Tomato (Solanum lycopersicum) fruit quality and yield are highly dependent on adequate uptake of nutrients. Potassium, magnesium and calcium are essential elements that influence fruit quality traits such as colour, uniformity of ripening, hollow fruit, fruit shape, firmness and acidity. Sodium is not an essential element for tomato and can detrimentally compete with the absorption of potassium and calcium. Daily intakes of potassium, magnesium and calcium in human diets are typically below healthful levels, while sodium intake is often excessive. The objective of this study was to compare 52 diverse commercially important varieties of tomato for concentrations of potassium, magnesium, calcium and sodium in fruits. The tomatoes were produced in replicated plots in Geneva, NY in 2010 and 2011. Multiple fruits per plot were harvested vine-ripe, homogenized and assayed for cations. Analysis of variance showed significant differences among the 52 varieties for all four traits, i.e. cation concentrations (df = 51, P < 0.0001–0.0034) and no significant differences between years for any trait (df = 1, P = 0.3432–0.6770). Factor analysis showed a strong interrelationship between potassium and magnesium that was independent of calcium and sodium. Potassium and magnesium were highly significantly correlated with each other (r = 0.64, P < 0.0001). No other correlations between pairs of traits were observed. Results supported a genetic basis for potassium, magnesium, calcium and sodium concentrations that was consistent across environments (i.e. years). Results can contribute to the development of cultivars with favourable cation profiles in terms of human health and fruit quality.

A world-wide coconut germplasm collection (79 genotypes) was analyzed for genetic diversity and population structure based on 48 simple sequence repeat (SSR) loci. The genotypes displayed moderately high amount of genetic diversity, which was strongly structured according to geographical origins. Number of SSR alleles ranged from 2 to 7 with an average of 4.1 per locus. Gene diversity (expected heterozygosity) estimates ranged from 0.162 to 0.811 with a mean of 0.573. Polymorphism information content values ranged from 0.149 to 0.785 with an average of 0.522. Hierarchical clustering analysis grouped the genotypes into two major clusters with two sub-groups in each, which corresponded with the geographic origins. The first cluster comprised of ‘Tall’ genotypes originated from Indo-Atlantic and South Asia regions. The second cluster comprised mostly of ‘Dwarf’ genotypes and some Tall genotypes which originated from Indo-Pacific and South-East Asia regions. Model-based clustering by STRUCTURE analysis also supported the presence of clear genetic structuring in the collection with two major populations (K = 2) and four sub-populations (K = 4). The proportion of SSR locus-pairs in linkage disequilibrium was low (2.4%). Association analysis in a subset of 44 genotypes detected a single SSR locus, CnCir73 (chromosome 1) putatively associated with fruit yield component traits, which corresponded with a previously mapped quantitative trait locus in coconut.

Direct sowing of rice in a flooded paddy field is a beneficial cultivation practice for water use and labour efficiency, compared to the transplanted cultivation. However, a drastic reduction in seedling emergence under flooded paddy fields is a serious constraint especially when the seeds fell at deeper soil layers. Suitable rice germplasm for the direct sowing in flooded paddy fields could ensure the success of this cultivation practice. Instead of laborious field-based screening systems, a pot-based screening method was adopted for simplicity and efficient evaluation of seedling emergence of a subset of world rice germplasm (n = 75) at different sowing depths. As a result, two rice genotypes, ‘Vary Futsi’ (landrace from Madagascar, non-glutinous, subspecies Indica) and ‘Dahonggu’ (landrace from China, non-glutinous, subspecies Indica), with consistently better seedling emergence were identified from a wide range of rice germplasm. These genotypes could serve as excellent parents for the breeding program in developing new rice cultivars with the improved seedling emergence in flooded paddy fields. There were no significant differences in the seedling emergence rate in flooded paddy conditions among the groups from various agro-geographical regions.

