Rice yield improvement is required to support increasing global rice demand. However, the limited genetic diversity within the cultivated rice gene pool may be a major obstacle. Australian wild rice which has been largely genetically isolated from cultivated rice might be a new source of genetic variation for use in improving rice production. The physical properties of Oryza australiensis and of the two perennial Australian Wild rice taxa-belonging to the A genome wild rice were evaluated. Seeds collected from rice in the wild were generally smaller than those from domesticated rice. The wild rice A genome collections were classified as extra-long paddy rice with grains that were long or medium, while O. australiensis was categorized as long paddy rice with a short grain. However, these wild rices were slender compared with domesticated rice. The grain colour of these wild rices varied from light red brown to dark brown compared with domesticated rice which is brighter, with less redness and more yellowness than the wild rice. The physical characteristics of the grains of the Australian wild rice indicate that these rice grains may be successfully processed using current rice processing techniques and may be a useful novel food especially in the coloured rice market.

The north-western Himalaya is one of the rich repositories of wheat genetic resources because of the preponderance of locally developed traditional crop varieties owing to high agro-climatic heterogeneity and local socio-cultural diversity. In the present study, 100 wheat landraces of this diversity rich region were evaluated for variability in physical parameters of seed to understand the basis of resistance against rice weevil, Sitophilus oryzae. The evaluation was based on the parameter of growth index (GI) of S. oryzae in different landraces. GI was correlated with different quantitative physical seed parameters, viz. hardness, length, width, length × width, test weight and qualitative parameter seed colour were studied to work out if these were related to resistance/susceptibility. Based on the parameter of GI, the six landraces viz. IC266831, IC266872, IC393109, IC392578, IC444217 and IC589276 were identified as resistant. Correlation coefficients between GI of S. oryzae and physical parameters of wheat landraces indicated that GI had significant positive relation with length × width (r = +0.573) and test weight (r = +0.549) indicated that small seeds confer resistance to S. oryzae. Also significant negative relation (r = −0.457) with GI of S. oryzae and seed hardness, indicated that hard seeds were relatively more resistant to S. oryzae.

The recent introduction of Illumina single nucleotide polymorphism (SNP) arrays is an important step towards comprehensive genome-wide studies of genetic diversity in wheat. In this study, 90 cultivars of hexaploid spring wheat growing in Kazakhstan were genotyped using the high-density wheat 90 K Illumina SNP array. The analysis allowed the identification of 30,288 polymorphic SNPs. A subset of 3541 high-quality SNPs were used for a comparison of 690 wheat accessions representing landraces and varieties, including those from Asia, Australia, Canada, Europe, Kazakhstan, USA and other parts of the world. Phylogenetic analysis showed a clear separation of wheat cultivars according to their geographic origin. In the phylogenetic tree, accessions from Kazakhstan and the USA formed two neighbouring clusters with a common node, and they were distinct from accessions from other regions of the world, including Europe. The results provide important new insights into the genetic relationships between diverse wheat accessions.

Soybean is a leading oilseed crop in India, which contains about 40% of protein and 20% of oil. Core collection will accelerate the management and utilization of soybean genetic resources in breeding programmes. In the present study, eight agromorphological traits of 3443 soybean germplasm were analysed for the development of core collection using the principal component score (PCS) strategy and the power core method. The PCS strategy yielded core collection (CC1) of 576 accessions, which accounted for 16.72% of the entire collection (EC). The analysis based on the power core programme resulted in CC2 of 402 accessions, which accounted for 11.67% of the EC. Statistical analysis showed similar trends for the mean and range estimated in both core collections and EC. In addition, the variance, standard deviation and coefficient of variance were in general higher in core collections than in the EC. The correlations observed in the EC in general were preserved in core collections. A total of 311 and 137 unique accessions were found in CC1 and CC2 in addition to 265 accessions that were found to be common in both core collections. These 265 common accessions were the most diverse core sets, which accounted for 7.64% of the EC. We proposed to constitute an integrated core collection (ICC) by integrating both common and unique accessions. The ICC comprised 713 accessions, which accounted for about 20.62% of the EC. Statistical analysis indicated that the ICC captured maximum variation than CC1 and CC2. Therefore, the ICC can be extensively evaluated for a large number of economically important traits for the identification of desirable genotypes and for the development of mini core collection in soybean.

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.

