Genetic diversity and relationship of 92 bread wheat (Triticum aestivum L.) genotypes from India and exotic collections were examined using simple sequence repeat (SSR) markers and phenotypic traits to identify new sources of diversity that could accelerate the development of improved wheat varieties better suited to meet the challenges posed by heat stress in India. Genetic diversity assessed by using 82 SSR markers was compared with diversity evaluated using five physiological and six agronomic traits under the heat stress condition. A total of 248 alleles were detected, with a range of two to eight alleles per locus. The average polymorphic information content value was 0.37, with a range of 0.04 (cfd9) to 0.68 (wmc339). The heat susceptibility index was determined for grain yield per spike, and the genotypes were grouped into four categories. Two dendrograms that were constructed based on phenotypic and molecular analysis using UPGMA (unweighted pair group method with arithmetic mean) were found to be topologically different. Genotypes characterized as highly heat tolerant were distributed among all the SSR-based cluster groups. This implies that the genetic basis of heat stress tolerance in these genotypes is different, thereby enabling wheat breeders to combine these diverse sources of genetic variability to improve heat tolerance in their breeding programmes.

Genebanks are important suppliers of genetic resources to the genomics research community, and access to the resulting information will allow traditional genebank users to better select genetic material for their breeding and scientific programmes. We discuss herein a possible solution to interconnect these data automatically based on semantic web technology.

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.

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.

The red algal genus Porphyra is sister to the genus Pyropia, the single most valuable marine crop in the Orient. We developed microsatellite loci for the red alga Porphyra umbilicalis, a widespread species in the Northern Atlantic. Enriched DNA libraries were constructed and 68 loci were screened for amplification and polymorphism. Seven polymorphic microsatellite markers were isolated using 44 individuals collected from four natural populations. The number of alleles per locus ranged from two to 12. Null alleles were detected in three loci. Among the markers reported, we tested also cross-amplification with two other Porphyra spp. These polymorphic microsatellite markers should be useful for investigating population genetic structure of P. umbilicalis in the North East Atlantic.

Low-temperature stress is an important factor affecting the growth and development of rice in temperate and high-elevation areas. In this study, 220 germplasm lines were used for screening of tolerant genotypes, validation of molecular markers and identification of robust markers for seedling-stage chilling stress tolerance to be used in marker-assisted breeding (MAS) programme. The temperature regimes imposed in the growth chamber simulated cold-stress injuries at the seedling stages of the germplasm lines. The genotypes were classified into six classes: those having susceptible genotypes were classified into moderately and highly susceptible types, while tolerant types into moderately tolerant, tolerant, highly tolerant and very highly tolerant classes. Genotypes namely Langma, Umleng-1 and Geetanjali showed survival up to 25 d, which were better than the positive check Kalinga-III surviving up to 20 d under chilling stress. Ten simple sequence repeat (SSR) markers were tested for differentiation of genotypes. Individual use of SSR markers like RM284, RM286, RM85, RM341 and RM5746 can be applied in MAS breeding including combination use of non-pair markers like RM284, RM239 and RM85, which was even better than the combined use of RM284 and RM85. However, combined use of all ten markers can most effectively be employed for cold tolerance through MAS breeding.

Castor is a prime industrial crop belonging to a monotypic genus and its genetic improvement depends on creating desired variability in the primary gene pool. This study reports the development of tetraploid castor plants through colchicine treatment. Seeds of three castor genotypes were soaked in aqueous solutions of colchicine with variable concentrations, and the LD50 value was determined. Of 1010 treated field-raised plants, three were identified as potential polyploids based on increases in a guard cell size and reductions in the number of stomata. The putative polyploid plants were selfed and the progeny were subjected to meiotic analysis. All the progeny were found to be tetraploid. The pairing of chromosomes was abnormal with univalent to octavalent configurations during meiosis-I, but the later parts of meiosis were normal. Seasonal variations in pollen fertility indicated the possible role of temperature-sensitive male sterility in causing the sterility in tetraploid plants. The tetraploid plants were phenotypically comparable with their diploid counterparts, but produced substantially bigger seeds. Thus, these tetraploid plants are valuable resources for basic and applied research in castor.

