In order to utilize germplasm resources more efficiently for peanut (Arachis hypogaea L.) genetic improvement, a core collection of 576 accessions and a primary mini core collection of 298 accessions were developed previously from a collection of 6839 cultivated peanut lines stored at the Oil Crops Research Institute of Chinese Academy of Agricultural Sciences at Wuhan. For an efficient evaluation and characterization of the most useful agronomic and disease-resistant traits, an even smaller collection of peanut accessions that represent a spectrum of phenotypes could be more desirable. For this reason, a mini-mini core collection with 99 accessions from the core accessions was developed based on the analysis of 21 morphological traits. It was demonstrated that there were no significant differences between the core and mini-mini core collections in 20 out of the 21 morphological traits studied. Further, the mini-mini core collection captured the ranges of all of the 21 traits displayed in the core collection. The newly developed mini-mini core collection was assessed for resistance to bacterial wilt disease caused by Ralstonia solanacearum. Two accessions showing a high level of resistance to bacterial wilt were identified, demonstrating the usefulness of the mini-mini core collection. The mini-mini-core collection provides a more efficient means of germplasm evaluation and will be resequenced as part of the International Peanut Genome Consortium sequencing project at the UC-Davis Genome Center.

An assessment of morphological variation among 70 accessions of greater yam (Dioscorea alata L.) collected throughout Malaysia was made. Data of 47 morphological variables measured from the accessions were subjected to multivariate analysis using principal component (PCA) and cluster analysis (CA). The PCA results indicated that the characters contributing largely to the species variability were those related to the shape, size and flesh colour of underground tubers; shape and colour of aerial tubers; position, shape, size and vein colour of the leaves; petiole colour; shoot growth rate; and number of days for shoots to germinate. The two-dimensional plot of the first two PCs showed a separation between accessions of purple tuber groups and those of white tuber groups, but was unable to distinguish accessions according to tuber shape groups, i.e. irregular, oblong and round, as revealed by visual observation. The dendrogram of CA revealed four major groups of D. alata in Malaysia, which supported the PCA grouping. This study demonstrated that D. alata in Malaysia consists of numerous genotypes revealing wide inter- and intra-group variability.

Successful development of new sorghum cultivars and hybrids to ensure sustainable production depends largely on the availability of genetic resources with desirable traits such as pest resistance. Our recent research has focused on improvement of crop protection against greenbugs using the worldwide germplasm collection and genomics-based approaches. First, we conducted the systematic evaluation of a worldwide germplasm collection in order to identify new sources of greenbug resistance. Twenty-one resistant lines were identified, which offered new sources of resistance to sorghum breeding. Molecular markers used to assess the genetic diversity among those resistant lines suggested relatively diverse resistant sources in the sorghum germplasm collection. More recently, a mapping project was executed to associate the resistance genes with sorghum chromosomes. The mapping data indicated one major and a minor quantitative trait loci reside on chromosome 9 and are responsible for resistance to greenbug. In addition, cDNA microarrays were used to monitor greenbug-induced gene expression in sorghum plants. This study has developed a transcriptional profile for sorghum in response to greenbug attack, which provides us with useful molecular information for discovery of greenbug resistance genes and a better understanding of the genetic mechanisms controlling host defences in sorghum.

Plant genetic resources are raw materials and their use in breeding is one of the most sustainable ways to conserve biodiversity. The ICRISAT has over 120,000 accessions of its five mandate crops and six small millets. The management and utilization of such large diversity are greatest challenges to germplasm curators and crop breeders. New sources of variations have been discovered using core and minicore collections developed at the ICRISAT. About 1.4 million seed samples have been distributed; some accessions with specific attributes have been requested more frequently. The advances in genomics have led researchers to dissect population structure and diversity and mine allelic variations associated with agronomically beneficial traits. Genome-wide association mapping in sorghum has revealed significant marker–trait associations for many agronomically beneficial traits. Wild relatives harbour genes for resistance to diseases and insect pests. Resistance to pod borer in chickpea and pigeonpea and resistance to rust and late leaf spot in groundnut have been successfully introgressed into a cultivated genetic background. Synthetics in groundnut are available to broaden the cultigen's gene pool. ICRISAT has notified the release of 266 varieties/cultivars, germplasm, and elite genetic stocks with unique traits, with some having a significant impact on breeding programs. Seventy-five germplasm lines have been directly released for cultivation in 39 countries.