Sensitivity of alfalfa to acidity and aluminium (Al) toxicity in soil is the major limiting factor in broadening of its growing area. Due to lack of Al tolerance in primary alfalfa germplasm, there is a need for transfer of genes for Al tolerance from other Medicago germplasm. One of the identified sources of Al tolerance is M. sativa ssp. caerulea accession PI 464724, which was used as a female parent in our study. The objectives of this study were: (i) obtaining the tetraploid offspring from 2x–4x M. sativa ssp. caerulea – M. sativa ssp. sativa spontaneous crosses, and (ii) development of a breeding strategy for Al/acid tolerance in alfalfa, using M. sativa ssp. caerulea as a source of Al tolerance. Out of eleven fully developed plants, five were morphologically similar to M. sativa ssp. caerulae, while six plants were similar to M. sativa ssp. sativa. All tested plants were fertile, with the pollen viability ranging from 21.45 to 97.09% and the average number of ovules per plant from 8.80 to 12.29. Eleven SSR primer pairs confirmed the hybrid nature of M. sativa ssp. caerulae × M. sativa ssp. sativa offspring. Both the Cluster Analysis and the Principal Coordinates Analysis separated plants in the caerulae type from plants in the sativa type, with one exception. Strategies based on conventional and molecular marker breeding efforts could lead towards development of tolerant alfalfa cultivars and successful crop production on acidic, Al-contaminated soils.

Triticum monococcum ssp. monococcum has useful traits for bread wheat improvement. The synthesis of Triticum turgidum–T. monococcum amphiploids is an essential step for transferring genes from T. monococcum into bread wheat. In this study, 264 wide hybridization combinations were done by crossing 60 T. turgidum lines belonging to five subspecies with 83 T. monococcum accessions. Without embryo rescue and hormone treatment, from the 10,810 florets pollinated, 1983 seeds were obtained, with a mean crossability of 18.34% (range 0–89.29%). Many hybrid seeds (90.73%, 923/1017) could germinate and produce plants. A total of 56 new amphiploids (AABBAmAm) were produced by colchicine treatment of T. turgidum × T. monococcum F1 hybrids. The chromosome constitution of amphiploids was characterized by fluorescence in situ hybridization using oligonucleotides probes with different chromosome and sub-chromosome specificities. Sodium dodecyl sulphate polyacrylamide gel electrophoresis analysis indicated that the Glu-A1m-b, Glu-A1m-c, Glu-A1m-d and Glu-A1m-h proteins of T. monococcum were expressed in some amphiploids. Despite resistance reduction in several cases, 45 out of 56 amphiploids exhibited resistance to the current predominant Chinese stripe rust races at both the seedling and adult plant stage. These novel amphiploids provide new germplasm for the potential improvement of bread wheat quality and stripe rust resistance.

To promote the utilization of West and Central African (WCA) genetic resources of pearl millet [Pennisetum glaucum (L.) R. Br.], this study aimed at agro-morphological characterization of selected accessions from the pearl millet reference collection, established by the Generation Challenge Program and the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). A total of 81 accessions were included, comprising 78 landraces originating from 13, predominantly WCA countries and three improved cultivars. All 81 accessions were evaluated together with 18 checks for resistance to the parasitic weed Striga hermonthica (Del.) Benth. in an artificially infested field at one location in Niger. Determined by available seed quantity, 74 accessions were characterized together with seven checks in the rainy season 2009 in field trials under low-input and fertilized conditions in Nigeria, Niger and Mali, respectively. Wide ranges were observed for various traits. Several accessions were identified as sources for specific traits of interest, i.e. long panicles, high-grain density, earliness, Striga resistance and stable yielding across environments. The observed yield inferiority of all Genebank accessions compared with checks may indicate lost adaptation or inbreeding depression due to an insufficient effective population size during multiplication. A principal component analysis revealed an immense diversity but also strong admixture among the tested accessions, i.e. there were no clearly distinct groups. The seed of all genotypes is available from ICRISAT. The online availability of the characterization data is expected to facilitate efficient use of these pearl millet accessions by breeding programmes in WCA and worldwide.

