two check varieties were evaluated under six environments (two planting dates for 2 years at one location and two planting dates for 1 year at another location). Lutein concentrations were influenced by genotype, environment and genotype × environment interactions. Genotypes with late maturity and low lutein concentrations were more stable than those with early maturity and high concentrations. Early (May) planting resulted in greater lutein concentrations than late (June) planting. Among the genotypes evaluated, PI603423B (7.7 μg/g) and PI89772 (5.8 μg/g) had the greatest mean lutein concentrations and exhibited medium and high stability across the six environments, respectively. Thus, these genotypes may be useful for breeding soybeans with high and stable seed lutein concentrations.

An interspecific hybrid Jatropha curcas (Jc) × Jatropha integerrima (Ji) was developed between jatropha (Jc) from Mexico and Ji from Thailand. Jc is a large canopy plant with soft wood, while Ji is a tall plant with semi-hard wood. The F1 hybrid and their parents were grown under field conditions at a spacing of 1 m × 1.5 m. One-year-old plants were harvested and determined for biomass yield, calorific value and chemical composition of wood, as well as for heterosis (hybrid vigour) of these characters. The F1 plants gave an average fresh wood weight of 18.07 kg/plant, a moisture content of 46.56%, a dry wood weight of 9.56 kg/plant and a wood density of 0.62 g/cm3. The F1 hybrid had less ash (2.60%) than Jc (6.93%), but a higher heat value of wood (18.73 MJ/kg) than Jc (17.77 MJ/kg). Heterosis over mid-parent was very high and positive in dry wood weight, fresh wood weight and number of secondary branches at 542, 310 and 450%, respectively, while negative heterosis was found in moisture content ( − 24.86%). The desirable traits found in the F1 hybrid can be fixed by cutting propagation of the selected plants.

Nitrogen fixation in legumes is an important agricultural trait that results from symbiosis between the root and rhizobia. To understand the molecular basis of nodulation, recent research has been focused on the identification of nodulation-related genes by functional analysis using two major model legumes, Medicago truncatula and Lotus japonicus. Thus far, three important processes have been discovered, namely Nod factor (NF) perception, NF signalling and autoregulation of nodulation. Nevertheless, application of the results of these studies is limited for non-model legume crops because a reference genome is unavailable. However, because the cost of whole-transcriptome analysis has dropped dramatically due to the Next generation sequencer (NGS) technology, minor crops for which reference sequences are yet to be constructed can still be studied at the genome level. In this study, we sequenced the leaf and root transcriptomes of Vigna angularis (accession IT213134) and de novo assembled. Our results demonstrate the feasibility of using the transcriptome assembly to effectively identify tissue-specific peptide clusters related to tissue-specific functions and species-specific nodulation-related genes.

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.

The wheat landraces collected by Dr Hitoshi Kihara et al. from Afghanistan, the place of secondary origin of wheat, are an untapped genetic resource for mining novel alleles. In this study, approximately 400 landraces were collected from seven agroecological zones and characterized using diversity array technology and single-nucleotide polymorphism markers, as well as diagnostic molecular markers at important loci controlling vernalization (Vrn), photoperiod response (Ppd), grain colour (R), leaf rust (Lr), yellow rust (Yr), stem rust (Sr) and Fusarium head blight (Fhb). A genome-wide marker array revealed a large amount of genetic diversity among the landraces, 53% of which were winter types, 43% were either spring types or facultative and 4% were either unknown or had Vrn-A1c – a rare spring allele that needs to be confirmed with additional genotyping and phenotyping. At Ppd, 97% of the lines carried a photosensitive allele. In the case of grain colour, classification based on dominant or recessive allelic combinations revealed that approximately 39% of the population is characterized by white grain. Four gene-specific markers that were targeted to identify loci for rust and Fhb resistance enabled us to identify 17 unique landraces with known resistance genes.

High-throughput genotyping using single-nucleotide polymorphisms (SNP) is one tool that can be used to study the genetic relationships between wild rice relatives and cultivated rice. In this study, a set of 96 indica–japonica SNP markers, which can differentiate indica and japonica subspecies of rice, were used to characterize 227 Oryza accessions including 93 AA genome accessions from seven wild Oryza species. A total of 72 markers of the 96 markers were selected for the phylogenetic study and allele polymorphism survey. A subset of SNP markers were present only in Oryza sativa and evolutionarily close species, Oryza nivara and Oryza rufipogon. These markers can be used for distinguishing cultivated rice from the other species and vice versa. Eight clusters were generated through phylogenetic analysis, and Oryza meridionalis and Oryza longistaminata appeared to be the most distantly related species to cultivated rice. In this study, Oryza barthii and Oryza glaberrima accessions were found to exhibit high genetic similarity. Across the wild species, more indica-type alleles were detected for most accessions. In this study, a set of markers selected to be informative across O. sativa accessions were used, but it will be interesting to compare the results of this study with SNP data obtained through next-generation sequencing in the future.

