Aegilops tauschii, the diploid progenitor of the wheat D-genome, is a valuable genetic resource for wheat breeders. In this study, we compared the efficiency of inter-simple sequence repeat (ISSR) (as an arbitrary technique) and start codon targeted (SCoT) (as a gene-targeting technique) markers in determining the genetic diversity and population structure of 90 accessions of Ae. tauschii. SCoT markers indicated the highest values for polymorphism information content, marker index and effective multiplex ratio compared to ISSR markers. The total genetic diversity (Ht) and genetic diversity within populations (Hs) parameters were comparably modest for the two marker systems. The results of the analysis of molecular variance showed that the genetic variation within populations was significantly higher than among them (ISSR: 92 versus 8%; SCoT: 88 versus 12%). Furthermore, SCoT markers discovered a high level of genetic differentiation among populations than ISSRs (0.19 versus 0.05), while the amount of gene flow detected by ISSR was higher than SCoT (2.13 versus 8.62). Cluster analysis and population structure of SCoT and ISSR data divided all investigated accessions into two and four main clusters, respectively. Our results revealed that SCoT and ISSR fingerprinting could be used to further molecular analysis in Ae. tauschii and other wild species. The high-genetic variability found in this study also indicates the valuable genetic potential present in the investigated Ae. tauschii germplasm, which could be utilized for future genetic analysis and linkage mapping in breeding programmes.

Apricot is considered an ecologically and economically important tree species of the stone-fruit crops that is widely grown in temperate regions of the world. Very few studies on apricot genetic diversity assessment have been carried out from the regions of Kashmir and Ladakh. In this backdrop, the present study was carried out to analyse the genetic diversity and population structure of 120 apricot genotypes collected from both the regions using 21 SSR markers. A total of 52 alleles were amplified with average values of marker index (MI) = 0.7084, resolving power (RP) = 2.8690, polymorphism information content (PIC) = 0.3132, Na = 2.317, Ne = 1.720, I = 0.572, Ho = 0.284, He = 0.360 and an average polymorphism of 91.2% per assay indicating high level of genetic diversity. The neighbour-joining (NJ) dendrogram generated three main clusters among selected apricot genotypes independent of their geographical locations. Interestingly, the result of the dendrogram coincides with the results of structure analysis which showed that the 120 apricot genotypes could be assigned to three (K = 3) sub-populations and the grouping of genotypes did not follow their geographical location suggesting that they share the same genetic pool. Moreover, analysis of molecular variance showed that 73% of the variation was attributed to differences within the individuals, 25% among individuals while only 2% of the variation was observed among the populations. The present study represents the most comprehensive analysis of the genetic diversity and population structure of apricot genotypes in Kashmir and Ladakh regions of India.

Peanut shell plays key roles in protecting the seed from diseases and pest infestation but also in the processing of peanut and is an important byproduct of peanut production. Most studies on peanut shell have focused on the utilization of its chemical applications, but the genetic basis of shell-related traits is largely unknown. A panel of 320 peanut (Arachis hypogaea) accessions including var. hypogaea, var. vulgaris, var. fastigiata and var. hirsuta was used to study the genetic basis of two physical and five microstructure-related traits in peanut shell. Significant phenotypic differences were revealed among the accessions of var. hypogaea, var. hirsuta, var. vulgaris and var. fastigiata for mechanical strength, thickness, three sclerenchymatous layer projections and main cell shape of the sclerenchymatous layer. We identified 10 significant single nucleotide polymorphisms (SNPs) through genome-wide association study (P < 5.0 × 10−6) combining the shell-related traits and high-quality SNPs. In total, 192 genes were located in physical proximity to the significantly associated SNPs, and 11 candidate genes were predicted related to their potential contribution to the development and structure of the peanut shell. All SNPs were detected on the B genome demonstrating the biased contribution of the B genome for the phenotypical make-up of peanut. Exploring the newly identified candidate genes will provide insight into the molecular pathways that regulate peanut shell-related traits and provide valuable information for molecular marker-assisted breeding of an improved peanut shell.