Chickpea (Cicer arietinum L.) is an important grain legume nutritionally balanced for human consumption. The physical properties of chickpea seeds are important for processing and storage as well as for assessing seed quality and the hydration properties related to cooking quality. The chickpea mini core collection (211 accessions) and four control cultivars were evaluated for seed morphological (seed colour, shape, dots on seed coat and surface texture); physical (seed moisture content, 100-seed weight, seed coat content, length, width, thickness, geometric mean diameter (GMD), surface area, sphericity, shape aspect, volume, bulk density, true density and porosity); and hydration traits (hydration capacity, hydration index, swelling capacity and swelling index). Highly significant differences were observed for all the seed traits in the mini core collection. Correlation coefficients indicated that accessions with high or more seed weight, GMD, sphericity, seed shape aspect, swelling capacity and swelling index would be useful for utilization in research. The results of this study have refined the seed traits of chickpea and resulted in identifying several desirable accessions in the mini core. Some of these accessions were previously identified as promising sources for important agronomic and nutritional traits and for resistance to biotic and abiotic stresses and will be useful sources to develop high-yielding cultivars with desirable seed physical and hydration quality.

In this study, the transcriptome of Vitis flexuosa leaves inoculated with Elsinoe ampelina was analysed to identify useful genes and elucidate their function and differential expression patterns through assembly and annotation gene ontology of data from sequencing short reads on the Illumina platform. We assembled ~121 million high-quality trimmed reads using Velvet and Oases with optimal parameters into a non-redundant set of 70,899 transcripts ( ≥ 200 bp in length). The transcripts exhibited an average length of 1138 bp and a N50 length of 1695 bp, with the largest contig length being 9623 bp. Functional categorization revealed the conservation of genes involved in various molecular functions, including protein binding (21.1%) and oxidoreductase activity (11.7%), in V. flexuosa. The V. flexuosa transcript set generated in this study will serve as a resource for gene discovery and development of functional molecular markers.

Selecting desired agronomic traits may lead to a loss of genetic diversity in crop species. A molecular investigation was conducted to determine how well a set of olive (Olea europaea L.) accessions sampled in Moroccan traditional orchards represented the entire Moroccan olive diversity range. We therefore collected, in traditional agroecosystems from northern and central Morocco, a total of 88 olive trees chosen for their agronomic traits based on local farmers' knowledge. Using 12 SSR loci, 45 trees (51.1%) had a genotype identical to the ‘Picholine Marocaine’ variety, while the remaining samples were classified into 27 different SSR profiles. Two categories of genotypes were identified: (i) genotypes closely related to the ‘Picholine Marocaine’ variety and probably resulting from intensive vegetative propagation from a limited number of clones, and (ii) genotypes displaying a high number of dissimilar alleles which may have originated from selected spontaneous seedlings. A significant difference in allelic richness was revealed between the 28 on-farm selected genotypes and the overall olive diversity, represented by 57 local genotypes, indicating that the on-farm selected trees represented a subsample of Moroccan genetic diversity. This could be explained by the prevalence of ‘Picholine Marocaine’ in traditional orchards, while some original genotypes with favourable agronomic traits resulting from local farmers' selection were also identified. Applying an ethnobotany approach combined with criteria to fulfil farmers' household needs could be particularly relevant and better explain the obtained results.

Genetic resource conservation is widely acknowledged as important. The implementation of conservation requires an insight into the distribution of genetic diversity at the scale of small regions or villages. We present an analysis of rice diversity at such a scale, in a region where traditional farming still prevails. Regional allelic diversity was comparable to that noted worldwide for Asian rice (Oryza sativa), but not as high for African rice (O. glaberrima). Each village pooled more than half of the regional allelic diversity. Genetic differentiation between varieties from the same village accounted for 70% of the regional variation. The differentiation associated with lowland and upland rice-growing ecosystems was 23%, while that associated with differences between villages within the same ecosystem was 7%. In the upland ecosystem, geographical distance had a significant effect on the FST between pairs of villages. In the lowland ecosystem, differences in soil salinity between villages affected FST. Genetic diversity within a single village may have up to three components: an ancient glaberrima component shared with neighbouring or ethnically related villages; a relatively ancient sativa component which was hardly or no longer shared with other villages due to local differentiation; and a recently introduced sativa component shared with other villages. Genetic resource conservation could be achieved, in terms of allelic diversity, through stratified sampling according to described genetic differentiation factors, whereas current farming systems must be preserved to ensure conservation of the diversity of allelic associations.

