Development of a representative and well-diversified core with minimum duplicate accessions and maximum diversity from a larger population of germplasm is highly essential for breeders involved in crop improvement programmes. Most of the existing methodologies for the identification of a core set are either based on qualitative or quantitative data. In this study, an approach to the identification of a core set of germplasm based on the response from a mixture of qualitative (single nucleotide polymorphism genotyping) and quantitative data was proposed. For this purpose, six different combined distance measures, three for quantitative data and two for qualitative data, were proposed and evaluated. The combined distance matrices were used as inputs to seven different clustering procedures for classifying the population of germplasm into homogeneous groups. Subsequently, an optimum number of clusters based on all clustering methodologies using different combined distance measures were identified on a consensus basis. Average cluster robustness values across all the identified optimum number of clusters under each clustering methodology were calculated. Overall, three different allocation methods were applied to sample the accessions that were selected from the clusters identified under each clustering methodology, with the highest average cluster robustness value being used to formulate a core set. Furthermore, an index was proposed for the evaluation of diversity in the core set. The results reveal that the combined distance measure A1B2 – the distance based on the average of the range-standardized absolute difference for quantitative data with the rescaled distance based on the average absolute difference for qualitative data – from which three clusters that were identified by using the k-means clustering algorithm along with the proportional allocation method was suitable for the identification of a core set from a collection of rice germplasm.

Chilli (Capsicum spp.) is an economically important vegetable and spice. The Tropical Vegetable Research and Development Center, Kasetsart University, Kamphaeng Saen Campus has collected more than 2500 chilli germplasm accessions since 1989. Investment to maintain and evaluate such a large germplasm collection is high. For efficient germplasm management and to reduce the cost of germplasm maintenance, a core collection needs to be established. Therefore, this study aimed to investigate the genetic diversity of chilli germplasm using microsatellites. A total of 230 chilli germplasm accessions were evaluated using ten anchored Capsicum microsatellite loci. These loci generated 42 alleles with a size ranging from 87 to 323 bp. The average polymorphic information content was 0.57, ranging from 0.414 to 0.681, and the probability of identity (PI) ranged from 0.17 to 0.49. The combined PI of the ten microsatellite loci was 2.30 × 10− 6. The similarity index ranged from 0.29 to 1.00. The 230 chilli accessions were divided into two major groups. Group I comprised mainly C. annuum, and group II comprised all four Capsicum species with the majority being C. frutescens, C. chinense and C. baccatum. The matrix comparison showed that a cophenetic correlation of 0.798 indicated the best fit of the obtained dendrogram. The PowerCore program selected 28 representative chilli accessions to form a core collection, which maintained a similar level of diversity to that of the overall 230 chilli accessions. The representative alleles in those 28 core accessions equalled all the alleles present in the entire collection.

Accurate knowledge of intra-specific diversity of underutilized crop species is a prerequisite for their genetic improvement and utilization. The diversity of 77 accessions of African yam bean (AYB, Sphenostylis stenocarpa) was assessed by amplified fragment length polymorphism (AFLP) markers. A total of EcoRI/MseI primer pairs were selected and 227 AFLP bands were generated, of which 59(26%) were found to be polymorphic in the 77 accessions of AYB. The most efficient primer combination for polymorphic detection was E-ACT/M-CAG with a polymorphic efficiency of 85.5%, while the least efficient was E-AGC/M-CAG with a polymorphic efficiency of 80.6%. The Jaccard genetic distance among the accessions of AYB ranged between 0.048 and 0.842 with a mean of 0.444. TSs98 and TSs104B were found to be the most similar accessions with a genetic similarity of 0.952. The neighbour-joining dendrogram grouped the 77 accessions of AYB into four distinct clusters comprising 8, 20, 21 and 28 accessions. The major clustering of the accessions was not related to their geographical origin. Cluster I was found to be the most diverse. The mean fixation index (0.203) and the mean expected heterozygosity (0.284) revealed a broad genetic base of the AYB accessions. The same germplasm set was previously evaluated for several agro-morphological traits. As the collection of additional AYB germplasm continues, the phenotypic profile, the clustering of the accessions and the AFLP primer combinations from this study can be used to augment breeding programmes.