Two aphid-transmitted RNA viruses, broad bean wilt virus 2 (BBWV2) and cucumber mosaic virus (CMV), are the most prevalent viruses in Korean pepper fields and cause chronic damage in pepper production. In this study, we employed a screening system for pathotype-specific resistance of pepper germplasm to BBWV2 and CMV by utilizing infectious cDNA clones of different pathotypes of the viruses (two BBWV2 strains and three CMV strains). We first examined pathogenic characteristics of the BBWV2 and CMV strains in various plant species and their phylogenetic positions in the virus population structures. We then screened 34 commercial pepper cultivars and seven accessions for resistance. While 21 pepper cultivars were resistant to CMV Fny strain, only two cultivars were resistant to CMV P1 strain. We also found only one cultivar partially resistant to BBWV2 RP1 strain. However, all tested commercial pepper cultivars were susceptible to the resistance-breaking CMV strain GTN (CMV-GTN) and BBWV2 severe strain PAP1 (BBWV2-PAP1), suggesting that breeding new cultivars resistant to these virus strains is necessary. Fortunately, we identified several pepper accessions that were resistant or partially resistant to CMV-GTN and one symptomless accession despite systemic infection with BBWV2-PAP1. These genetic resources will be useful in pepper breeding programs to deploy resistance to BBWV2 and CMV.

Milk thistle, Silybum marianum (L.) Gaertn. (Asteraceae), is an economically important medicinal plant utilized for silymarin production. Moreover, the species has been positively evaluated for vegetable oil and biomass production. Despite these positive characteristics, milk thistle is still marked by traits that are typical of undomesticated species (most importantly natural fruit dispersal at maturity) and requires further genetic improvement for its complete exploitation. This manuscript summarizes all the information collected through time about a collection of nine milk thistle wild and mutant lines and it discusses the possible further utilization of these genotypes. The accessions are characterized by interesting traits related to: fruit silymarin composition (S. marianum chemotype A and B), fruit fatty acid composition (high oleic and high stearic acid lines), fruit condensed tannins content, vegetative biomass composition (modification of xylans or lignin content), vegetative biomass structure (dwarf and tall lines), modifications of leaf variegation (hypervareigated line) and different types of fruit shatter resistance at maturity. All the lines underwent subsequent generations of selfing and are stable for all the described traits. The accessions will be made available at the Genebank of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK, Gatersleben) and may prove to be a useful genetic material for the improvement of qualitative fruit traits (silymarin quality, fatty acid composition) and for the further development of shatter-resistant S. marianum genotypes towards the complete domestication of this promising species.

Melon (Cucumis melo L.) is an economically important vegetable crop worldwide. Karnataka state of southern India is rich in melon landraces and wild relatives, which are potential sources of genetic diversity for crop improvement. Here we report on the collection, characterization and documentation of previously unexplored landrace and wild material to broaden the availability of this genetic diversity for use in melon improvement. Accessions of botanical groups, momordica, kachri, chandalak, reticulatus, acidulus and indicus, intermediate forms of acidulus and momordica, and three melons of an unknown group were sourced directly from farmers of eight agro-ecological regions. Twenty-three representative melon landraces and wild relatives, along with four reference varieties of different botanical groups, were evaluated for agronomic traits during the year 2016. Very wide and distinctive genetic variations were observed among the melon accessions for ovary characters, sex expression, days taken to first fruit maturity, external and internal fruit traits, and fruit cracking (splitting). The remarkable variability displayed among the melon accessions as observed from the study demonstrates the importance of them as a valuable genetic reservoir for melon improvement.

