Profiling and association mapping of grain metabolites in a subset of the core collection of Chinese rice germplasm (Oryza sativa L.)

In this study, metabolic profiles of a set of 48 rice germplasms from the Chinese core collection were obtained by gas chromatography and time-of-flight mass spectrometry (GC-TOF-MS). Forty-one metabolites were identified and relatively quantified according to the internal standard (IS). Wide ranges of variations for all metabolites were observed among rice accessions. The maximum/minimum ratios varied from 4.73 to 211.36. The metabolites were categorized into seven groups based on their chemical characteristics. Clustering analysis and a correlation network showed that most of the metabolites had variations among rice accessions in the same direction. Using 218 molecular markers, association mapping was conducted to identify the chromosomal loci influencing the concentrations of identified metabolites. Twenty markers were identified associating with the concentrations of 29 metabolites [-lg(P) > 3]. Allelic effects were investigated in detail in two markers (RM315 and RM541) as examples.     

Development of NIRS equations for food grain quality traits through exploitation of a core collection of cultivated sorghum

A sorghum core collection representing a wide range of genetic diversity and used in the framework of a sorghum breeding and genetics program was evaluated by near-infrared reflectance spectroscopy (NIRS) to predict food grain quality traits: amylose content (AM), protein content (PR), lipid content (LI), endosperm texture (ET), and hardness (HD). A total of 278 sorghum samples were scanned as whole and ground grain to develop calibration equations. Laboratory analyses were performed on NIRS sample subsets that preserved the core collection racial distribution. Principal component analysis performed on NIRS spectra evidenced a level of structure following known sorghum races, which underlined the importance of using a wide range of genetic diversity. Performances of calibration equations were evaluated by the coefficient of determination, bias, standard error of laboratory (SEL), and ratio of performance deviation (RPD). Ground grain spectra gave better calibration equations than whole grain. PR equation (RPD of 5.7) can be used for quality control. ET, LI, and HD equations (RPD of 2.9, 2.6, and 2.6, respectively) can be used for screening steps. Even with a small SEL in whole sample analysis, a RPD of 1.8 for AM confirmed that this variable is not easy to predict with NIRS.     

Establishment of sesame germplasm core collection in China

A sesame core collection containing 453 accessions was established by assessing genetic diversity of 4251 accessions collected in China. The accessions in the whole collection were grouped based on their origin, varietal and agro-ecological type. A computer program was used to cluster the data of 14 traits from the random small sample. Ward's method was chosen as the desirable method for clustering sesame germplasm resources. A set of technical methods for establishing core collection has been developed through determining the number of selected accessions based on the diversity distribution. The agronomic traits of the pre-selected core collection were investigated and tested in three ecological locations in China for two years. Among six qualitative traits, including plant type and flower color in a total of 5304 accessions, 97.85% was completely the same as the original data, and three quantitative traits, including growth period and plant height, were significantly and positively related with the original data. The representativeness assessment of the final core collection indicated that 35 phenotypes of 10 qualitative traits in the core collection were basically similar to those of the pre-selected core collection. Six feature values such as mean, standard deviation etc. of four quantitative traits including oil content and 1000-seed weight were close to those of the pre-selected core collection. The final core collection possessed a fair representativeness of the pre-selected core collection.     

Assembling a core collection from the flax world collection maintained by Plant Gene Resources of Canada

Between 1998 and 2008, numerous projects were conducted by the Canadian national genebank, Plant Gene Resources of Canada, for the regeneration, characterization and evaluation of the whole flax (Linum usitatissimum L.) germplasm collection. The whole collection comprised 3378 accessions and, according to the passport data, several of these were probably genetically very similar or even identical. Therefore, a subset of 381 accessions was selected that represented the diversity found in the whole collection. Sampling accessions from the whole collection was made using characterization and evaluation data and followed six different methods: (1) For seven qualitative characters, each unique combination of character expression was represented by three accessions; (2) for quantitative characters, a fixed number of accessions representing the lowest and highest observed values was included; (3) for stem fibre content, disease ratings, seed vigour and drought tolerance, a fixed number of accessions with desirable performance was included; (4) a subset of the 57 most distinct accessions based on RAPD markers was included; (5) a subset of 40 pure lines that were created based on extreme low and high values for 1000 seed weight, seed oil content and fatty acid profiles was included; (6) a subset of fibre flax cultivars of known relevance in European flax breeding and another subset of flax cultivars of known relevance for North American linseed breeding were included. The goal was to maximize the diversity available in a limited number of flax accessions by preserving the range of variation present in the whole collection, while improving evenness. The core collection was assembled in response to requests by flax breeders. This paper compares distribution parameters in the whole and core collections.     