Old germplasm is an important genetic resource for enhancing modern crops with new alleles. In the present study, the genetic diversity of 52 historic varieties and landraces of bread wheat originated from the Western (Bulgaria) and Northeastern (Ukraine, Russia and Georgia) regions of the Black Sea basin was assessed based on microsatellite markers and agronomic characteristics. A set of 24 markers detected a total of 263 alleles at 25 microsatellite loci, with an average number of 10.5 alleles per locus and an average polymorphic information content (PIC) of 0.74. A total of 63 alleles at 22 loci were unique, being specific to a particular accession. Half of the alleles (132) were regionally specific, and the rest were common between the Western and Northeastern accessions. The latter group was characterized with greater total and private allelic richness, a higher number of unique alleles and a higher average PIC. The population was found to be very heterogeneous (average heterogeneity 41%), with the Northeastern pool (52.8%) being more diverse than the Western pool (30.9%). Most of the accessions of the Western group clustered together, and the rest were distributed among the subclusters of the Northeastern germplasm. Large inter-group differences in the frequencies of alleles ranging from 3.1 at Xgwm294-2A to 16.7 at Xgwm333-7B were observed. This variation might partly account for the differences in certain yield-related traits. The Northeastern accessions had significantly longer spikes with more number of spikelets. Some issues related to germplasm preservation in seed genebanks are discussed herein. The large molecular variation observed could be utilized by breeders for the selection of diverse parents, or by researchers for the production of mapping populations.

The regions of north-eastern Ethiopia are known for their high levels of sorghum genetic diversity, and for being drought prone. For centuries, sorghum has been developed and maintained by farmers for its adaptation to the marginal and heterogeneous environment of these regions. The objective of this study was to examine the genetic diversity and population structure of 200 sorghum landraces collected from seven lowland districts, using 30 microsatellite markers sampled from all linkage groups of the sorghum genome. Both distance-based and model-based analytical approaches were used to analyse the data. The data analysis revealed that there was a large variation among all the markers under study. The values of polymorphic information content ranged from 0.26 to 0.88, with a mean value of 0.61, reflecting the high discriminating ability of the markers studied. The mean value of total gene diversity was 0.69, which partitioned 86% among the landraces and 14% within the landraces. Gene diversity among the landraces was largely due to the variation among the genotypes within the geographic origins. Landraces sampled from different collection sites appeared to cluster together, indicating the existence of a high level of gene flow among the sites of collection. This indicates that a relatively small, random collection of landraces would capture the bulk of genetic diversity in the target area. A moderately high level of genetic differentiation and a relatively low level of gene flow were observed between sorghum races and maturity groups. Given that the target area is marginal, drought prone and heterogeneous, the study of genetic diversity among sorghum landraces could serve as an important indicator of valuable alleles for drought tolerance in future sorghum improvement programmes.

The development of modern approaches to the genetic improvement of the tree crops Ilex paraguariensis (‘yerba mate’) and Ilex dumosa (‘yerba señorita’) is halted by the scarcity of basic genetic information. In this study, we characterized the implementation of low-cost methodologies such as representational difference analysis (RDA), single-strand conformation polymorphisms (SSCP), and reverse and direct dot-blot filter hybridization assays coupled with thorough bioinformatic characterization of sequence data for both species. Also, we estimated the genome size of each species using flow cytometry. This study contributes to the better understanding of the genetic differences between two cultivated species, by generating new quantitative and qualitative genome-level data. Using the RDA technique, we isolated a group of non-coding repetitive sequences, tentatively considered as Ilex-specific, which were 1.21- to 39.62-fold more abundant in the genome of I. paraguariensis. Another group of repetitive DNA sequences involved retrotransposons, which appeared 1.41- to 35.77-fold more abundantly in the genome of I. dumosa. The genomic DNA of each species showed different performances in filter hybridizations: while I. paraguariensis showed a high intraspecific affinity, I. dumosa exhibited a higher affinity for the genome of the former species (i.e. interspecific). These differences could be attributed to the occurrence of homologous but slightly divergent repetitive DNA sequences, highly amplified in the genome of I. paraguariensis but not in the genome of I. dumosa. Additionally, our hybridization outcomes suggest that the genomes of both species have less than 80% similarity. Moreover, for the first time, we report herein a genome size estimate of 1670 Mbp for I. paraguariensis and that of 1848 Mbp for I. dumosa.