Acetohydroxyacid synthase (AHAS) inhibiting herbicides have played a significant role in effective weed control in the cultivation of sunflower since their discovery. The development of sunflower lines and hybrids resistant to these herbicides made their post-emergence application possible. In this study, wild Helianthus species were screened phenotypically for imidazolinone (IMI) and sulfonylurea (SU) resistance by herbicide spray and for allelic variations at Ahasl1 (Ahas1 large subunit) locus using simple sequence repeat and single nucleotide polymorphism markers. Helianthus praecox accession 1823 plants showed promising resistance to three classes of SU-based herbicides and Helianthus nuttallii accession NUT05 plants remained green for a longer time after imazethapyr spray. A total of 50 accessions belonging to 21 wild Helianthus species of different ploidy levels were analysed for allelic variation along with some parents of commercial sunflower hybrids. None of the wild species showed the resistant allele (Ahasl1-1) similar to SCG101 (IMI-resistant line), although it is present in some of the parental lines of hybrids. However, the parental lines having Ahasl1-1-type allele failed to survive the field dose of imazethapyr spray. Inter-species and inter-accessional allelic variation could be observed among the species. PRA1823 and NUT05 showed repeat length variations at Ahasl1 locus. Sequencing of full length Ahasl1 gene from both these accessions did not reveal any resistance mutations in the protein sequences. The molecular basis of the phenotypes identified in this study could be explored further and utilized in breeding programmes for imparting herbicide resistance in cultivated hybrids across sunflower growing regions of the world.

Substantial variation in phenotypic traits and ISSR fingerprinting was observed among twenty populations of Achillea fragrantissima (Forssk.) Sch. Bip. in Egypt. Such variation was reflected in the clustering of the examined populations into two major groups: one representing populations in the mountainous area of South Sinai and the other comprising populations growing at low elevations in the middle of Sinai and the desert west of the Suez Canal from Suez in the east to Cairo in the west. Five populations in the eastern part of Sinai near Nuwieba and Taba on the Gulf of Aqaba were loosely assigned to the first group. The populations growing at high elevations in South Sinai, under lower temperature and higher humidity, were characterized by a higher number of total and polymorphic ISSR markers compared with other populations. Unique ISSR markers were more often observed in the fingerprinting of seven populations including five populations growing in the high mountains of Saint Catherine in South Sinai and two populations growing at low elevations but at Wadi Hof south-east of Cairo. Interestingly, unique bands were found in the populations that possessed traits associated with larger plant size and seed yield as well as better vigour. These are important criteria for the selection of A. fragrantissima populations for conservation and sustainable commercial use.

Cassava germplasm collection is important for the preservation of genetic variability, allowing the development of improved cultivars with desirable traits such as drought and disease tolerance, better starch quality and yield. Therefore, the assessment of diversity in cassava germplasm maintained by farmers is important for maintaining biodiversity and crop improvement. Herein, we report genetic diversity relationships of 52 farmer-preferred cassava landraces from the eastern zone of Tanzania based on morphological descriptors and single nucleotide polymorphisms (SNPs). Cluster analysis was performed for both morphological traits (genetic distance 1.18–0.15) and SNPs (genetic distance 0.078–0.002). The analysis revealed that there were a total of 17,393 variant positions, and that several of the SNPs were distributed across all the chromosomes. The abundance of SNP varied remarkably among the 18 cassava chromosomes, with chromosome 2 having the highest number of SNPs (1335) and chromosome 18 having the lowest number of SNPs (734). The power of SNPs in distinguishing morphologically similar landraces was shown. Both analyses did not group landraces according to geographical locations, suggesting that farmers were moving cassava germplasm to different areas. Their diversity was mainly due to adaptation and preferential selection by farmers. This further implied that within a geographical location, the cultivars were more diverse and there was no misnaming of cassava cultivars by farmers. The collection revealed a wide range of genetic diversity, and represented a valuable resource for trait improvement, allowing the capture of farmer-preferred traits in future cassava breeding programmes.

Durum wheat (Triticum durum) is predominantly grown as spring type and depending on the production area autumn or spring sowing is used. For the durum production in Austria and Germany, autumn sowing has several advantages, such as yield increase and stability, but this requires the selection for winter hardiness including a good frost tolerance. The aim of this study was to support breeding of winter durum and to facilitate genomic approaches by molecularly characterizing a panel of 170 diverse winter and 14 spring durum lines employing a genotyping-by-sequencing approach. We obtained an unprecedentedly high number of 30,611 polymorphic markers covering the entire genome. The principal coordinate analysis and the cluster analysis revealed the absence of a major population structure but a tendency of lines to group according to their country of origin. Linkage disequilibrium was found to decay within a short distance of approximately 2–5 cM and also showed variable patterns along chromosomes. In summary, our results can assist breeding of durum wheat and pave the way for genomic approaches towards knowledge-based winter durum breeding.