An analysis of isozymic loci polymorphism in the core collection of the Polish Pisum genebank

The investigated material consisted of the core collection of the Polish Pisum gene bank at Wiatrowo and represented a described, monohybrid variation (type lines for characters/genes and their initial lines, tester lines with markers and lines from wild taxa, 266 accessions in total). A polymorphism in 18 isozymic loci was analyzed (Lap-1, Px-1, Aat-p, Aat-m, Aat-c, Pgm-c, Pgm-p, Gpi-c, Idh, Acp-1, Skdh, Est-1, Est-2, Est-3, Aldo, 6Pgd-p, 6Pgd-c, Dia-1). The practical outcome of the analysis was a selection of lines with a high number of fast or slow isozymic alleles, useful as tester lines with markers for chromosome mapping. A polymorphism was stated in all investigated loci with 2 to 4 alleles ranging from very fast, fast, slow to very slow. Fast and slow alleles occurred in all loci. In 11 loci the incidence of fast alleles was higher than slow ones. Conversly, slow alleles occurred more frequently than fast ones in 5 loci. Additionally, there was a low incidence of a very fast allele in 7 loci and of a very slow allele in 3 loci. A slow allele was rare in 2 loci. Primitive lines and land races were a source of these rare alleles. It is suggested to consider a frequent allele of a given locus found in a group of wild lines as a so-called wild type of Pisum.     

Biomass production and related characters in the core collection of Pisum germplasm

Retention of residue on the soil surface following harvest is an effective method of reducing soil erosion from both wind and water. The pea crop produces small amounts of residue to effectively reduce soil erosion. Severe erosion occurs in pea production areas such as the Palouse Region of the US Pacific Northwest (PNW) when low residue crops such as spring pea or lentil are followed by fall-sown wheat. The current study was conducted to determine the range of total aboveground biomass (TAB), seed yield, and straw (residue) production from the plant identification (PI) accessions that comprise the core collection of Pisum germplasm. In addition, the potential for increasing seed yield and straw production simultaneously was evaluated. Three hundred and ninety PI accessions were screened in the field in 1996 and 1997. The variation for TAB, seed yield and straw production among the PI accessions exceeded that of the controls both years. Seed yield was positively correlated with straw production (r = 0.81, p< 0.01) indicating that seed and straw production can be increased simultaneously through positive selection for both traits. Significant favorable variation is present among accessions in the USDA core collection of Pisum germplasm which could be used to increase both seed yield and total biomass production of adapted breeding lines.     

Quantitative analysis of anticancer 3-deoxyanthocyanidins in infected sorghum seedlings

3-Deoxyanthocyanidins are structurally related to the anthocyanin pigments, which are popular as health-promoting phytochemicals. Here, it is demonstrated that the 3-deoxyanthocyanidins are more cytotoxic on human cancer cells than the 3-hydroxylated anthocyanidin analogues. At 200 microM concentration, luteolinidin reduced the viability of HL-60 and HepG2 cells by 90 and 50%, respectively. Sorghum is a major source of 3-deoxyanthocyanidins, which are present as seed pigments and as phytoalexins responding to pathogen attack. On the basis of the collision-induced dissociation spectra of luteolinidin and apigeninidin, an LC-MS/MS method, operating in multiple-reaction monitoring mode, was developed for the specific detection and accurate quantification of these compounds in complex mixtures, which may be difficult to analyze using absorbance measurements. The results demonstrated that inoculated sorghum seedlings could be utilized for convenient and large-scale production of 3-deoxyanthocyanidins. A quantity of almost 270 microg/g (fresh weight) of luteolinidin was produced 72 h after fungal inoculation of 1-week-old seedlings.     

Oil and meal characteristics of core and non-core safflower accessions from the USDA collection

Germplasm evaluation of ex situ collections is needed to document collection characteristics, enhance utilization, and to determine collection needs. The objectives of this study were to (1) provide oil and meal evaluation information for a major portion of the United States Department of Agriculture (USDA) safflower (Carthamus tinctorius L.) collection, (2) compare ranges, variances and means between 203 core and 797 non-core accessions, and (3) determine if region of origin could be differentiated based on accession oil and meal characteristics. Means of the core and non-core accessions differed for % oil, palmitic acid, stearic acid, -tocopherols, and phenolic glucosides (both bitter and cathartic) (P<0.05). Differences between linoleic acid, oleic acid and -tocopherol means were not significant, and the variance between core and non-core accessions differed only for palmitic acid. Thus the core was not fully representative of the non-core accessions, but did capture a large fraction of the diversity in oil and meal factors present. Accessions from the Americas, China, South-West Asia, and South-Central Asia were differentiated using canonical discriminate analysis, but these regions overlapped to varying degrees with the E. European, Mediterranean, and E. African regions. Variation in % oil and fatty acids were generally more important than tocopherols and phenolic glucosides in differentiating accessions on a regional basis. The check cultivars Montola 2001 (high oleic) and Morlin (high linoleic) had oil and fatty acid content comparable to the maximums found in the collection. The ranges for tocopherols and phenolic glucosides among collection accessions, however, exceeded those of the cultivars, suggesting that collection accessions could be useful for genetic manipulation of these factors.     