Niche modelling software can be used to assess the probability of detecting a population of a plant species at a certain location. In this study, we used the distribution of the wild relatives of lettuce (Lactuca spp.) to investigate the applicability of Maxent species distribution models for collecting missions. Geographic origin data of genebank and herbarium specimens and climatic data of the origin locations were used as input. For Lactuca saligna, we varied the input data by omitting the specimens from different parts of the known distribution area to assess the robustness of the predicted distributions. Furthermore, we examined the accuracy of the modelling by comparing the predicted probabilities of population presence against recent expedition data for the endemic Lactuca georgica and the cosmopolitan Lactuca serriola. We found Maxent to be quite robust in its predictions, although its usefulness was higher for endemic taxa than for more widespread species. The exclusion of occurrence data from the perceived range margins of the species can result in important information about local adaptation to distinct climatic conditions. We discuss the potential for enhanced use of Maxent in germplasm collecting planning.

Mungbean yellow mosaic virus (MYMV) is a disastrous pathogen of mungbean. It is widespread in most of southern India and no complete resistance has been identified among its commercial cultivars. Two isolates of MYMV, representing its diversity, were used to assess and characterize the susceptibility reaction of all the three species of Vigna. The seeds were agroinoculated with the virus and the presence of the viral DNA was confirmed after 12 d by reverse transcriptase-polymerase chain reaction (RT-PCR) analysis after which the plants were monitored for the expression of symptoms. All of the 20 accessions of Vigna radiata and ten accessions of Vigna mungo were systemically infected with MYMV, and they all produced typical symptoms. On the other hand, the 24 accessions of Vigna umbellata were found to be resistant to both the isolates. For additional affirmation, three representative accessions of V. radiata and V. mungo and all the accessions of V. umbellata were agroinoculated, and quantitative RT-PCR was performed for the quantitative detection of the MYMV. The mRNA transcripts of MYMV were detected in V. radiata and V. mungo plants but not in the V. umbellata plants. Researching the molecular basis of the resistance in V. umbellate against MYMV might definitely be very constructive for developing resistant varieties of mungbean on a commercial scale. This genetic quality offering resistance to MYMV could also be incorporated into V. radiata/V. mungo by means of interspecific crosses.

This study examined variation in seed zinc (Zn) in a local upland rice germplasm that may affect adaptation in a system of slash-and-burn. Individual seed Zn in farmers' seed lots of local upland rice varieties from a slash-and-burn system was evaluated by staining with dithizone (DTZ). Concentration of Zn in the farmers' seed lots and their single-seed descent genotypes grown at Chiang Mai University was determined by chemical analysis. The DTZ staining of individual seeds in most of the farmers' seed lots covered the intensity of standards that ranged from 19 mg Zn/kg (RD21) to 31 (Nam Roo) mg Zn/kg. Zinc content by chemical analysis was closely correlated with the weighted-average staining for each seed lot. Almost all of the single-seed descent genotypes had higher seed Zn than RD21; two-thirds were higher than Nam Roo. The variation within seed lots detected by DTZ staining was confirmed by seed Zn in the single-seed descent genotypes. Evolutionary adaptation to soil with limited Zn, exacerbated by alkalinity of the ash from slash-and-burn, is made possible by variation in seed Zn among individuals growing together in the same field, and benefits the eaters with Zn-enriched seed.

Centella asiatica (L.) Urban is an important herbaceous medicinal plant with a worldwide distribution. The herb possesses a medicinal value and is used extensively in traditional systems of medicine. The medicinal properties of the herb are attributed to the presence of characteristic triterpenoids and their saponins in the leaves. The major triterpenoids are asiaticoside, madecassoside and their aglycones asiatic acid and madecassic acid, respectively, among others. The present study reports a remarkable qualitative and quantitative variability in secondary metabolites in different accessions of C. asiatica L. as determined by high-performance liquid chromatography (HPLC) analysis. The accessions analyzed in this study can be considered as the core set of discrete chemotypes of C. asiatica. Considerable and contrasting biochemical variations were observed in the terpenoid profiles of the chemotypes. From the basic and applied phytochemical utility, this chemotypic variability in the total content of triterpenoids is important and interesting.