Castor is an industrially important oilseed crop. Vascular wilt caused by the soil borne fungus Fusarium oxysporum f. sp. ricini is a serious disease of castor. Use of resistant cultivars is the only viable option for management of wilt disease problem in castor production. Excellent sources of resistance to wilt have been found in castor germplasm. In this study, a set of four castor inbred lines (48–1, CI-1, AP42 and AP48) was characterized for inheritance of resistance to wilt by studying segregating populations generated by crossing these inbred lines with eight different susceptible genotypes. An artificial screening method (sick pot) with a new scoring system (days to wilt) was used for evaluation of plant progenies for reaction to the pathogen infection. The reaction of F1s indicated that the nature of resistance in 48–1, CI-1 and AP48 is recessive whereas it was dominant in AP42. Inheritance results from eight F2 populations showed that resistance to wilt is conferred by a single locus in one population and at least two loci, which interact in complementary way, in other seven populations. Different modes of inheritance were also observed when the same resistant source was crossed with different susceptible parents, indicating the possible role of genetic backgrounds in determining resistance. Overall, the results suggested that Mendelian resistance to wilt is predominant in the castor genotypes, which can be exploited for breeding cultivars. Particularly, AP42 with dominant nature of resistance will be of great interest to hybrid breeding.

The Greek lentil landrace ‘Eglouvis’ is cultivated continuously at the Lefkada island for more than 400 years. It has great taste, high nutritional value and high market price. In the present study, we used morphological and molecular markers to estimate genetic diversity within the landrace. Morphological analysis was based on characteristics of the seed. Molecular analysis was performed using simple sequence repeat (SSR) molecular markers in a high-resolution melting (HRM) approach. ‘Samos’ and ‘Demetra’, two of the most widely cultivated commercial lentil varieties in Greece, were used for comparisons. Morphological analysis was performed with 584 seeds randomly selected from a lot. Analysis of seed dimensions and colour distributed the samples in different categories and highlighted the phenotypic variability in ‘Eglouvis’ lentil seeds. Genetic variability was estimated from 91 individual DNA samples with 11 SSR markers using HRM analysis. Genotyping was based upon the shape of the melting curves and the difference plots; all polymerase chain reaction products were also run on agarose gels. Genetic distances of individuals and principal coordinates analysis suggested that ‘Eglouvis’ landrace has a unique genetic background that significantly differs from ‘Samos’ and ‘Demetra’ and no overlapping could be detected. Genetic variability within the ‘Eglouvis’ landrace can be considered in targeted breeding programs as a significant phytogenetic resource of lentils in Greece.

Stripe rust, caused by Puccinia striiformis f.sp. tritici (Pst), is an important disease of winter wheat in Central Asia. Stripe rust races contain diverse virulence/avirulence patterns and change rapidly. Therefore the objectives of this research were to: (i) examine current pathotype variability of Pst races collected from Kazakhstan and Uzbekistan and (ii) evaluate stripe rust resistance in leading cultivars and advanced breeding lines targeted to those regions. Analyses of 152 Pst samples showed diverse virulence patterns with avirulence to Yr5, Yr10 and Yr15 being common. Most of identified races are among the rare. Analysis of a mixed Pst population showed 10 distinct pathotypes with frequencies ranged from 1.2 to 8.7%. The virulence patterns ranged from least ‘31–1.5’ and X-1.5 to highly virulent ‘86 + E16’. Seedling evaluation of 62 genotypes using the 10 pathotypes showed variations for resistance. Bunyodkor and Barhayot showed resistance to all pathotypes. Five Yr genes were postulated. Yr1 in KR12-5075, and Yr6 in KR11-03 and KR12-5003 were postulated. Yr5 combined with Yr10 and Yr15 genes were determined in Bunyodkor. The wheat genotypes also showed different levels of resistance in adult plant stage under field conditions. Twenty genotypes showed <20% severity in both Kazakhstan and Uzbekistan. The disease severity on several genotypes differed in this countries, suggesting different Pst populations in the two countries. Several resistant genotypes were identified, which should be further evaluated for release as new varieties or used in breeding programmes. Two resistant lines from this study were identified as new varieties in Georgia and Uzbekistan.

