We now understand that many different types of DNA structural polymorphisms contribute to functional diversity of plant genomes, including single nucleotide polymorphisms, insertions of retrotransposons and DNA transposons, including Helitrons carrying pseudogenes, and other types of insertion–deletion polymorphisms, many of which may contribute to the phenotype by affecting gene expression through a variety of mechanisms including those involving non-coding RNAs. These polymorphisms can now be probed with tools such as array comparative genomic hybridization and, most comprehensively, genomic sequencing. Rapid developments in next generation sequencing will soon make genomic sequencing of germplasm collections a reality. This will help eliminate an important difficulty in the estimation of genetic relationships between accessions caused by ascertainment bias. Also, it has now become obvious that epigenetic differences, such as cytosine methylation, also contribute to the heritable phenotype, although detailed understanding of their transgenerational stability in crop species is lacking. The degree of linkage disequilibrium of epialleles with DNA sequence polymorphisms has important implications to the analysis of genetic diversity. Epigenetic marks in complete linkage disequilibrium (LD) with DNA polymorphisms do not add additional diversity information. However, epialleles in partial or low LD with DNA sequence alleles constitute another layer of genetic information that should not be neglected in germplasm analysis, especially if they exhibit transgenerational stability.

In this study, 123 almond (Prunus dulcis (Mill.) D.A. Webb) trees identified among traditional orchards in the Algarve region and 53 trees of the local field collection managed by the regional office of the Portuguese Ministry of Agriculture (DRAALG) were assessed using isozyme, inter-single sequence repeat and simple sequence repeat or microsatellite techniques for the evaluation of genetic diversity and genetic relatedness and identification of new accessions for the field collection. The isozyme analysis allowed the distribution of the 176 plants into 13 different classes of enzyme similarity, while the use of DNA markers increased the distribution of the analysed trees among 140 discriminating DNA patterns. Multiple cases of homonymy and synonymy were identified in the local germplasm. Some traditional varieties, such as Lourencinha, appeared to be relatively homogeneous, while other local denominations, e.g. Galamba, included diverse genotypes. Of the 13 commercial varieties analysed in this study, 11 assembled in one major cluster clearly differentiated from the majority of the local genotypes. These results reinforced the perception that the Algarve traditional germplasm constitutes an important repository of genetic diversity, eventually carrying alleles of high agricultural interest such as the recently identified Phomopsis resistance in the traditional variety Barrinho Grado.

Knowledge of linkage disequilibrium (LD) patterns is considered a prerequisite for effective association mapping studies. However, no LD analysis in the Argentine public temperate maize collection has been reported to date. In this study, a panel of 111 temperate maize inbreds genotyped at 74 single sequence repeats (SSRs) loci was used to assess LD, genetic diversity and population structure to evaluate the suitability of the panel for association mapping. Mini-core sets were also designed for in-depth phenotyping and allele mining purposes. The panel consisted of: (1) locally developed orange flint germplasm; (2) temperate inbred lines with Iowa Stiff Stalk Synthetic background; and (3) eight historic flint lines, some of them from the Cuarentín race. As a result, four subpopulations were defined. Joint analysis of population structure and combining ability allowed identifying two main heterotic patterns. High molecular diversity, a low extent of LD and a high ratio of linked to unlinked SSR loci pairs in significant LD were detected indicating the suitability of the entire collection for association mapping. The fact that the LD extent in the mini-core sets was similar to that observed in the entire collection and that only a small percentage of allelic richness was reduced suggests that these mini-core sets are suitable to capture diversity, exploit phenotypic variance and discover useful variants representative of the entire collection.