Characterization of core collection of lentil germplasm for phenology, morphology, seed and straw yields

Increasing and maintaining crop residues in predominantly cereal-based rotations of the US Pacific Northwest is critical to controlling soil erosion. The core collection of lentil (Lens culinaris Medik.) germplasm comprising 287 accessions was evaluated for variation in phenological, morphological and growth parameters including seed yields and residue amounts over a two-year period under conventional tillage and no-till conditions. The objectives of this study were (i) assess lentil genetic variation in germplasm for variation in biomass production and seed yield, (ii) assess the relationship of phenological and morphological traits with biomass and seed yield and (iii) identify high biomass producing germplasm for use as parents in the breeding program. Days to flowering and days to maturity ranged from 31 to 78 and from 71 to 106 days, respectively. Time to flowering in terms of cumulative heat units was a more efficient measurement than days to flowering. Plant height and plant canopy width had a significant association with total biomass, seed yield and residue amounts. Total biomass ranged from 788–6389 kg ha^–1 under conventional tillage, while the range under no-till conditions was 1045–6195 kg ha^–1. Most of the lines with higher biomass also produced the highest seed yields and residue amounts. Overall, only one accession produced more residue than `Laird'. In the more favorable environment of 1997, six accessions exceeded the control cultivars, `Laird' and `Indianhead', for residue amounts, and seven and twenty-four accessions exceeded control cultivars, `Pardina' and `Brewer', for seed yield. Results indicated that plant height, canopy width at maturity and seed yield explained most of the variation in biomass and residue production. Large seeded germplasm consistently had a longer reproductive growth period than small seeded accessions and had 17%, 7% and 21% more biomass, seed yield and residue, respectively. Our data indicated significant variation in lentil germplasm for biomass, seed yield and residue amounts to warrant their use in the breeding program.     

Variation in shoot and root characteristics and their association with drought tolerance in lentil landraces

Lentil (Lens culinaris Medikus subsp. culinaris), generally grown as a rainfed crop, is often subjected to drought. Drought tolerance is closely related to the distribution of root systems in the soil. We studied seedling shoot and root characters in a set of eight randomly selected lentil genotypes collected from Ethiopia, India, Iran, Syria and ICARDA. Each group of genotypes represents a specific adaptation to the environmental conditions associated with its area of origin. The genotypes were evaluated during two seasons (1997 –1999) under field conditions. Thirty-five-day-old seedlings grown in pots in the open air were assessed for stem length, stem weight, taproot length, lateral root number, total root length and total root weight. Combined analyses over 2 years showed that these characters exhibited significant genotypic variability. Stem length, taproot length and lateral root number were highly correlated, both amongst themselves and with yield. High heritability estimates provided reliability in screening based on these traits. Regression analysis showed that stem length alone accounted for 85% of the variance that occurred in seed yield per plant. Cluster analysis showed that the landraces that originated in Iran and Syria, and the breeding lines developed at ICARDA are distinctly different from the lentil accessions that originated in countries at more southerly latitudes (India and Ethiopia). However, of the total of 40 genotypes, only one line (ILL 6002) was strikingly different from all other test genotypes. This line exhibited significantly superior root and shoot traits and yield, and, therefore, is a valuable germplasm for breeding drought tolerant cultivars.     

Character analysis and numerical classification in a wheat collection from Sicily

Summary A study was undertaken using 48 characters observed in plants, spikes and seeds in order to determine the amount of information of different characters and their taxonomic importance in tetraploid wheat samples from Sicily. A classification of the material was also attempted using similarity indices.The most important characters appear: leaf pubescence, glume colour and length, and seed colour. Using all characters, similarity indices among samples were computed and a classification was worked out. This classification, which is very similar to those proposed by various scientists, produces hierarchical groups, showing different levels of merging, and offers very interesting hypotheses on the evolution of the Siciliandurum wheats.