Extensive studies of genetic diversity and population structure important for conservation of wild sorghum are yet lacking in Ethiopia, the centre of origin for cultivated sorghum. To assess both genetic diversity and the probability of gene flow between wild and cultivated types, collections of wild Sorghum bicolor were made from regions in Ethiopia where wild and cultivated sorghum coexist. Morphological data were recorded in situ for both quantitative and qualitative characters from 30 populations in five diverse geographical regions and eight agroecologies. High phenotypic diversity was observed among the wild and weedy sorghum populations. The overall standardized Shannon–Weaver diversity index (H′), computed from the frequencies of all qualitative traits, ranged from 0.47 to 0.98 with an average value of 0.76. Moreover, warm semi-arid lowland (SA2) agroecologies, which contain Tigray populations, supported the highest diversity for these traits. Subspecies verticilliflorum and drummondii (the two major subspecies of wild S. bicolor) were observed in diverse habitats throughout northern and central Ethiopia. In some areas, weedy types showed domestication traits including the absence of awns and reduced seed shattering. The existence of morphologically intermediate forms indicates that gene flow between cultivated and wild forms has likely occurred. Deployment of transgenic crop sorghum, therefore, would pose a distinct risk for transgene movement into wild Ethiopian populations.

Rhubarb includes approximately 60 species in the genus Rheum. It has been utilized for thousands of years for medicinal purposes, but only recently identified for its culinary use. In the mid 1700s, edible petioles were discovered on seedlings from rhubarb species. Hundreds of cultivars have since been identified for a wide range of uses from tarts to wine. Unfortunately, propagation by seed and irregular naming has resulted in a plethora of similarly named cultivars and multitude of phenotypes. Fifteen morphological characters were evaluated to differentiate rhubarb cultivars in the USDA, ARS Rheum collection in Palmer, Alaska. Two years of morphological data, focusing on horticultural characteristics indicated variation between the years. To improve cultivar resolution, the results suggest using 1 year's data instead of combining data from different years. The mean °Brix observed was 3.8, with a range from 2.2 to 6.1. Flesh colour and basal skin colour were poorly correlated (R2 = 0.462); overall skin colour was more red at the base than in the middle of the petiole. Rhubarb character categories, in particular petiole number and petiole base thickness, need to be modified to better anticipate the range of expected values, and thereby contribute improved reproducibility and reliability to separate cultivars based on morphological characters.

Cultivated pigeonpea has a narrow genetic base. Wild relatives play an important role in the efforts to broaden its genetic base. In this report, we present a successful wide-cross between the cultivated pigeonpea and Cajanus lanceolatus, a wild relative from the secondary gene pool, native to Australia, with desirable traits such as frost and drought resistance. A range of F1 progeny were obtained and the resultant F1 hybrid plants set mature pods and seeds. The hybrids had intermediate morphology, sharing the traits of both the parents. All the F1 hybrids flowered profusely. Some of the hybrids were completely male sterile and some were partially fertile with pollen fertility ranging from 35 to 50 %. Meiotic analysis of the fertile F1 hybrids revealed a high degree of meiotic chromosome pairing between the two parental genomes. Meiotic analysis of the sterile F1 hybrids revealed that the breakdown of microsporogenesis occurred at the post-meiotic stage after the formation of tetrads. Fertile plants formed regular bivalents with normal disjunction, except for occasional asynchrony at meiotic II division.

Spelt (Triticum spelta L.) is hulled wheat which was widely cultivated in Spain until the first half of the 20th century and is still cultivated in Asturias (northern Spain). Much of the variability of this species has been preserved, but little evaluation has been carried out. We describe the characterization of some of these spelt lines for several quantitative traits, including plant height and awnedness.

In this study, 15 morphological traits and 16 microsatellite markers were used to assess the morphological variability and structure of 68 (33 local and 35 foreign) almond accessions (Prunus dulcis (Mill.) D.A. Webb). Extensive phenotypic diversity was found among the accessions, and results indicated a high variation in leaf and fruit traits. Varieties were separated into two distinct groups with a similarity coefficient of 0.761. Morphological traits were categorized by principal component analysis into five components, which explained 86.5% of the total variation. Nut and kernel traits were dominant in the two first components, accounting for 49.4% of the variation. By contrast, leaf traits accounted for 18.4% of the variation in the third component. The results of molecular analysis (Bayesian clustering approach) did not correspond to morphological groupings, and the second approach was more discriminate. The combination of both approaches revealed the richness among the collected plant materials, which will be useful in breeding programmes of this species.