Identification of sugarcane hybrids is difficult when selections are based solely on morphological traits. Our objective was to combine morphological traits and molecular marker analysis to select F1 hybrids from two separate crosses between Djatiroto, a clone of Saccharum spontaneum, and elite sugarcane clones, LCP 85-384 (Cross 97-3144) and CP 62-258 (Cross 97-3146). The maternal inflorescences of Djatiroto were emasculated by submersion in a circulating 45°C hot-water tank for 10 min to minimize self-fertilization. Cross 97-3144 produced 4.7 g of seeds with 338 viable seeds per gram and Cross 97-3146 produced 2.4 g of seeds with 166 viable seeds per gram. After greenhouse germination, 96 progeny from each cross were evaluated in a field plot. Evaluations were conducted on the ratoon crops for stalk diameter (mm), juice Brix (percentage soluble solids), and a randomly amplified polymorphic DNA (RAPD) marker OPA-11-366 that was reproducibly amplified through PCR from the elite clones, but not the maternal S. spontaneum clone. Fifty progeny (52.1%) from Cross 97-3144 and 36 progeny (37.5%) from Cross 97-3146 inherited the RAPD marker. Five putative F1 progeny were selected from each cross, namely US 99-43, US 99-44, US 99-45, US 99-46 and US 99-47 from Cross 97-3144, and US 99-48, US 99-49, US 99-50, US 99-51 and US 99-52 from Cross 97-3146, based on their relatively larger stalk diameter, higher Brix and inheritance of the RAPD marker. The hybrid nature of these selected progeny was verified with sugarcane microsatellite markers. This is the first report of the development of Saccharum hybrids with the cytoplasm of S. spontaneum for breeding purpose through a combination of conventional and molecular breeding approaches. Availability of these F1 hybrids could enhance the genetic diversity of Saccharum germplasm and has enabled sugarcane geneticists and breeders to explore the possible contribution of S. spontaneum cytoplasm in the development of new sugarcane cultivars.

Nicaragua is located in the Mesoamerican diversity centre for common beans (Phaseolus vulgaris L.). Yet, there is insufficient knowledge of the molecular characteristics of most common bean landraces in Nicaragua. The objectives of the present study were to investigate the genetic diversity of common bean landraces and to identify promising sources of genetic variation for breeding purposes. Two cultivars and 40 landraces never studied before were selected from a collection based on the geographic origin, seed coloration and information provided by farmers. Fourteen microsatellite markers distributed in different linkage groups were analysed. The study revealed that there is a high genetic diversity (mean 8.9 alleles per locus). The populations showed structuring into three groups where seed weight had a strong relationship with population clustering. At least 20% of the populations hold promising allelic variation and potential for good market acceptance that could be maximized in breeding programmes. Additionally, four markers revealed a high correlation with seed length, width and weight, suggesting that marker-assisted selection for these yield-determinant traits could be straightforward. Nonetheless, more marker–trait associations should be addressed in order to enforce this practice.

The starchy corms of taro (Colocasia esculenta) are consumed throughout the tropics and are essential for food security in many developing countries. Taro corms are increasingly processed into fries, chips, flours or flakes in urban areas, and varieties with attractive corm flesh colours are now needed. The identification of flavonoids in taro corms would add value to this crop. The present study developed a high-performance thin layer chromatography (HPTLC) protocol for the high-throughput screening of flavonoids in taro germplasm. Overall, 350 different accessions were analysed including 259 varieties from Vanuatu, one from Vietnam, eight from Thailand, eight from the Philippines, six from Malaysia, two from Japan and 18 from Indonesia. Forty-eight breeding lines (hybrids) including 21 from Vanuatu, 21 from Samoa, four from Hawaii and two from Papua New Guinea were also analysed. Ten flavones, namely luteolin-6-C-hexoside-8-C-pentoside, schaftoside, luteolin-3′,7-di-O-glucoside, homoorientin, isovitexin, orientin, luteolin-4′-O-glucoside, luteolin-7-O-glucoside, vitexin and apigenin-7-O-glucoside, were successfully detected in the corm and are responsible for the attractive yellow colour of the flesh and fibres. Quantitatively, luteolin-6-C-hexoside-8-C-pentoside and schaftoside were the most important of all the detected flavonoids. However, only 18% of the varieties analysed presented these two compounds and 80% presented poor flavonoid composition. No geographical structure of the variation was detected and the most flavone-rich varieties originated from Vanuatu, Thailand, the Philippines, Malaysia and Indonesia. The compounds detected in the present study were significantly and positively correlated, suggesting that there is potential for fast improvement through controlled crosses, subsequent evaluation of full-sib progenies and cloning of elite individuals.