Development of winter wheat (Triticum aestivum) synthetics started at CIMMYT-Mexico in 2004, when winter durum wheat (Triticum turgidum) germplasm from Ukraine and Romania was crossed with Aegilops tauschii accessions from the Caspian Sea region. Chromosomes were doubled after pollination and embryo rescue, but chromosome number and cytological validation was not performed. F2 populations were grown in Mexico and were shipped to Turkey in 2008. During 2009–2015, these populations were subjected to rigorous pedigree selection under dry, cold, disease-affected environments of the Central Anatolian Plateau. The wide segregation and partial sterility observed in 2009 gradually decreased and, by 2016, most of the F8 single spike progenies demonstrated good fertility and agronomic performance. Since 2013, lines have been selected from synthetic populations and evaluated at multiple sites. Superior lines were characterized for resistance to leaf, stripe and stem rust, plant height, and reaction to common bunt and soil-borne pathogens. Thousand kernel weight of many lines exceeded 50 g, compared with the check varieties that barely reached 40 g. Threshability of synthetic lines varied from 0 to 95%, demonstrating genetic variation for this important domestication trait. Screening against Hessian fly, sunny pest and Russian wheat aphid identified several resistant genotypes. Both durum and Aegilops parents affected synthetic wheat traits. Several studies are underway to reveal the genetic diversity of synthetic lines and the basis of resistance to diseases and insects. This synthetic germplasm represents a new winter bread wheat parental pool. It is available upon request to interested breeding/research programmes.

The dwarfing wheat (Triticum aestivum L.) breeding has promoted a dramatic increase in yields. Since the utilized dwarfing genes in wheat are very limited, identification of novel dwarfing genes is necessary for improving the genetic diversity of wheat. In this study, more than 300 dwarfing wheat lines from induced mutation were screened by kompetitive allele-specific PCR and gibberellin (GA) treatment. The 17.49% of Rht-D1b and 1.37% of Rht-B1b dwarfing mutants were identified in this mutant group. Additionally, Rht-D1b mutants showed more effective in reduction of plant height and higher 1000-grain weight comparing with that of Rht-B1b mutants. By combing with comparison of yield components and expression profile of GA biosynthetic genes with wild-type, the GA-responsive mutant dm15 without directly involvement in GA metabolism, significantly increased 1000-grain weight but no change of other yield components in two locations of field experiments. Meanwhile, another elite mutant dm11 with change of GA biosynthetic genes expression was also identified. These mutants will be promising candidates for dwarfing wheat breeding.

Here we review the potential of ILB 938 (IG 12132 – doi: 10.18730/60FD2), a unique faba bean accession originating from the Andean region of Colombia and Ecuador, maintained at ICARDA – International Center for Agricultural Research in the Dry Areas, with resistance to multiple biotic and abiotic stresses and carrying some useful morphological markers. It has been used as a donor of leaf-related drought adaptation traits and chocolate spot (Botrytis fabae) resistance genes in faba bean breeding programmes worldwide. From generated populations of recombinant inbred lines, quantitative traits loci associated with these useful traits have been mapped. Other markers, such as a lack of stipule-spot pigmentation and clinging pod wall, show the presence of unusual changes in biochemical pathways that may have economic value in the future.