Beachpea (Vigna marina) is a halophytic wild leguminous plant which occurs throughout tropical and subtropical beaches of world. As quantitative trait loci (QTLs) for salt tolerance in V. marina and its crossability with other Vigna species are known, the current study was undertaken to know the presence of these QTLs in the V. marina accessions along with check varieties of pulses. Accordingly, 20 Vigna genotypes (15 accessions of V. marina collected from sea-shore areas of Andaman and Nicobar Islands along with five check varieties of green gram and black gram) were subjected to molecular characterization using seven simple sequence repeat (SSR) markers associated with salt tolerance. Of the markers used, only four SSR markers amplified in the studied germplasm. Number of alleles detected per primer and size of alleles ranged from 1 to 3 and 100 to 325 bp, respectively. Polymorphism information content and heterozygosity values ranged from 0.305 to 0.537 and 0.375 to 0.612, respectively. Three major clusters, cluster I, II and III were obtained at Jaccard's similarity coefficient value of 0.48 through the un-weighted paired group method with arithmetic means method of cluster analysis. It grouped green gram and black gram genotypes in clusters I (04) and II (01), whereas all V. marina genotypes were grouped in cluster III (15). Principal co-ordinate analysis explained 85.9% of genetic variation among genotypes which was further confirmed by cluster analysis. This study indicated the effectiveness of SSR markers in separating cultivated Vigna species from wild V. marina. The findings will be useful for transferring trait of robust salt tolerance of V. marina in cultivated Vigna species using marker-assisted breeding.

White Guinea yam (Dioscorea rotundata Poir.) is indigenous to West Africa, a region that harbours the crop's tremendous landrace diversity. The knowledge and understanding of local cultivars’ genetic diversity are essential for properly managing genetic resources, conservation, sustainable use and their improvement through breeding. This study aimed to dissect phenotypic and molecular diversity of white yam cultivars from Benin using agro-morphological and single nucleotide polymorphism (SNP) markers. Eighty-eight Beninese white Guinea yam cultivars collected through a countrywide ethnobotanical survey were phenotyped with 53 traits and genotyped with 9725 DArT-SNP. Multivariate analysis using phenotypic traits revealed 30 traits as most discriminative and explained up to 80.78% of cultivars’ phenotypic variation. Assessment of diversity indices such as Shannon–Wiener (H′), inverse Shannon (H.B.), Simpson's (λ) index and Pilou evenness (J) based molecular and phenotypic data depicted a moderate genetic diversity in Beninese white Guinea yam cultivars. Genetic differentiation of cultivars among country production zones was low due to the high exchange of planting materials among farmers of different regions. However, there was high genetic diversity within regions. Hierarchical clusters (HCs) on phenotypic data revealed the presence of two groups while HCs based on the SNP markers and the combined analysis identified three genetic groups. Our result provided valuable insights into the Beninese white Guinea yam diversity for its proper conservation and improvement through breeding.

Distant hybridization of cereals is often impaired by fertilization barriers. Haploid induction through intergeneric crossing is well developed in wheat but has not been successful in rice due to incompatibility issues. The present study was thus undertaken to identify fertilization barriers that hinder the compatibility of the rice cultivar Punjab Rice 121 with maize and pearl millet lines as pollinators. A total of 37,357 spikelets were pollinated, yielding 494 caryopses upon supplementation with auxins. The resultant caryopses, arising from true intergeneric crosses, lacked embryos. Imaging of the pollinated pistils at different intervals indicated that intense callose depositions block the release of generative nuclei to the ovule in these wide crosses. Rice spikelets pollinated with rice pollen (cis-generic crosses) exhibited positive indicators of fertilization reaction at the micropyle. While the cis-generic crosses initiated true caryopsis formation after 24 h, no comparative reaction was observed in the intergeneric crosses. The current survey underlines that the rice female gametophyte presents a strong pre-fertilization barrier to foreign pollen. This barrier may be modulated in the future by altering genotype and auxin combinations.

