Sustainable development of a breeding programme depends on having sufficient genetic variability to achieve genetic gains in each selection cycle. The aim of this study was to molecularly characterize families of the oil palm, Elaeis guineensis Jacq., of different origins using microsatellite molecular markers. The value of the observed heterozygosity was higher than that of the expected heterozygosity in all of the progenies. The coefficients (GST= 0.207 and FST= 0.174) and AMOVA showed genotypic differences among the evaluated families. Likewise, this was reflected in the groups obtained by the dendrogram and principal coordinate analyses. This difference could have evolved due to the enrichment of some of the families with germplasm from different origins. Therefore, genetic relationships estimated from molecular data would be convenient to select families more distant from each group and palms more distant from each family selected to reserve genetic variability. This information will guide us in the decision-making process when planning breeding programmes focused on crosses to develop new populations with an acceptable broad genetic base and adaptability. In this way, sources of resistance to biotic and abiotic factors can be identified for the development of new varieties with competitive advantages for the sector.

The genebank at ICRISAT, Patancheru, India conserves a total of 19,063 pearl millet landraces from latitudes ranging from 33.00° in the Southern Hemisphere (SH) to 34.37° in the Northern Hemisphere (NH). In the present study, the NH was found to be the major region for growing pearl millet landraces (80.5%). More landraces were found at lower latitudes ( < 20°) in both hemispheres than at higher latitudes. The latitude range of 10°–15° in the NH and 15°–20° in the SH were found to be important source regions for the prevalence of pearl millet, with 39.6% and 13.1% in the world collection of landraces, respectively. Landraces from lower-latitude regions on either side of the equator varied widely for all traits. Landraces from the 5°–10°N latitude region flowered late and grew tall in the rainy and post-rainy seasons and produced more tillers. Landraces from the 10°–15°N latitude region produced few tillers and had long and thick panicles with larger seeds. Long-bristled bird-resistant landraces were considerable at latitudes of 10°–15°S and 20°–25°S. The minimum temperature at the collection sites was found to be one of the important factors for determining the patterns of the prevalence of pearl millet across the latitudes. Late-maturing, tall and high-tillering landraces from lower-latitude regions were better sources for fodder production. Early-maturing landraces producing long and thick panicles with large seeds from mid-latitude regions (15°–20°) in both hemispheres were useful for developing high-yielding cultivars. Using the latitudinal patterns of diversity in pearl millet landraces, missions may be launched to explore high-diversity, under-collected and threatened areas for the collection of materials of interest at latitudes of 15°–20°.

The characterization of genetic diversity and structure for improved cultivated varieties/elite lines is tremendously important to assist breeders in parental selection for inbred and hybrid breeding and heterotic group construction. In this study, a total of 737 improved indica varieties/lines developed recently and/or widely used by present indica breeding programmes worldwide were genotyped with a 384-single-nucleotide polymorphism assay. Model-based population structure analysis revealed the presence of two major groups with six subgroups (SGs), wherein no clear correlation was found between the groups/SGs and breeding programmes or geographical origin of the accessions. Over half of the accessions (51.8%) appeared to have less than 0.6 memberships assigned to any one of the six model-based groups, highlighting the wide range of gene flow within improved indica varieties/lines and the genetic integration of valuable alleles shared by ancestries among improved high-yielding varieties/lines through germplasm exchanges. Distance-based clustering revealed that Latin-American cultivated indica lines have tended to form their own ecological cline, which could serve as a potential heterotic ecotype for hybrid rice breeding, although they are still closely related to Asian indica lines. African cultivated indica lines, on the other hand, have not yet formed their own ecological cline. It was also observed that the most well-known hybrid rice parents, Zhenshan97B and Minghui63, were unexpectedly clustered in the same SG with a relatively narrow genetic distance, which suggests that a significant genetic distance between parents is not a prerequisite for all elite hybrid rice lines with high heterosis.

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.

To develop synthetic varieties (Syn) of broccoli for organic agriculture, we initiated a breeding programme from a landrace (LR). A Syn was obtained through a farmer-assisted selection programme that mirrors the original LR. The diversity level of the Syn was assessed using 14 putatively neutral microsatellite markers (simple sequence repeats (SSR)) and seven SSR related to genes involved in flowering control. Four commercial F1 hybrids were also assessed. Despite the strict selection procedure applied by the farmer to reproduce the LR annually and to obtain the Syn, the detected diversity level was high and similar to that of non-selected LRs. The possible reasons for these genetic outcomes (i.e. SSR position in the genome and farmer selection methods) are discussed here.