In a germplasm bank collection the conservation and characterization of genetic resources is a prerequisite in order to use the material in breeding projects aiming the creation of new cultivars. In the present study, 54 Prunus salicina domestica and Prunus domestica genotypes (including seven Greek cultivars), maintained in the ex situ National Genebank Collection of Greece, were classified using microsatellite (simple sequence repeat, SSR) markers on high resolution melting (HRM) analysis. The SSR primer pairs were chosen from the published literature as originally designed on Prunus species. This combined approach was used to genotype all plum accessions of the collection highlighting the benefits of either method (HRM and SSRs) for cultivar identification. Dendrograms for P. domestica and P. salicina and a combined one with all the genotypes assayed were produced. A total of 15 from the 19 P. domestica accessions analysed, including all the Greek accessions but ‘Avgati Skopelou’, were grouped into the same clade in the combined dendrogram, whereas the remaining four were dispersed into the P. salinica clades. Bayesian structure analysis confirmed that ‘Avgati Skopelou’ differs from the rest of the Greek plum cultivars since it was not grouped into the same cluster. The combination of HRM and SSRs, provided a considerably faster, cost-effective, closed-tube microsatellite genotyping method for molecular characterization of plum cultivars.

Characterization of high-molecular-weight (HMW) glutenins is an important criterion for identifying genotypes with good bread-making quality. In synthetic hexaploids (SHs), the D-genome encodes several allelic variants of HMW glutenins that require proper identification prior to their utilization for bread wheat (BW) improvement. In this study, SHs with promising agronomic features were characterized for HMW glutenin composition. Seven different allelic variants were observed at the Glu-Dt1 locus, three of which (1Dx1.5+1Dy10, 1Dx1.5+1Dy12.2 and 1Dx2.1+1Dy10) have not been previously reported in existing BW germplasm. The results also showed a variety of D-genome-encoded subunits along with superior glutenin alleles in the B-genome (1Bx7+1By8, 1Bx6+1By8 and 1Bx13+1By16). About 63% of these SHs encoded favourable allelic variants of HMW glutenins, which make them a good choice for improvement in wheat bread making. Glu-Dt1 encoded favourable allelic variants (1Dx5+1Dy10 and 1Dx1.5+1Dy10) that are frequently observed in SHs can be easily incorporated into BW through recombination breeding.

Investigation of genetic diversity and the relationships among varieties and breeding lines is of great importance to facilitate parental selection in the development of inbred and hybrid rice varieties and in the construction of heterotic groups. The technology of single nucleotide polymorphism (SNP) is being advanced for the assessment of population diversity and genetic structures. We characterized 215 widely cultivated indica rice varieties developed in southern China and at the International Rice Research Institute (IRRI) using IRRI-developed SNP oligonucleotide pooled assay (OPA) to provide grouping information of rice mega-varieties for further heterotic pool study. The results revealed that the Chinese varieties were more divergent than the IRRI varieties. Two major subpopulations were clustered for the varieties using a model-based grouping method. The IRRI varieties were closely grouped and separated clearly from the majority of the Chinese varieties. The Chinese varieties were subclustered into three subgroups, but there was no clear evidence to separate the Chinese varieties into subgroups geographically, indicating a great degree of genetic integration of alleles and shared ancestries among those high-yielding modern varieties.

Fungal blast disease is one of the major constraints in finger millet production. Breeding for disease resistance in finger millet, needs characterization of genetic polymorphism among and between the resistant and susceptible genotypes. In total, 67 finger millet genotypes, which are resistant or susceptible to fungal blast disease, were analysed using sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers to assess genetic variations and select diverse parents. Twelve each of SRAP and SSR primers produced 95.1 and 93.1% polymorphic bands and grouped them into unweighted pair-group method with arithmetic average clusters. Two of the finger millet genotypes, IE 4709 (blast resistant) and INDAF 7 (susceptible) were distinguished as most diverse genotypes as parents. Several genotype-specific bands observed with SSR primers are potential in developing genotype-specific markers. A high genetic diversity within the resistant and susceptible genotypes, rather than between them, was revealed through Nei's gene diversity (h) index and analysis of molecular variance. The finding helps us to understand the extent of genetic polymorphism between blast disease resistant and susceptible finger millet genotypes to exploit in resistance breeding programs.