UK agriculture is undergoing significant change with reduced subsidies for food production, increasing consumer demands for food safety and traceability, and environmental concerns including climate and demographic change. The International Treaty on Plant Genetic Resources for Food and Agriculture adopted by the United Nations Food and Agriculture Organisation supports the use of genetic resources for research and breeding. Mining genetic resources for useful genetic variation is perceived as a major benefit of genebanks. However, utilization by breeders may be constrained by poor characterization of genetic resources, a widening gap between improved and unimproved material, and the disruption of well- adapted genotypes during introgression. Breeders working with grasses and forage legumes for sustainable agriculture are fortunate in the wealth of genetic variation available both within the primary species of interest and among related species. New DNA technologies allow more targeted approaches to the use of these genetic resources. Possibilities for gene transfer between related species using conventional techniques expand the available gene pools while potential use of genetic transformation extend these even further.

Belgian agriculture could decrease its heavy dependency on imported protein crops by a local production of soybean. Unfortunately, soybean production is hampered by Belgium's short and cold growing season. We evaluated 409 varieties, breeding lines and genebank accessions planted at two planting dates in a row-plot experiment to explore the genotypes that are suitable for growing in Belgium. The current MG000 varieties may require additional crossings with very early-maturing genotypes to guarantee an optimal and safe harvest. Within such crossings, care must be taken to maintain the indeterminate or semi-determinate growth habit. Vegetative development was negatively correlated with flowering date and maturity date, but positively correlated with cold tolerance. Seed quality was mainly affected by mould infection (associated with strong lodging and late maturity) and mottling caused by soybean mosaic virus. Planting 3 weeks earlier resulted in 8 d earlier flowering and 7 d earlier maturing, without significant losses in seed yield per plant. The results of this row-plot experiment hold promise to select for genotypes adapted to the Belgian conditions.

Drought is a devastating factor for crop production worldwide. Therefore, an experiment was conducted to study genetics for some agro-physiological traits in cotton under drought stress. The 13 parental cotton genotypes along with their 30 F1 hybrids were planted under normal and drought conditions. The mean performance of the genotypes was assessed through principal component and heat map analyses. The principal component analyses revealed 53.99 and 53.15% in the first two principal components of variability for normal and drought conditions, respectively. Heat map analysis revealed that three cotton genotypes i.e. FH-207 × NS-131, FH-207 × KZ-191 and S-15 × AA-703 attained higher values for all the traits except for canopy temperature under drought conditions. These crosses may proliferate to further filial generations to identify transgressive segregates for drought tolerance. The heritable differences of F̅1 and mid-parent showed dominance and non-additive gene action under drought conditions. Heritable differences between F̅1 and P̅1 showed over dominance and partial dominance under drought conditions. Heritable differences between F̅1 and P̅2 indicated negative over dominance and partial dominance for all traits under drought conditions. Proline contents and the bolls per plant showed high heritability and genetic advance through additive gene action. Therefore, these two traits can be used as a means of selection in future breeding programmes of drought tolerance.

The bell-type pepper cultivar Golden California Wonder, a source of resistance to southern blight, was crossed with the susceptible cultivar Sweet Banana. The F1, F2 and backcross progenies of this cross and the parental lines were evaluated in an inoculated field study for their reactions to Sclerotium rolfsii Sacc. A categorical rating system was used to rate plants for severity of wilting and severity of stem-lesion development. The plants within all three non-segregating populations (the resistant parent, the susceptible parent and the F1) displayed a range of reactions to S. rolfsii. Variable reactions to S. rolfsii among homogeneous pepper populations were expected because this phenomenon is well documented in the literature and we had observed similar responses in field trials conducted over multiple years. The high level of variation for reactions to S. rolfsii exhibited by the parental and F1 hybrid populations and the categorical system of rating individual plants placed severe limitations on the effective use of any quantitative type of analysis. Accordingly, a weighting procedure was used to correct the F2 and backcross populations based on frequencies of apparent mis-classifications in the parental and F1 populations. Examination of the comparative frequency distributions of the parental and progeny populations and examination of the weighted segregation data suggest that the southern blight resistance in ‘Golden California Wonder’ is conditioned by a single recessive gene. The level of resistance conditioned by this reputed recessive gene appears high enough to recommend it for use in pepper breeding programmes.