Population structure and linkage disequilibrium (LD) were investigated in a set of 395 bread wheat landraces including 154 spring, 193 winter, two facultative wheat and 46 unknown growth type collected from different geographical regions of Iran. A total of 53 microsatellite markers distributed in three genomes of wheat were assayed for polymorphism. The 312 polymorphic alleles were served to estimate population structure and analyse the genome-wide LD. The number of alleles ranged from 2 to 18 with an average of 5.89 alleles/locus. Mean of polymorphic information content was 0.6 with a range of 0.15–0.86 and gene diversity varied from 0.16 to 0.88 with an average of 0.64. The population of landraces was highly structured and based on distance-and model-based cluster analyses the 395 landraces were assigned into eight subpopulations: SG1–SG8. Population structure estimates based on simple sequence repeat (SSR) marker data were quantified in a Q matrix and used in calculation of LD between pair of markers. A low overall LD level found in 12–13% (166) of the SSR marker pairs showed significant pairwise LD in r2 ≥ 0.01 and P ≤ 0.001 and six pair showed r2 ≥ 0.05 with P ≤ 0.001. LD clearly decays within the genetic distance of 40–60 cM with r2 ~ 0.05. The results of this study should provide valuable information for future association mapping using this wheat collection.

It is known that genetic diversity is the most important factor in classical and modern plant breeding. The considerable increase in the number of transgenic crops reveals the value of new plant genetic resources. In this study, a set of 12 wheat progenitors were screened for tissue culture parameters such as callus induction, callus weight, regeneration capacity of callus and callus efficiency using mature embryos. Embryos were excised from imbibed seeds of the progenitors. The excised embryos were placed scutellum upwards in dishes containing 2 mg/l 2,4-dichlorophenoxyacetic acid (2,4-D) for callus induction. The developed calli and regenerated plants were maintained on 2,4-D free MS medium. When mature embryos of 12 wheat progenitors (Aegilops sp. and Triticum sp.) were compared, significant differences were detected in callus induction frequency, weight of callus, regeneration capacity and culture efficiency. A significant genotypic effect was observed on the culture responses. Of the 12 wheat progenitors tested, Aegilops umbellulata had the highest regeneration capacity of callus. Aegilops biuncialis created the most regenerable calli because of the highest callus induction and culture efficiency. In the experiment, callus induction was significantly correlated with callus weight (r= 0.820) and regeneration capacity (r= 0.955). Weight of callus was significantly correlated with regeneration capacity (r= 0.740), while there was no significant correlation between callus induction frequency and culture efficiency (r= 0.350). Our results showed that, generally, mature embryos of some Aegilops and Triticum species have a high regeneration capacity, and therefore, can be used as an effective explant source for the successful application of biotechnology in crop improvement.

Hybrid breeding relies on selection of genetically unrelated and complementary parents for key traits. The objective of this study was to examine genetic variation and identify unique sorghum genotypes using phenotypic and simple sequence repeat (SSR) markers and to determine their relationships with combining ability and heterosis for grain yield. A total of 32 landraces and four cytoplasmic male sterile (CMS) lines were phenotyped using 25 agro-morphological traits and genotyped with 30 polymorphic SSR markers. The landraces were crossed with four CMS lines using a line × tester mating design. The 128 hybrids, 36 parentals and four check varieties were field-evaluated using a 12 × 14 alpha lattice design with three replications. General combining ability (GCA), specific combining ability (SCA) and heterosis for grain yield were determined. Genetic distance estimates ranged from 0.39 to 0.60 and 0.50 to 0.79, based on phenotypic and SSR markers, respectively. Landraces 72572, 75454, 200654, 239175, 239208, 244735A and 242039B and CMS lines ICSA 743 and ICSA 756 displayed positive and significant GCA effects for grain yield. Based on the SCA effects of yield, lines were classified into three heterotic groups aligned to the different cytoplasmic systems of testers. Lines with high GCA effects rendered hybrids with highly significant SCA effects with high mid-parent heterosis (MPH) for grain yield. Both marker systems were effective in demarcating sorghum genotypes that provided desirable cross-combinations with high combining ability effects and MPH for grain yield. The selected genotypes are recommended as potential parents for sorghum hybrid breeding in moisture stress environments.