Groundnut is one of the most important oilseed crops in the world. Bacterial wilt, caused by Ralstonia solanacearum E. F. Smith, is one of the major biotic constraints to groundnut production particularly in South-East Asia and East Africa. Several sources of resistance to bacterial wilt have been identified through field screening of groundnut germplasm. The aim of the present study was to quantify the genetic diversity among selected bacterial wilt-resistant lines, in comparison with the levels of variation observable within the cultivated A. hypogaea gene pool. Thirty-two SSR markers were used to assess the degree of molecular polymorphism between 46 selected genotypes revealing 107 alleles, of which 101 (99.4%) were polymorphic with gene diversity scores ranging from 0.103 to 0.669, averaging 0.386. Cluster and multidimensional scaling analysis revealed two distinct groups within the germplasm broadly corresponding to the two subspecies (hypogaea and fastigiata) of A. hypogaea. However, accessions of varieties peruviana and aequatoriana grouped together with the varieties from subsp. hypogaea, rather than grouping with the other varieties of subsp. fastigiata. Analysis of molecular variance (AMOVA) revealed that 15% of the total observed variation was accounted for by disease response groups. This analysis will be useful in the selection of parental genotypes for mapping populations and breeding programmes attempting to broaden the genetic base of future groundnut cultivars. In particular, this opens up significant opportunities for the development of intraspecific mapping populations that will be highly relevant to modern groundnut breeding programmes.

Germplasm molecular and phenotypic characterization is instrumental to its utilization and to genetic variability incorporation into rice breeding programmes. The diversity within 192 Japanese rice accessions was analysed for 22 agro-morphological traits and 24 single sequence repeat markers. A total of 181 alleles were detected, 38 of which were exclusive. The number of alleles/marker ranged from 2 to 16, with an average of 7.54 alleles/locus and the He value ranged from 0.01 to 0.82, with an average of 0.46. The accessions showed diversity at molecular and phenotypic level and few showed also good agronomic performance. Tocher's method applied on a total-dissimilarity matrix was used to determine cluster formation of 13 diversity groups. Most of the accessions (81%) were clustered within a group, whereas eight accessions (Kyuushuu, Eika Ine, Ishiwari Mochi, Col/Fukui/1965, Ookuma Nishiki, Suzume Shirazu, Iwate Ryoon and Toga) did not cluster with other accessions.

A natural population of Vriesea friburgensis var. paludosa was genetically and demographically characterized. Four selected enzymatic systems were used. In total, 10 allozymic loci were analysed. The proportion of polymorphic loci was 70% and the number of alleles per locus was 2.3· The mean observed and expected heterozygosities were 0.234 and 0.226, respectively. An excess of heterozygotes was revealed by the value of the fixation index (—0.035). These indices showed the presence of high levels of genetic diversity in the population studied. A demographic survey revealed almost six times more vegetative than sexually reproductive plants. Reproductive plants were found only in clusters. The genetic diversity exhibited by this population, associated with vegetative as well as sexual propagation, resulting in clusters or colonies, would allow the employment of a sustainable management strategy for species conservation as well as its exploitation as an ornamental.

Pepper (Capsicum sp.) is important in human diets in many parts of the world and a major source of several antioxidants, including carotenoids, ascorbic acid, tocopherols and phenolics. More information on genetic diversity within Capsicum for antioxidant (AO) content and antioxidant activity (AOA) could contribute to improved human health. We evaluated 46 Capsicum accessions from AVRDC—the World Vegetable Center Capsicum core collection for content of nine AO (five carotenoids, ascorbic acid, tocopherols α and γ, and total phenolics) and two AOA assays for 2 years in south Taiwan. Ample genetic diversity exists within C. annuum to increase AO content. Based on dry weight values, non-pungent C. annuum entries as a group were significantly greater than pungent entries for contents of β-cryptoxanthin (36%), ascorbic acid (65%), total phenolics (36%) and α-tocopherol (11%). Group means of the brown-fruited entries exceeded the means of red-fruited entries for capsanthin (34%), zeaxanthin (37%), lutein (36%), β-cryptoxanthin (71%), β-carotene (82%), ascorbic acid (19%) and α-tocopherol (40%). Red-fruited C. annuum entries ‘Verdano Poblano’ and ‘Guajillo Ancho’ from Mexico ranked among the entries highest for all carotenoids, ascorbic acid and α-tocopherol. The inhibition of lipid peroxidation (ILP) assay could be adopted for AOA characterization or selection because of high variation among entries and consistent entry performance over years. ILP was positively correlated with phenolics (r=0.72**) and ascorbic acid (r=0.58**) contents. Significant positive correlations were detected between most carotenoids as well as a significant positive correlation between ascorbic acid and total phenolics contents (r=0.78**).

Genetic variation in wild soybean (Glycine soja Sieb. and Zucc.) is a valuable resource for crop improvement efforts. Soybean is believed to have originated from China, Korea, and Japan, but little is known about the diversity or evolution of Korean wild soybean. Therefore, in this study, we evaluated the genetic diversity and population structure of 733 G. soja accessions collected in Korea using 21 simple sequence repeat (SSR) markers. The SSR loci produced 539 alleles (25.7 per locus) with a mean genetic diversity of 0.882 in these accessions. Rare alleles, those with a frequency of less than 5%, represented 75% of the total number. This collection was divided into two populations based on the principal coordinate analysis. Accessions from population 1 were distributed throughout the country, whereas most of the accessions from population 2 were distributed on the western side of the Taebaek and Sobaek mountains. The Korean G. soja collection evaluated in this study should provide useful background information for allele mining approach and breeding programmes to introgress alleles into the cultivated soybean (G. max (L). Merr.) from wild soybean.