Addressing the impact of heat stress during flowering and grain filling is critical to sustaining wheat productivity to meet a steadily increasing demand from a rapidly growing world population. Crop wild progenitor species of wheat possess a wealth of genetic diversity for several biotic and abiotic stresses, and morphological traits and can serve as valuable donors. The transfer of useful variation from the diploid progenitor, Aegilops tauschii, to hexaploid wheat can be done through the generation of synthetic hexaploid wheat (SHW). The present study targeted the identification of potential primary SHWs to introduce new genetic variability for heat stress tolerance. Selected SHWs were screened for different yield-associated traits along with three advanced breeding lines and durum parents as checks for assessing terminal heat stress tolerance under timely and late sown conditions for two consecutive seasons. Heat tolerance index based on the number of productive tillers and thousand grain weight indicated that three synthetics, syn9809 (64.32, 78.80), syn14128 (50.30, 78.28) and syn14135 (58.16, 76.03), were able to endure terminal heat stress better than other SHWs as well as checks. One of these synthetics, syn14128, recorded a minimum reduction in thousand kernel weight (21%), chlorophyll content (2.56%), grain width (1.07%) despite minimum grain-filling duration (36.15 d) and has been selected as a potential candidate for introducing the terminal heat stress tolerance in wheat breeding programmes. Breeding efforts using these candidate donors will help develop lines with a higher potential to express the desired heat stress-tolerant phenotype under field conditions.

In many regions of the world, the cultivation of landraces is still common, in particular in centres of crop diversity. Significant effort has been put into ex situ conservation of landraces but limited data exist on the changes in genetic diversity that occur over time in farmers’ fields. We assessed temporal changes in barley landrace diversity in Jordan using seed samples collected in 1981 and 2012 from the same locations. We did not observe significant changes in the amount of genetic diversity, but samples collected in 2012 were more homogenous and less locally distinct. In two sites, we observed replacement of the old material. We observed a change in phenotype, and phenotypes were found to be more homogeneous among sites in 2012. Climate changed significantly over the study period, becoming hotter and dryer, but we did not identify any correlation between the changes in climate and genetic and phenotypic variations. While the amount of genetic diversity in terms of allelic richness and number of multi-locus genotypes has been maintained, local distinctiveness among landrace barley populations in Jordan was reduced.

Occurrence of drought under rainfed conditions is the foremost factor responsible for yield reduction in soybean. Developing soybean cultivars with an inherent ability to withstand drought would immensely benefit the soybean production in rainfed areas. In the present study, F2 derived mapping populations were developed by crossing drought tolerant (PK 1180, SL 46) and susceptible (UPSL 298, PK 1169) genotypes to investigate the inheritance of seedling survival drought mechanisms and to identify simple-sequence repeat (SSR) markers associated with them, using bulked segregant analysis. Parents as well as a F2 derived mapping population were screened for drought tolerance based on seedling survivability under controlled conditions. Segregation analysis of F2 population derived from a cross between PK 1180 × UPSL 298 was previously shown to have a 3:1 tolerant to susceptible ratio and a probability of 0.61 at a χ2(3:1) value of 0.258. This was confirmed in another F2 population derived from a cross between PK 1169 × SL 46 with a χ2(3:1) value of 0.145 obtained at a probability of 0.70. One SSR marker Satt277 showed polymorphism between contracting bulks (tolerant and susceptible) out of 50 polymorphic markers identified during parental polymorphism. Single marker analysis suggested that the marker, Satt277 is linked to seedling survival drought tolerance and is located on chromosome linkage group C2 (chr 6) with a map distance of 3.40 cM. The tolerant genotypes identified could be used as a donor in soybean improvement programs. The marker identified can be used in marker-assisted selection while screening large collection of germplasm.