Drought stress ‘particularly at seedling stage’ causes morpho-physiological differences in wheat which are crucial for its survival and adaptability. In the present study, 209 recombinant inbred lines (RILs) from synthetic wheat (W7984)× ‘Opata’ (also known as SynOpRIL) population were investigated under well-watered and water-limited conditions to identify quantitative trait loci (QTL) for morphological traits at seedling stage. Analysis of variance revealed significant differences (P < 0.01) among RILs, and water treatments for all traits with moderate to high broad sense heritability. Pearson's coefficient of correlation revealed positive correlation among all traits except dry root weight that showed poor correlation with fresh shoot weight (FSW) under water-limited conditions. A high-density linkage map was constructed with 2639 genotyping-by-sequencing markers and covering 5047 cM with an average marker density of 2 markers/cM. Composite interval mapping identified 16 QTL distributed over nine chromosomes, of which six were identified under well-watered and 10 in water-limited conditions. These QTL explained from 4 to 59% of the phenotypic variance. Six QTL were identified on chromosome 7B; three for shoot length under water-limited conditions (QSL.nust-7B) at 64, 104 and 221 cM, two for fresh root weight (QFRW.nust-7B) at 124 and 128 cM, and one for root length (QRL.nust-7B) at 122 cM positions. QFSW.nust-7B appeared to be the most significant QTL explaining 59% of the phenotypic variance and also associated with FSW at well-watered conditions. These QTL could serve as target regions for candidate gene discovery and marker-assisted selection in wheat breeding.

Shortawn foxtail (Alopecurus aequalis Sobol.) is an invasive and highly troublesome weed species originating from North America that has become widespread across China. Since its proliferation seriously threatens crop production worldwide, understanding its genetic diversity is critical for developing a forecasting system for integrated pest management plans. To accelerate the application of molecular markers in A. aequalis, this study aimed to develop a set of expressed sequence tag-simple sequence repeat (SSR) markers using previous high-throughput sequencing data. In this study, a total of 1411 SSR loci were identified from 95,479 unigenes. Tri-nucleotide repeat motifs were the most abundant type with a frequency of 66.27%, followed by di- (24.95%) and tetra-nucleotide (8.78%). Among the loci, 584 primer pairs were successfully designed for marker development. Subsequently, a subset of 36 primer pairs was randomly selected and synthesized, of which 12 (33.33%) pairs successfully revealed abundant allelic polymorphism. Additionally, to investigate their utility, the genotypes of 160 individuals from 20 natural populations representing diverse wild genotypes of A. aequalis were analysed by using these 12 polymorphic markers. These novel SSR markers developed here are reliable and useful for genetic analysis on this invasive plant and will greatly enrich its genetic resource.

ICAR-Directorate of Cashew Research is the nodal agency for conducting cashew research and manages the largest field gene bank in India. Cashew is a perennial tree and needs more land and other resources to maintain accessions. Conservation through seeds is not feasible because of cross-pollination. Tissue culture efforts to regenerate plants from mature explants are not successful. Therefore, efficient management of the filed gene bank particularly utilization requires designation of the core collection representing the spectrum of diversity present in the entire collection. In this study, a relatively new technique, the advanced M strategy with heuristic approach was deployed to develop the core collection. Sixty-eight morphometric characters of 478 accessions were subjected to analysis resulting in the core collection of 49 accessions. Further, another core collection of same number was constituted by K-Means clustering to compare the efficiency of two approaches. The validation parameters like mean difference, variance difference, coincidence rate, variable rate and class coverage among others were employed for comparative analysis. The results of these parameters revealed that the core collection designated by heuristic approach was better able to efficiently represent and retain the diversity of the entire collection compared with the core identified by clustering approach. Future conservation and breeding efforts will be focused on establishing a separate block in the field gene bank having 49 accessions of cashew core collection.

We developed a multiplex PCR DNA marker for quick and easy identification of the AAGG-genome timopheevii lineage, including Triticum timopheevii, Triticum araraticum and hexaploid Triticum zhukovskyi (AAAmAmGG), and the AABB-genome emmer wheat lineage, including Triticum durum, Triticum dicoccum and Triticum dicoccoides. Distinguishing between tetraploid AAGG- and AABB-genome wheat species based on morphology is known to be difficult. This multiplex PCR system is based on the simultaneous PCR amplification of two chloroplast regions, matK and rbcL. The matK region molecularly distinguishes the two lineages, whereas the rbcL region is a positive control amplicon. We also examined whether the simple sequence repeat is a fixed mutation within species, using genetic resources in the collection of KOMUGI, Kyoto University, which comprises accessioned species collected across diverse geographical areas. The multiplex PCR marker distinguished AAGG from AABB species with complete accuracy.