The genus Vicia L., one of the earliest domesticated plant genera, is a member of the legume tribe Fabeae of the subfamily Papilionoideae (Fabaceae). The taxonomic history of this genus is extensive and controversial, which has hindered the development of taxonomic procedures and made it difficult to identify and share these economically important crop resources. Species identification through DNA barcoding is a valuable taxonomic classification tool. In this study, four DNA barcodes (ITS2, matK, rbcL and psbA-trnH) were evaluated on 110 samples that represented 34 taxonomically best-known species in the Vicia genus. Topologies of the phylogenetic trees based on an individual locus were similar. Individual locus-based analyses could not discriminate closely related Vicia species. We proposed a concatenated data approach to increase the resolving power of ITS2. The DNA barcodes matK, psbA-trnH and rbcL were used as an additional tool for phylogenetic analysis. Among the four barcodes, three-barcode combinations that included psbA-trnH with any two of the other barcodes (ITS2, matK or rbcL) provided the best discrimination among Vicia species. Species discrimination was assessed with bootstrap values and considered successful only when all the conspecific individuals formed a single clade. Through sequencing of these barcodes from additional Vicia accessions, 17 of the 34 known Vicia species could be identified with varying levels of confidence. From our analyses, the combined barcoding markers are useful in the early diagnosis of targeted Vicia species and can provide essential baseline data for conservation strategies, as well as guidance in assembling germplasm collections.

Wild apricot (Prunus armeniaca L.) is an economically important fruit crop for folk and marginal farmers and local tribal populations in the high-altitude difficult terrains of north-western Himalayas in Jammu and Kashmir and Himachal Pradesh states of India. This is a multi-purpose fruit tree species which, besides its fresh edible fruits, is preserved for use in diverse ways depending upon the type of cultivar. Seed kernel of apricot is used as edible nut and for the production of edible oil. In the present study, 147 diverse accessions of wild and cultivated apricot belonging to 28 folk cultivars were collected and characterized for fruit, stone and kernel characters. Indigenous traditional uses and importance of fruits and kernels of these folk cultivars have been recorded and described. Promising table-type cultivars identified were Margulam, Lodi, Shakarpara, Narmo and Khurmani, while drying-type cultivars were Halman, Shakarpara, Rakchey Karpo and Tachu. Cultivars Chuli and Shadi were the most common types and widely distributed with vast variability, while other cultivars had localized presence. Some of these folk cultivars have high potential for promotion as commercial cultivars of apricot in this high-altitude area basically depending upon traditional production system. Genetic resource management including collection, characterization and documentation of existing variability of apricot is of immense importance for safe conservation and commercialization of potential cultivars to enhance farmer's livelihood in this fragile agroecosystem.

Ilex paraguariensis, commonly known as yerba mate, is a tree species native to South America. Its commercial value is due to the manufacturing of teas, with potential also in the pharmacological and cosmetic industries. Vegetative propagation of yerba mate is considered an innovation to the traditional production systems based on sexual propagation. The present study aimed to evaluate the rhizogenic potential and chemical attributes of mini-cuttings from 15 yerba mate genotypes, as well as to verify the correlation between phytochemical and rooting-related variables. Mini-cuttings were collected from a pre-existing mini-clonal hedge and the experimental design was completely randomized, with 15 treatments (genotypes), four replications and 10 mini-cuttings per plot. After 120 days, mini-cuttings were assessed regarding rooting, mortality, callogenesis and leaf retention percentages, percentage of mini-cuttings with both calluses and roots, number of roots and average root length. At the time of collection, subsamples from each plot were used for phytochemical analyses including total phenolic compounds, protein, caffeine and theobromine contents and antioxidant activity. Rooting percentages ranged from 5 to 72.5%, with significant variation among genotypes. Adventitious rooting and phytochemical profile of yerba mate mini-cuttings are genotype-dependent. Leaf retention is a relevant factor in the rooting of yerba mate mini-cuttings and the levels of total phenolic compounds, antioxidants and theobromine present in mini-cuttings are negatively correlated components to Ilex paraguariensis adventitious rooting.

Seed protein content is one of the most important traits controlled by quantitative trait loci (QTLs) in soybean. In this study, a Glycine soja accession (ZYD2738) was crossed with two elite cultivars Jidou 12 and Jidou 9 separately and subsequently the resulting F2:3 populations were used to identify QTLs associated with seed protein content. Protein contents in either population appeared to have a normal distribution with transgressive segregation. A total of five QTLs associated with high protein content were identified and mapped to chromosomes 2, 6, 13, 18 and 20, respectively. Of these QTLs, three (qPRO_2_1, qPRO_13_1 and qPRO_20_1) were identified in the same region in both the populations, whereas the other two (qPRO_6_1 and qPRO_18_1) were mapped in two different regions. qPRO_2_1 appears to be a novel protein QTL. qPRO_6_1, qPRO_18_1 and qPRO_20_1 had additive effects on seed protein content, while qPRO_13_1 had an over-dominant effect on seed protein content. These QTLs and their linked markers could serve as effective tools for marker-assisted selection to increase seed protein content.