Amylose-free (waxy) maize has been a vegetable (cooked ears) and staple food in Southeast Asia for centuries, resulting in hundreds of landraces (LRs) across the region. The recessive waxy allele induces soft grains with preferred cooking and flavour properties. We hypothesized that eating preferences resulted in the additional selection for different starch properties, reflected in altered starch granule morphology or amylopectin structure. A total of 41 LRs were available as starting material that had been used by different ethnic groups in Vietnam and Thailand. Unluckily, some LR were not pure waxy, but we successfully regained the original pure waxy status for most. Twenty LR were chosen for analysis of starch traits according to their purity. Four different waxy mutations were identified, including two unknown alleles. This is a strong proof for parallel independent selection of waxy maize in the region. Starch granule morphology and size were similar among all LRs. Gelatinization properties differed only between waxy and wild-type LR, and all waxy LR were comparable to a commercial waxy hybrid. The fine structure of waxy amylopectin had fewer short chains compared with that in wild-type. So far, the differences observed in starch properties are likely associated exclusively with the waxy trait. Despite the strong selection for amylose-free starch, there was no evidence for additional region wide selection for other special starch properties in our collection. In conclusion, all analyses did not encourage further targeted research on allelic variation of other starch metabolism genes for future use in the food and feed industry.

The genebank at ICRISAT, India that serves as a world repository for sorghum germplasm conserves 39,234 accessions from 93 countries, including 6249 from seven South Asian countries: Afghanistan (6), Bangladesh (9), India (6101), the Maldives (10), Nepal (8), Pakistan (90) and Sri Lanka (25). A total of 5340 georeferenced accessions were used to identify gaps, and 5322 accessions that were characterized at ICRISAT were used to assess the diversity in the collection. Accessions of basic races varied widely than those of intermediate races for flowering in the postrainy season, plant height in both rainy and postrainy seasons, panicle exsertion, panicle length and width, seed size and 100 seed weight. Landraces from India were late flowering, tall and produced stout panicles and larger seeds. Landraces from Pakistan flowered early in both seasons and produced stout panicles and those from Sri Lanka were late flowering and tall in both seasons, produced more basal tillers and stout panicles. A total of 110 districts in 20 provinces of India, 13 districts in three provinces of Pakistan, three districts in Bangladesh and five districts in four provinces of Sri Lanka were identified as geographical gaps. Sorghum bicolor subsp. verticilliflorum, S. halepense and S. propinquum were identified as taxonomic gaps in the collection. Therefore, it is suggested to explore the districts identified as gaps to enrich the variability in the world collection of sorghum at ICRISAT.

Purple- and red-fleshed potato cultivars constitute a great source of phenolic compounds, which may promote human health. Since the characterization of potato germplasm is a key step during the breeding process, the classification of high anthocyanin-producing tetraploid genotypes may facilitate the incorporation of phenolic-related traits in a potato breeding programme. A set of 18 high anthocyanin-producing underutilized tetraploid cultivars, which have been previously classified in terms of phytochemical content, have been characterized by both microsatellite markers (simple sequence repeat, SSR) and morphological descriptors. A wide genetic variability was found using 11 highly discriminatory SSR markers. The collection also displayed a large amount of variation for most morphological traits. The neighbour-joining trees defined by SSR markers and morphological descriptors revealed genetic and phenotypic relatedness of the potato genotypes. Despite the complexity of tetrasomic inheritance, high anthocyanin-producing tetraploid cultivars should be considered for potato breeding since they are adapted to long-day conditions and do not present undesirable characteristics that are found in native accessions or landraces.

Bitter gourd (Momordica charantia L.) is an important market vegetable in the tropics. The objectives of this study were to (1) conduct a preliminary evaluation of genetic diversity in bitter gourd flesh (without seeds) for phytonutrient (carotenoid, ascorbic acid and tocopherol) contents with the aim to understand which phytonutrients might be increased through breeding, (2) assess the association between fruit traits and phytonutrient contents and (3) evaluate the effect of the fruit harvest stage on phytonutrient contents. A total of 17 diverse bitter gourd entries of various commercial market types were evaluated for fruit traits and phytonutrient contents for 2 years. Significant differences (P= 0.05) among the entries were detected for total carotenoids, total tocopherols, dry matter and fruit traits. Mean total carotenoid contents of the entries ranged from 10 to 1335 μg/100 g fresh weight in year 1 and 10 to 1185 μg/100 g fresh weight in year 2. Mean ascorbic acid contents were 69 and 61 mg/100 g fresh weight in year 1 and year 2, respectively. Total tocopherol contents among the entries ranged from 480 to 1345 and 445 to 2145 μg/100 g fresh weight in year 1 and year 2, respectively. Total carotenoid and ascorbic acid contents were highest at 12 days after fruit set (DAFS), but total tocopherol contents were highest from 14 to 20 DAFS. A 100 g portion of bitter gourd fruit can meet 190, 17 and 8% of the recommended daily allowances of vitamin C, vitamin E and vitamin A, respectively, for adults.