Recombinant inbred lines (RILs) generated from a cross between a cultivated species and its wild progenitor species serve as important germplasm for introgressing valuable genes from a wild species to a cultivated species. During this breeding process, it is equally important to prevent the loss of agronomically important genes in the cultivated species. In an effort to establish an efficient selection system for the single Rsv1 gene conferring durable resistance to soybean mosaic virus (SMV) in the soybean cultivar Hwangkeum (also known as Suweon 97), which is a parent of a RIL population from Hwangkeum (cultivated soybean) × IT182932 (wild soybean), in the present study, we unexpectedly identified an additional necrosis-conditioning gene unmasked by a recombination in the middle of the Rsv1-containing nucleotide-binding leucine-rich repeat gene cluster region and the Rsv3 gene in Hwangkeum. Thus, Hwangkeum contains at least three SMV resistance genes consisting of two tightly linked genes at the Rsv1 locus and the Rsv3 locus. The results of this study provide additional important information for use of the Hwangkeum genome in soybean breeding programmes.

Genetic variation in wild soybean (Glycine soja Sieb. and Zucc.) is a valuable resource for crop improvement efforts. Soybean is believed to have originated from China, Korea, and Japan, but little is known about the diversity or evolution of Korean wild soybean. Therefore, in this study, we evaluated the genetic diversity and population structure of 733 G. soja accessions collected in Korea using 21 simple sequence repeat (SSR) markers. The SSR loci produced 539 alleles (25.7 per locus) with a mean genetic diversity of 0.882 in these accessions. Rare alleles, those with a frequency of less than 5%, represented 75% of the total number. This collection was divided into two populations based on the principal coordinate analysis. Accessions from population 1 were distributed throughout the country, whereas most of the accessions from population 2 were distributed on the western side of the Taebaek and Sobaek mountains. The Korean G. soja collection evaluated in this study should provide useful background information for allele mining approach and breeding programmes to introgress alleles into the cultivated soybean (G. max (L). Merr.) from wild soybean.

Adzuki bean (Vigna angularis [Willd.] Ohwi & H. Ohashi) is one of the most important legume crops cultivated in East Asia and northern South Asia. Despite its agronomic importance, the lack of available sequence information has made it difficult to improve important agronomic traits. In the present study, we performed de novo assembly of transcript sequences produced by short-read sequencing to construct 59,860 full-length protein-coding sequences in adzuki bean. These genes were subjected to a BLASTP search to identify putative homologues of the 84 Arabidopsis genes involved in the circadian clock and photoperiodic flowering pathway. A large proportion of these Arabidopsis genes were found to be conserved in adzuki bean. However, there were no homologues of six genes including FLOWER LOCUS D (FD) and LEAFY (LFY). Furthermore, the phylogenetic relationships of 25 highly homologous matches to CONSTANS (CO) or CONSTANS-LIKE (COL) of Arabidopsis indicated the lack of a CO orthologue in adzuki bean. FLOWER LOCUS T (FT) and its homologues were found to have two homologous counterparts in adzuki bean. This study provides primary genetic resources that may be useful for producing adzuki bean with improved flowering and fruiting performance in response to environmental changes.

Mutation breeding techniques have been used to induce new genetic variations and improve agronomic traits in soybean. In Korea, the Korea Atomic Energy Research Institute (KAERI) has unique radiation facilities to induce plant mutations and has been conducting soybean mutation breeding programmes since the mid-1960s. Until now, the KAERI has developed five soybean mutant cultivars exhibiting early maturity, high yield and seed-coat colour change. In this paper, we review these five mutant cultivars in terms of how to successfully induce unique agronomic characteristics through mutation breeding programmes. A number of induced mutants exhibiting null lipoxygenase enzymes, altered protein patterns or Kunitz trypsin inhibitor activity could serve as genetic resources for the genetic analysis of target genes, and one mutant population has been developed for a reverse genetic study.

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.

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.

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.

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.