Cultivated soybeans [Glycinemax (L.) Merr.] have various flower colours such as dark purple, purple, light purple, pink, magenta, near white and white. About one-third of the soybean accessions in the United States Department of Agriculture – Germplasm Resource Information Network (USDA-GRIN) Soybean Germplasm Collections have white flowers and are the second dominant accessions after the purple-flowered accessions. Earlier studies have shown that the w1 recessive allele of the W1 gene encoding flavonoid 3′,5′-hydroxylase produces white flowers. In the present study, we aimed to understand why the white-flowered accessions have become abundant among the cultivated soybeans and what their genetic and regional origin is. For this purpose, 99 landraces with white flowers and 39 landraces with purple flowers from eight Asian countries and Russia were analysed with regard to the nucleotide sequences of the W1 locus. We not only found that the w1 alleles of the 99 white-flowered landraces were identical to those of the white-flowered Williams 82, but also found that these w1 alleles displayed no polymorphism at all. By carrying out a phylogenetic analysis, we were able to identify a group with W1 alleles from which the w1 allele might have diverged.

Nagaland is one of the eight states in the north-eastern region of India, where a considerable diversity exists in cultivated rice. Recent exploration in this tribal-dominated state has resulted in a collection of 130 rice accessions growing under diverse agroecological conditions. The agromorphological characterization data of 124 rice landraces revealed a significant variability in plant architecture and grain morphological and quality traits. Multivariate analyses including principal component analysis (PCA) and cluster analysis were performed to assess the patterns of morphological variation. The PCA extracted 12 components, which explained 75.4% of the total variation for 38 quantitative and qualitative traits. The cluster analysis grouped 124 rice landraces into five clusters, and the number of landraces in each cluster ranged from 1 to 59. The correlations among the traits are discussed, which will be useful in considering traits for genetic improvement in grain yield and quality. The landraces have been conserved in the national genebank for further utilization.

Tomato is a pivotal vegetable crop worldwide concerning human nutrition, economy and in service to biotechnology. Tomato leaf curl virus (ToLCV) is a begomovirus transmitted through the whitefly (Bemisia tabaci) and is responsible for severe losses in tomato production. In this context, the current investigation was carried out to determine heterotic combiners with high yield, resistance to ToLCV and mode of gene action for economically important traits. For this, 11 prescreened inbred lines were crossed in a half diallel fashion to generate 55 F1 hybrids. The 55 crosses with 11 parents and commercial checks were evaluated for different horticultural traits and resistance to ToLCV. The molecular validation with SCAR markers TG0302 and SCAR1 confirmed the presence of ToLCV-resistant genes in parents and their crosses. The hybrid IIHR-2902 × IIHR-2852 showed the presence of both Ty-2 and Ty-3 alleles in the homozygous state. The estimation of σSCA2 and σGCA2 was significant. It also indicated that the genetic control of target traits was under additive and non-additive gene effects. The values of σA/D2 along with σGCA2/σSCA2 found to be less than unity indicates the preponderance of non-additive gene action in the expression of the studied traits except for percent disease incidence. The parental line IIHR-2919 was the best combiner for fruit and yield traits. The cross combinations IIHR-2913 × IIHR-2898 exhibited significantly higher economic heterosis for yield along with the presence of Ty-2 and Ty-3 genes. The study paves the way for breeding high yielding and ToLCV-resistant hybrids in tomato.