Nested association mapping (NAM) captures the best features of both linkage and association mapping and enables the high power and high resolution of quantitative trait locus mapping through joint linkage-association analysis. In the current study, NAM population was developed by hybridizing JS 335, a popular variety of central India with 20 diverse soybean genotypes. The parents used in the study have various traits of economic importance such as drought and water-logging tolerance, bacterial pustule and yellow mosaic virus resistance, wider adaptability, resistance to mechanical damage and higher yield potential. High variability in the F2 populations of 20 crosses for grain yield and days to maturity indicated scope for development of high-yielding varieties. Genetic variability studies, correlation, regression, principal component analysis (PCA) and genetic diversity analyses were carried out in 900 NAM-recombinant inbred lines (RILs) derived from 11 crosses. Correlation and regression analysis indicated a significant positive effect of biomass, pods/plant, harvest index, branches/plant, nodes/plant and plant height on grain yield. Genetic diversity analysis grouped 900 NAM-RILs into 10 clusters. PCA revealed first two principal components to explain 63.78% of total variation mostly contributed by grain yield, biomass and number of pods. The inbred lines developed in this study will serve as an elite soybean genetic resource in understanding the genetic architecture underlying different traits of economic significance.

Drought is the major abiotic constraint to the rice production in the rain-fed areas across Asia and sub-Saharan Africa. Wild species of Oryza offer a wide spectrum of adaptive traits and can serve as potential donors of biotic and abiotic stress tolerance. At the Punjab Agricultural University, we are maintaining an active collection of 1630 accessions of wild species germplasm (AA, CC, BBCC and CCDD) of rice. These accessions were screened to assess genetic variation for drought tolerance under field conditions. Severe water stress was imposed at the late vegetative stage by withholding water initially for 25 d and then extended further to 35 d during kharif season in the years 2013–14 and 2015–16. The tolerance score for drought stress was based on the extent of leaf rolling and leaf drying. Based on the 2 years’ data, seven accessions from Oryza rufipogon, four from Oryza longistaminata and one each from Oryza officinalis and Oryza latifolia were found tolerant to drought stress. These selected accessions were further phenotype for root morphology. The average root length among the selected accessions ranges between 36 and 80 cm and the number of primary roots vary from 30 to 87 cm. The O. rufipogon accession IRGC 106433, O. longistaminata accession IRGC 92656A, O. officinalis accession IRGC 101152 and O. latifolia accession IRGC 80769 showed approximately 2–2.5 times longer root length and number than the indica rice elite cultivar PR121. The results indicated potentiality of selected wild species germplasm for conferring drought tolerance to the elite cultivars.

A collection of 120 Ethiopian tetraploid wheat accessions was analysed for high-molecular weight (HMW) glutenin subunit, low-molecular weight (LMW) glutenin subunit and omega gliadin composition by SDS–PAGE. For the HMW glutenin subunits, a new allelic variant, 2****, was detected which has not been previously described at the Glu-A1 locus. A high proportion of Glu-A1x banding pattern was observed in durum wheat. For the Glu-B1 locus four different banding patterns were detected. Among those HMW glutenin subunits, 7+8 were the most common, while subunits 14+15 and 6+8 were found to be rare. A high degree of variation was evident for the LMW glutenin subunits and D-zone omega gliadins. The association of the composition of the gluten with quality has been discussed. This wide variation can be used in improving the quality of wheat and to widen its genetic base.

Aegilops markgrafii is a useful source of genes encoding both resistance to biotic stress and high seed lysine content. Bread wheat/Ae. markgrafii introgression lines expressing leaf rust resistance were developed from a cross between a leaf rust-resistant Ae.markgrafii accession and the susceptible bread wheat cultivar ‘Alcedo’. The content of introgressed segments present in five sister introgression lines was assessed with the help of chromosome-specific simple sequence repeats (SSRs). One of the lines was used as a parent of a 140 individual F2 mapping population, by crossing with the leaf rust-susceptible bread wheat cv. ‘Borenos’. The population was tested for susceptibility or resistance to leaf rust, and linkage analysis indicated the presence of a quantitative trait locus (QLr.ipk-2A) originating from the Ae. markgrafii parent, mapping to the distal segment of chromosome arm 2AS.