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.

Cultivated pigeonpea has a narrow genetic base. Wild relatives play an important role in the efforts to broaden its genetic base. In this report, we present a successful wide-cross between the cultivated pigeonpea and Cajanus lanceolatus, a wild relative from the secondary gene pool, native to Australia, with desirable traits such as frost and drought resistance. A range of F1 progeny were obtained and the resultant F1 hybrid plants set mature pods and seeds. The hybrids had intermediate morphology, sharing the traits of both the parents. All the F1 hybrids flowered profusely. Some of the hybrids were completely male sterile and some were partially fertile with pollen fertility ranging from 35 to 50 %. Meiotic analysis of the fertile F1 hybrids revealed a high degree of meiotic chromosome pairing between the two parental genomes. Meiotic analysis of the sterile F1 hybrids revealed that the breakdown of microsporogenesis occurred at the post-meiotic stage after the formation of tetrads. Fertile plants formed regular bivalents with normal disjunction, except for occasional asynchrony at meiotic II division.

Seeds of wild and cultivated species of Luffa were studied to determine the variability in morphological (seed size, colour, seed-coat surface and 100-seed weight) and biochemical (oil and protein) characteristics. A total of 80 accessions of three cultivated species (71 accessions) and three wild species (9 accessions) of Luffa under the present investigation from diverse regions (12 states of five regions) of India showed variations in seed size, colour, seed-coat surface, 100-seed weight, and seed protein and oil contents both within the accessions of the same species and between different species. Significant variability in seed morphological traits was observed. Both seed oil and soluble seed protein contents were highest in some accessions of the cultivated species (25–27% oil and 8–10% protein, respectively, on a fresh seed weight basis). Using the 2D scatter plot diagram derived from the principal components analysis, the morphological and biochemical traits of the 80 Luffa accessions classified the wild species into one cluster (cluster I) and the cultivated species into a second major cluster (cluster II). The present investigation on the correlation between seed morphology and biochemical traits in the cultivated and wild species of Luffa can help in identifying the genotypes of Luffa species with valuable traits for further exploring the potential of this valuable crop as a source of edible oil, food and fodder in edible seed types or as a source of industrial oil/biodiesel in non-edible seed types. The protein-rich seed could be further explored to be utilized in the fortification of food products for value addition.

A rare aberrant fruit phenotype was found in cacao (Theobroma cacao L.) in St Augustine, Trinidad. Double fructification instead of single fructification on a single pedicel was observed. The aberration probably occurred as a result of the formation of two pistils in a single flower. Fruits matured as normal, and fruit morphology and seed number were within the range of that reported for normal fruits of the accession observed in Trinidad. The plant is under investigation and the impact of this finding is highlighted.

Sesame (Sesamum indicum L.) is one of the oldest oil crops and is widely cultivated in Asia and Africa. The aim of this study was to assess the genetic diversity, phylogenetic relationships and population structure of 277 sesame core collection accessions collected from 15 countries in four different continents. A total of 158 alleles were detected among the sesame accessions, with the number varying from 3 to 25 alleles per locus and an average of 11.3. Polymorphism information content values ranged from 0.34 to 0.84, with an average of 0.568. These values indicated a high genetic diversity at 14 loci both among and within the populations. Of these, 44 genotype-specific alleles were identified in 12 of the 14 polymorphic simple sequence repeat markers. The core collection preserved a much higher level of genetic variation. Therefore, 10.1% was selected as the best sampling percentage from the whole collection when constructing the core collection. The 277 core collection accessions formed four robust clusters in the unweighted pair group method and the arithmetic averages (UPGMA) dendrogram, although the clustering did not indicate any clear division among the sesame accessions based on their geographical locations. Similar patterns were obtained using model-based structure analysis and country-based dendrograms, as some accessions situated geographically far apart were grouped together in the same cluster. The results of these analyses will increase our understanding of the genotype-specific alleles, genetic diversity and population structure of core collections, and the information can be used for the development of a future breeding strategy to improve sesame yield.