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Merkmalsanalyse und numerische Klassifikation an einer Weizen-Kollektion aus Sizilien

Zusammenfassung Untersucht wurden 48 Pflanzen-, Ähren- und Kornmerkmale an Proben tetraploider Weizen aus Sizilien, um den Informationsgehalt unterschiedlicher Merkmale und ihren taxonomischen Wert zu erfassen. Anhand von Ähnlichkeitsindices wurde auch eine Klassifikation des Materials vorgenommen.Als bedeutsamste Merkmale erscheinen: Blattpubeszenz, Spelzenfarbe und-länge und Kornfarbe. Auf der Grundlage aller Merkmale wurden Ähnlichkeitsindices zwischen den Proben errechnet und eine Klassifikation ausgearbeitet. Diese ist den Klassifikationen anderer Wissenschaftler sehr ähnlich, ergibt hierarchische Gruppen mit unterschiedlichem Ähnlichkeitsniveau und ermöglicht die Aufstellung einer interessanten Hypothese zur Evolution der sizilianischendurum- Weizen.

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Molecular and phenotypic characterization of a collection of white grain sorghum [Sorghum bicolor (L.) Moench] for temperate climates

Genetic Resources and Crop Evolution - Sorghum [Sorghum bicolor (L.) Moench] is a subsistence crop and the main food for populations in arid or semiarid regions and it is appreciated for the...     

Establishment of a core collection for maize germplasm preserved in Chinese National Genebank using geographic distribution and characterization data

Since the 1980s, a large collection of maize has been preserved in the China National Genebank. To facilitate the evaluation and utilization of these valuable germplasm resources, a core collection was established. The collection was firstly divided into two groups, i.e. the landraces and inbred lines. The percentage of the original collection to be included in the core was given as 7% based on a previous study of sampling strategies in maize. Each group was sequentially stratified based on administrative provinces or regions and kernel types, and a clustering method was applied in further stratification. A logarithmic strategy was used to determine the number of entries in the core at each step. The process resulted in the maize core comprising 951 landraces and 242 inbred lines. Shannon-Weaver diversity index and means were used to validate the core. The core can be used effectively in further in-depth research and maize improvement.     

Study of a germplasm collection of loquat (Eriobotrya japonica Lindl.) by multivariate analysis

Loquat species (Eriobotrya japonica Lindl.) originated in China, later was introduced in Japan. However, introduction in Europe occurred much later, in 18th century, it was introduced as an ornamental tree. Since then, the species was very well adapted to the Mediterranean climate, mainly in South East of Spain, where is located more than 50% of total European crop production. A European Project titled ‘Conservation, evaluation and collection of underutilized fruit species’ supported surveys and collection of plant material from these species in the Mediterranean basin countries. One of these surveys resulted in a germplasm collection of loquat established at IVIA, Valencia, Spain. This collection is being extended with new accessions collected across the world, currently the collection have 123 accessions under study. Germplasm management needs first a characterization of the plant material introduced and second diversity studies into the collection that could point out the variability pattern, to establish groups of accessions with similar traits and the most significant variables. These results allow organizing the information gathered for further uses. In this paper, 62 accessions from the IVIA germplasm collection were studied. Results from 43 variables were gathered and data studied by multivariate analysis. The analysis allowed summarizing the data tables with new variables containing most of the information. These results along with those obtained in the coming years will allow define a nuclear collection (minimum number of accessions that contained all the variability present in the collection).     

Agro-morphological variability and genetic diversity in linseed (Linum usitatissimum L.) germplasm accessions with emphasis on flowering and maturity time

Genetic Resources and Crop Evolution - Assessment of genetic diversity and extent of trait variation among germplasm accessions facilitate the effective use of genetic resources for varietal...     

Diltiazem influence on calcium and aluminum absorption by roots of three sorghum cultivars

Calcium (Ca⁺⁺) (10 mM) and Al⁺⁺⁺ (10 mM) ions were applied unilaterally in agar to primary roots of sorghum [Sorghum bicolor (L.) Moench.]. Both Ca⁺⁺ and Al⁺⁺⁺ caused unilateral growth “inhibitions and induced root curvature in cv Funk G522DR, SC574, and SC283 (acid soil stress sensitive, tolerant, and tolerant, respectively). Diltiazem (0.1 mM) [3‐(acetyloxy)‐5‐[2‐(dimethylamino)ethyl]‐2,3‐dihydro‐2‐(4‐methoxyphenyl)‐l‐5‐benzothiozepin‐4 (5H)‐one] inhibited Ca⁺⁺ absorption in Funk G522DR and SC283 but only partially influenced Ca⁺⁺ absorption by roots of SC574. Aluminum ion absorption by roots was inhibited in SC283 and SC574 but not in Funk G522DR.