Drought is a major concern among abiotic stresses in wheat (Triticum aestivum L.) production. Breeding resistant cultivars are the most effective means to manage drought stress. F6 recombinant inbred lines (RIL) derived from the cross of Berkut/Worrakatta were used to identify quantitative trait loci (QTL) for drought tolerance at germination stage under treatment of PEG6000 using the wheat 50 K single nucleotide polymorphism (SNP) array. Twenty-eight linkage groups were constructed, covering a length of 2220.26 cM. Eighteen QTL were detected based on the drought tolerance coefficients and D-value, explaining 2.7–6.5% of the phenotypic variances, in which 15 were likely to be novel. Three QTL, QGR.xjau-5AS, QCL.xjau-5AS and QD.xjau-5AS for GR, CL and D-value, respectively, at physical positions of 11.70–20.61 Mb between markers AX-111258240 and AX-94458300 on chromosome 5AS accounted for 3.4–4.8% of the phenotypic variances. Three QTL, QGP.xjau-5DL, QSH.xjau-5DL and QD.xjau-5DL for GP, SH and D-value, respectively, were flanked by markers AX-94524442 and AX-110998507 at 560.42–567.39 Mb on chromosome 5DL, accounting for 4.4–6.5% of the phenotypic variances. In addition, the candidate genes TraesCS5A02G022100, TraesCS5B02G014200 and TraesCS5D02G563900 were predicted. Based on transcriptional expression data, the results showed that the expression level of TaGATAs-5A, TaUbox-5B and TaGSTP-5D changed with the increase of treatment time under drought stress in tolerant and sensitive varieties. These are interesting targets in mining drought tolerance genes and the improvement of drought tolerance in wheat.

Due to the high yield losses caused by late blight in potato cultivation, the development of resistant pre-breeding material is of great importance for cultivar breeding. The gene pool of the Julius Kühn Institute (JKI) includes a large collection of resistant clones whose resistance has not yet been analysed in detail with markers for relevant resistance genes. A panel of 52 pre-breeding potato clones developed at the JKI via interspecific crosses and highly resistant to late blight were tested for the presence of seven resistance genes (Rpi-blb1/Rpi-sto1, Rpi-blb2, Rpi-blb3/R2/Rpi-abpt, R1, R3a, R3b, Rpi-phu1) and one QTL allele (QTL_phu-stn) from Solanum species S. bulbocastanum, S. demissum, S. phureja and S. stoloniferum, respectively. Molecular marker assays based on sequence-specific primers revealed that 36 of the 52 pre-breeding clones carried either 1, 2, 3 or 4 resistance genes introgressed from these wild Solanum species. Results indicate that these resistance genes were retained over generations of breeding. Although highly resistant to late blight, 16 pre-breeding clones did not carry any of these resistance genes. Resistance in the gene pool may, thus, be based not only on individual resistance genes but also on QTL effects. Results help to better understand both inheritance and expression of late blight resistance of this unique gene pool and may be used for breeding programmes.

Seeds kept in long-term storage are essential for maintaining genetic resources of crops and other plant materials in seed banks and national germplasm systems. But seeds undergo chemical changes over time as part of the ageing process that result in reduced germination rates and seedling normalcy. For example, oilseed crops such as peanuts are particularly vulnerable to oxidation and rancidification due to their high oil content. To test the effect of storage time on seed oil in peanuts, we grew different accessions and harvested fresh seeds to compare the oil composition of new seeds with seeds aged in storage for varying lengths of time. Out of the nine fatty acids detected and measured by gas chromatography, five including oleic, gadoleic, behenic, lignoceric and cerotic acids differed significantly between new and old seeds. Additionally, old seeds accumulated up to four oxidation products together averaging about 1% of the total oil composition. The concentration of these oxidation products was positively correlated with the age of the seeds, increasing linearly up to more than 6% of the total in the oldest seeds. The presence and concentration of oxidation products measured using simple chromatography techniques can be used as an initial indication of quality and viability in older seed inventories stored in germplasm repositories.