Transformations that farmers bring to their traditional farming systems and their impacts on the conservation and evolution of maize varieties over a 12-year period are investigated using a longitudinal analysis. Despite the increased introduction and supply of improved maize variety seeds in the Yucatan Peninsula, Mexico, over the last 12 years farmers continue to maintain a substantial amount of traditional maize variety diversity. Even with the increased availability of hybrid seeds, farmers in the community of Yaxcaba on average plant more than three quarters of their milpa fields to traditional maize varieties, with the latter one fourth predominately planted to a locally improved variety Nal Xoy, a farm cross of a traditional variety and an improved variety. We observed a significant reduction in yellow – x-Nuuk nal, a long-cycle traditional landrace, paralleled by an increase in short- and intermediate-cycle locally adapted improved maize varieties. We found great differences in the distribution of maize varieties by soil type, with modern varieties being targeted for the rarer, deeper and fine-grained soils, while traditional varieties predominate on the more prevalent stony and thin soils. Our results provide a picture in which most traditional maize varieties in Yaxcaba continue to be maintained by farmers, coexisting with locally adapted improved varieties on the same landscape, and allowing the continued evolution of maize populations.

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.

Niger (Guizotia abyssinica, L.) is a desirable oilseed crop for birdseed, especially for finches (Spinus spp.) because of its high ratio of unsaturated to saturated fatty acids and relatively high oil content. In 2012, phenotypic traits, seed oil and fatty acid content measurements were made on 14 plant introductions (PIs) from the United States Department of Agriculture germplasm collection. The PIs originated in Ethiopia (ten), India (three) and USA (one). The phenotypic traits analysed included seed/plant, branches/plant, capitula/plant1, average seed/capitulum and plant height. After initial assessments of the 14 PIs, three were selected for use as parents to produce two one-way and two two-way F1 crosses for the purpose of evaluating self-incompatibility (SI). Parent and F1 progeny seeds were planted in a greenhouse and transplanted to a field site at the East Tennessee Research and Education Center (2012, 2013 and 2014). Comparisons from 2012 showed seed oil of the 14 PIs ranging from 32.9 to 37.9% (PI 508076 (Ethiopia) and PI 509436 (India), respectively). Major fatty acids included stearic, palmitic, oleic and linoleic; with linoleic acid in highest amount. PI508079 (Ethiopia) had the best combination of seed yield, seed oil and linoleic acid content. Over 2013 and 2014, SI ranged from 91.1 to 100.0%. W6 18860 (USA) had the most self-compatibility, and the F1 plants generated from crosses between W6 18860 and other plants tended to be self-compatible when the former was used as a pollen recipient. The results obtained from this study should be useful for niger breeding and production purposes.

Heat stress greatly limits the productivity of wheat in many regions. Knowledge on the degree of genetic diversity of wheat varieties along with their selective traits will facilitate the development of high yielding, stress-tolerant wheat cultivar. The objective of this study were to determine genetic variation in morpho-physiological traits associated with heat tolerance in 30 diverse wheat genotypes and to examine genetic diversity and relationship among the genotypes varying heat tolerance using molecular markers. Phenotypic data of 15 traits were evaluated for heat tolerance under non-stress and stress conditions for two consecutive years. A positive and significant correlation among cell membrane stability, canopy temperature depression, biomass, susceptibility index and grain yield was shown. Genetic diversity assessed by 41 polymorphic simple sequence repeat (SSR) markers was compared with diversity evaluated for 15 phenotypic traits averaged over stress and non-stress field conditions. The mean polymorphic information content for SSR value was 0.38 with range of 0.12–0.75. Based on morpho-physiological traits and genotypic data, three groups were obtained based on their tolerance (HHT, MHT and LHT) levels. Analysis of molecular variance explained 91.7% of the total variation could be due to variance within the heat tolerance genotypes. Genetic diversity among HHT was higher than LHT genotypes and HHT genotypes were distributed among all cluster implied that genetic basis of heat tolerance in these genotypes was different thereby enabling the wheat breeders to combine these diverse sources of genetic variation to improve heat tolerance in wheat breeding programme.