The allelic variations at glutenin loci could significantly affect the bread baking quality, and specific glutenin alleles might be closely associated with greater gluten strength, which, in turn, is related to superior bread baking quality. In this study, allelic variations at Glu-1, Glu-A3 and Glu-B3 loci were evaluated in 222 Korean wheat landraces using gene-specific polymerase chain reaction (PCR) markers. Ten alleles were identified at Glu-1 loci. Glu-A1c, Glu-B1b, and Glu-D1a or Glu-D1f alleles were predominantly found at the respective loci and their frequencies were 86.5, 87.8 and 96.9 %, respectively. Seven Korean wheat landraces carried the Glu-D1d allele, and only one Korean wheat landrace (IT173162) achieved 10 points for the Glu-1 score. Fifteen alleles were identified at Glu-A3 and Glu-B3 loci; Glu-A3c and Glu-B3d or Glu-B3i alleles were commonly found at the respective loci and their frequencies were 77.0, 33.3 and 37.8 %, respectively. Glu-B3 alleles exhibited the highest genetic diversity than other alleles, while Glu-B1 and Glu-A1 alleles exhibited the lowest genetic diversity than other alleles. Twenty Korean wheat landraces had the Glu-A3d and Glu-B3b, Glu-B3d, Glu-B3f, Glu-B3g or Glu-B3i alleles, which were correlated with superior bread baking quality. Among these wheat lines, two (IT59787 and IT236544) carried the Glu-D1d allele.

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.

Several Desmodium species are adapted to the environment of Griffin, Georgia, USA. The determination of flavonoid concentrations, oil content and fatty acid compositions of 25 Desmodium accessions representing five species (D. discolor Vogel, D. incanum (G.Mey.) DC., D. intortum (Mill.) Urb., D. sandwicense E. Mey. and D. tortuosum (Sw.) DC.) would add value to the members of the genus Desmodium for possible use as livestock health supplements. In this study, the seeds of these 25 accessions were evaluated for flavonoid concentrations, oil content and fatty acid compositions using high-performance liquid chromatography, nuclear magnetic resonance and gas chromatography, respectively. Several accessions exhibited significantly greater values for all the traits than the controls. The Desmodium accessions produced significantly greater concentrations of quercetin and kaempferol than the best control accession (D. incanum, PI 477072). However, all the Desmodium accessions produced significantly greater concentrations of isorhamnetin and luteolin than the control accessions. All the Desmodium accessions had greater linoleic (18:2) and behenic (22:0) acid content than a couple of D. incanum control accessions in 2010 and 2011. Significant correlations were observed between several traits. The concentration of quercetin was significantly correlated with that of kaempferol (r2= 0.69***); however, the concentration of quercetin exhibited a significantly negative correlation (r2= − 0.41*) with that of isorhamnetin. Oil content was significantly correlated with palmitic acid (r2= 0.61**), stearic acid (r2= 0.81***), linolenic acid (r2= 0.58**) and lignoceric acid (r2= 0.80***) content. This information will assist breeders and other scientists in developing superior cultivars with optimum levels of flavonoid concentrations, oil content and fatty acid compositions for many of these Desmodium species.

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.

The secret art of silk culture along with mulberry seeds is presumed to have spread from China to other parts of the world including India through the famous Silk Road. In this study, we investigated a set of 36 important mulberry genotypes (designated as ‘breeders’ collection’) of historical importance that have been frequently used in Indian crop improvement programmes over the last five decades. This study is the first to employ a large number of microsatellite markers (140 screened; 70 used for profiling) to elucidate the diversity, structure and breeding history of mulberry. The cluster and STRUCTURE analysis corroborated with the known genetic relationships and origin. The groupings by STRUCTURE (k= 4) confirm parallel breeding efforts undertaken in the eastern, southern and northern regions of the country. The cultivar ‘Mysore Local’ shares a common parent with ‘Berhampore Local’, and this supports the historical records of its introduction from eastern India to the Kingdom of Mysore by the erstwhile ruler Tippu Sultan. The popular variety ‘Kanva-2’ shared a common male parent with the Japanese variety ‘Kousen’, supporting the contribution of exotic progenitors in Indian cultivars. The findings of this study will be useful in formulating new strategies for mulberry improvement and reveals the historical events of the introduction and spread of cultivated mulberry in the Indian subcontinent.