Seedling emergence is the preliminary factor defining wheat adaptability and stability under salt stress. This study was led to assess the salinity tolerance amongst 226 synthetic hexaploid wheats (SHWs) evaluated against two check cultivars, the tolerant ‘S-24’ and the susceptible ‘PBW-343’ at three sodium chloride treatments (0, 100 and 200 mM). Highly significant and positive correlation was observed between germination % and germination index (r = 0.85), and between seedling height and weight (r = 0.85). All four traits across three treatments were transformed into the salt tolerance trait index and salt tolerance index (STI). STI had significant positive correlation with all four parameters indicating reliability of this index for ranking the tolerance levels. STI-based 20 best performing genotypes were known as being promising candidates for wheat breeding. Local tolerant check was amongst the top three tolerant accessions. Two SHWs, AUS30288 {Croc_1/Aegilops squarrosa (466)} and AUS34444 {Ceta/Ae. squarrosa (872)} outperformed S-24 with STI of 61.8 and 55.7, respectively. SHW with same durum parents were included in tolerant and susceptible categories indicating that tolerance is contributed by the Ae. squarrosa syn. tauschii parent of SHWs. In conclusion, this baseline study revealed that continuous variation in the seedling emergence traits under salt stress is a conduit towards implementing genome-wide association studies. Likewise, new diversity has implications in development of salt tolerance germplasm after genetic dissection permitting unique Ae. squarrosa accessional diversity validation to target SHW donors for breeding.

Ninety-eight high-yielding recombinant inbred lines (RILs) of WAB638-1/PRIMAVERA rice were evaluated with the parents under reproductive stage drought stress. The study aimed at characterizing flowering time response under drought stress and consequently classifying the genetic resources for efficient use in breeding programmes. Two field trials were conducted during the 2016 and 2017 dry seasons using the randomized complete block design with two replications. In 2016, 12 RILs were evaluated with the parents for the rooting attributes under drought stress and well-watered treatments. Analysis of variance revealed a significant (P < 0.05) variation among the genotypes for the traits evaluated. Drought stress reduced most of the characters in this study, including grain yield. However, the inbred lines exhibited considerable tolerance to drought stress as indicated by yield-related stress indexes, including stress susceptibility and drought tolerance indexes. Delayed flowering (FD) was recorded in 75 genotypes (including WAB638-1), while 25 genotypes (including PRIMAVERA) had no delay under drought stress compared to the control. The genotypes were grouped into flowering delay (D) genotypes (FD > 1 d) and no delay (N) genotypes (FD < 1 d), which significantly differ (P ⩽ 0.05) for numbers of days to 50% flowering. The flowering delay genotypes may be suitable for intermittent drought, while genotypes with little or no delay may be selected for terminal drought conditions. There was a significant correlation (r > 0.5) between the root length and number of days to 50% flowering. The study indicated that root parameters, such as the root length, may contribute to the drought adaptation mechanisms of the RILs.

Jatropha curcas L. is a potential bioenergy crop but has a lack of improved cultivars with high yields and oil content. Therefore, increasing our understanding of J. curcas germplasm is important for designing breeding strategies. This study was performed to investigate the genetic diversity and population structure of Indonesian J. curcas populations from six different islands. To construct a reference, we de novo assembled the scaffolds (N50 = 355.5 kb) using 182 Gb Illumina HiSeq sequencing data from Thai J. curcas variety Chai Nat. Genetic diversity analysis among 52 Indonesian J. curcas accessions was conducted based on yield traits and single nucleotide polymorphism (SNP) markers detected by mapping genotyping-by-sequencing reads from Indonesian population to Chai Nat scaffolds. Strong variation in yield traits was detected among accessions. Using J. integerrima as an outgroup, 13,916 SNPs were detected. Among J. curcas accessions, including accessions from other countries (Thailand, the Philippines and China), 856 SNPs were detected, but only 297 SNPs were detected among Indonesian J. curcas populations, representing low genetic diversity. Through phylogenetic and structural analysis, the populations were clustered into two major groups. Group one consists of populations from Bangka and Sulawesi in the northern part of Indonesia, which are located at a distance of 1572.59 km. Group two contains populations from islands in the southern part: Java, Lombok-Sumbawa, Flores and Timor. These results indicate that introduction of diverse J. curcas germplasms is necessary for the improvement of the genetic variation in the Indonesian collections.