Momordica charantia L. (Cucurbitaceae) is a commonly cultivated functional food plant. In the present study, karyological variation among 34 accessions of M. charantia originating from the Indian subcontinent (Bangladesh, India and Pakistan) and Thailand was evaluated. Ploidy levels ranging from diploid (2n= 22) to hexaploid (2n= 66) were observed. Hexaploidy in M. charantia is reported herein for the first time. Chromosome length ranged from 0.8 to 2.9 μm. The hexaploid accessions had submetacentric and subtelocentric chromosomes. All accessions harboured median and submedian chromosomes. Only one hexaploid accession (TOT1140) had chromosomes with subterminal centromeres. There was considerable variation in chromosome length and chromosome arm ratio.

Two unique black pepper accessions with very long spikes, hitherto unreported in the world genepool of black pepper, were collected from the centre of origin of the species and characterized. The two accessions can be a valuable genetic source in the improvement of spike length.

Amphidiploids serve as a bridge for transferring genes from wild species into wheat. In this study, five amphidiploids with AABBUU and AABBNN genomes were produced by spontaneous chromosome doubling of unreduced triploid F1 gametes from crosses between diploid Aegilops (A. umbellulata accessions CIae 29 and PI 226500, and A. uniaristata accession PI 554419) and tetraploid Triticum turgidum (ssp. durum cultivar Langdon and ssp. dicoccum accessions PI 94 668 and PI 349045) species. The composition of high-molecular-weight glutenin subunits (HMW-GS) in these amphidiploids and in their parental A. umbellulata and A. uniaristata species was analysed. As expected, the amphidiploids from T. turgidum ssp. dicoccum accession PI 944668 or PI 349045 and A. umbellulata accession CIae 29 or PI 226500 and A. uniaristata accession PI 554419 showed the same HMW-GS patterns as those of their Aegilops parents, because HMW-GS genes were all silenced in the T. turgidum ssp. dicoccum parents. The amphidiploids from CIae 29 and Langdon inherited all of the HMW-GS genes from their parents except for the Uy type. Using 10 and 15% sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE) and 10% urea/SDS–PAGE, 11 Ux and ten Uy types in 16 combinations were observed in 48 A. umbellulata accessions, and two Nx and two Ny types in two combinations were detected in six A. uniaristata accessions. These novel HMW-GS variants may provide new genetic resources for improving the quality of wheat.

Inhibition of α-glucosidase activity is considered an effective means for controlling diabetes by regulating glucose uptake, and blueberries have been shown to possess high levels of inhibitory activity. In the present study, we examined the variations in α-glucosidase inhibition, phenolic and anthocyanin levels, and antioxidant capacity in the peel and pulp of 16 mixed-species rabbiteye hybrids (Vaccinium ashei Reade × Vaccinium spp.), one rabbiteye cultivar (V. ashei) and two highbush hybrids (Vaccinium corymbosum). Peel tissue had, on average, about four times higher levels of α-glucosidase inhibitory activity than pulp, and exhibited significantly higher levels of all other measured activities, even though the peel comprised only a small portion of the fruit. Significant variations in the levels of antioxidant activity were observed; however, no consistent differences were observed between the hybrids with various species composition. Significant positive correlations (r≥ 0.84) were found among α-glucosidase inhibitory activity, total anthocyanin (TA) and phenolic levels, and scavenging activity against ROO∙, ∙OH, 1O2 and H2O2 radicals in the extracts from the peel and pulp. There was a high correlation observed between α-glucosidase inhibitory activity levels and ROO∙(ORAC)peel (r= 0.95). A similarly high correlation with TApeel (r= 0.93) suggests that TA would be a suitable assay proxy if a broader genotypic evaluation of blueberry genotypes is desired.