Cinnamomum camphora (Lauraceae) is a well-known multipurpose tree with aromatic oils, insect-repellent effects and ornamental value. In this study, a total of 74,289 simple sequence repeats (SSRs) were found in 56,124 unigenes, of which 14,225 unigenes contained more than one SSR locus. Among these SSR loci, the mono-nucleotide repeats were the most frequent, with a frequency of 61.14%, followed by 24.87% di-nucleotide repeats and 12.87% tri-nucleotide repeats. Twenty-one polymorphic SSR markers were developed and validated in 45 camphor trees. The 21 loci were further examined for cross-species transferability in other six related species. The novel genic-SSR markers will not only benefit genetic diversity analysis and wild resources conservation of C. camphora, but also contribute to exploring the further evolutionary history and genetic differentiation pattern of Cinnamomum.

Aegilops tauschii, the D genome donor of wheat, is an invaluable source of genetic variability, which can be utilized for broadening the wheat gene pool. Linked leaf rust resistance and non-glaucousness genes transferred from Ae. tauschii to cultivated wheat variety WH542 were mapped in the present study. Genetic analysis in an F2 population from a BC3 plant derived from the cross Triticum durum cv. PBW114/Ae. tauschii acc. pau14195//4*T. aestivum cv. WH542 revealed monogenic dominant inheritance for both the traits. The leaf rust resistance and the non-glaucousness gene were tentatively named LrT and IwT, respectively. Leaf rust resistance gene exhibited all stage resistance. SSR markers Xbarc124, Xgdm5, Xgdm35, Xcfd51 and EST-derived markers Xcau96 and Xte6 on chromosome 2DS were linked with both genes. Chromosomal assignments of the genes were confirmed by testing linked SSR markers on Chinese Spring nulli-tetrasomics lines. SSR markers Xcau96 (1.6 cM) and Xbarc124 (0.6 cM) flanked LrT and Xgdm35 (4.1 cM) and Xte6 (2.5 cM) flanked non-glaucousness gene. LrT and IwT showed a recombination distance of 3.4 cM. Hence, IwT can be used as an easy to score morphological marker of LrT during its transfer to other glaucous backgrounds.

David Bond and Jean Picard, two leaders of European legume breeding, died within a few months of each other. On the basis of their agronomic and genetic training, they both met the challenge of breeding faba bean, a protein-rich species that had received little attention from breeders before the 1950s (Picard, 1953; Bond 1957). Both made great strides at modernizing their chosen crop by developing and applying new ideas and techniques, as well as generating new methods and genetic materials.

Bamboo shoots and leaves are valuable food sources for both humans and livestock. The USDA-ARS NPGS (National Plant Germplasm System) collections hold 93 bamboo species in 20 genera. Total leaf protein, amino acid composition and elemental content for these important genetic resources had never been quantified. Lack of nutrition information hinders germplasm utilization. The above-mentioned nutritional traits were evaluated from these 93 species in this study. Leaf protein content among bamboo species ranged from 8.12 to 16.33% with an average of 12.84%. This average was higher than 9.0% observed for switchgrass leaves, but considerably lower than 32.48% in cassava leaves. For 18 quantified amino acids, there was more than a twofold variation among the samples evaluated. For 12 quantified mineral elements, there was significant variability from the low end (4.2-fold, 2.27–9.52 mg/g calcium; 4.4-fold, 56.17–246.43 µg/g sodium) to the high end (61.5-fold, 17.67–1087.0 µg/g manganese; 40.8-fold, 42.0–1713.5 µg/g aluminium). Due to their variability in leaf nutritive value, bamboo species should be carefully chosen when they are used as a feedstock. The results from this study will be useful for the bamboo industry, producers and consumers.