Grasspea (Lathyrus sativus L.) is an annual, herbaceous, drought-resistant legume and staple crop in Asian and African countries. Little is known about the nature and the amount of genetic diversity present in existing grasspea seed collections, yet this information is pivotal for future breeding programmes, such as those striving to reduce high neurotoxin levels present in seeds. Here we report on the level of genetic diversity within a world-wide collection of L. sativus, determined by isozymatic analysis. Although grasspea is generally considered a predominantly self-pollinating species, we found that the population genetic structure of these accessions showed a considerable outcrossing rate of 36%. The identification of a mixed mating system in L. sativus has significant implications for collecting and multiplying genetic resources for conservation and for future breeding purposes. In addition, we determined the genetic closeness of grasspea accessions from different geographical regions around the world. While we noticed an allelic richness in this species that was conserved across the regions, we did not find any evidence of high genetic identity between accessions, even when originating from the same geographical location. Instead, we found that greater genetic variability existed at the intra-regional level than at the inter-regional level.

Out-crossing between genetically modified herbicide-tolerant (GMHT) and non-GM rape cultivars was studied using GMHT source field plots of approximately 0.8 ha. Levels of cross-pollination between adjacent fully fertile rape varieties declined rapidly with increasing distance from the interface between plots. A varietal association with low levels of male sterility showed higher levels of out-crossing than other varieties. Out-crossing data were used to compare negative exponential and inverse power-law models for their fit to describe the observed relationship between cross-pollination and distance from source. Results showed that the inverse power-law model provided a better fit of the data.

This study was conducted to characterize new plant type (NPT) traits among 650 genetically diverse rice genotypes of tropical japonica and indica and to establish an initial core set for NPT traits. Analysis of variance revealed highly significant differences among the genotypes for all the traits assessed except flag length and width and leaf angles. Dendrogram categorized the genotypes into five distinct duration groups. Genotypes viz., Pumphamah, IRGC5097, IRGC37015, IRGC43741, IRGC50448, IRGC53089, IRGC39111, IRGC18021, Haorei Machang, IRGC44069, IRGC8269, Thangmoi, IRGC33130 and IRGC29772 were identified as possessing strong culm. Long panicles with a length of more than 35 cm were found in IRGC8269, IRGC9147, IRGC14694, IRGC19642, IRGC27435, IRGC39111, IRGC31051, IRGC26011and IRGC25892. Ideal leaf angle of NPT genotypes of 5°, 10° and 20° of flag leaf, 1st and 2nd leaves was not found in any genotype but with a combination of 5°, 10° and 10° was observed in IRGC63102 and IRGC66644. NPT flag leaf length and width of 50 and 2 cm, respectively, was seen in ‘Kemenya Kepeu’ and ‘IRGC29772’. High grain number of more than 350 was observed in IRGC53089, IRGC31063 and Azhoghi. A total of 72 genotypes were found with a combination of one or more ideal plant type traits of which, hierarchical cluster analysis based on genetic distances selected 32 as NPT core set. This core set will serve as an ideal genetic resource for breeding programs aimed at NPT development.

Niger harbours a wealth of diversity of Africa's rice (Oryza glaberrima) and its related wild species. We therefore engaged in a collecting mission of rice species across growing regions and agrosystems in Niger. A total of 270 rice accessions were assembled, including 177 Asian rice (O. sativa) cultivars, 67 African rice landraces (O.glaberrima), 25 O. barthii and one O.longistaminata. We found most accessions (80.7%) along the Niger River and its tributary the Dallol Maouri. Many of the accessions, except those belonging to the wild O. barthii initially found around the Lake Chad region, were also collected along the Niger River. Drought, insects, birds, rice yellow mottle virus and bacterial blight were noted as major constraints on rice production. Accession naming by farmers was consistent within regions but seldom across regions. Based on the recorded agro-morphological traits, the germplasm was classified into three clusters: (1) O. longistaminata with floating African landraces and late-maturing floating Asian rice; (2) lowland O.barthii and African landraces; (3) a mixture of irrigated Asian rice with lowland accessions of both cultivated species. The phenotypic variability of the germplasm collection, as measured by the Shannon–Weaver diversity index, was relatively high (H′ = 0.69), with accessions in the irrigated agrosystem being less diverse than those in the traditional agrosystems. There was no significant difference in the magnitude of diversity between the main eco-geographical zones and between the clusters. However, some traits contributing the most to this diversity were different. This study suggested a substantial germplasm exchange between regions in Niger.