The use of characterisation data to establish the Indian mungbean core collection and assessment of genetic diversity

A representative core set of well characterised Indian mungbean collection was developed using information on passport, characterisation and evaluation data. Initial diversity groups of the accessions comprising the whole collection were formed based on six major crop growing zones and a separate group for a few accessions from diverse exotic sources. Principal components score strategy was found to be most useful in maximising the selection inertia than strictly random sampling in all individual groups. A total of 152 accessions were extracted and the validity of their representativeness was established by comparing its diversity with that of the whole collection. Shannon diversity index for qualitative characters and certain statistical parameters for quantitative variables were used for measuring the diversity of the accessions in the core set and that of the whole collection. The representative core set was subjected to multivariate analysis for assessment of genetic diversity and also the variation patterns for discriminating among accessions to facilitate the users for easy accessibility, and effective and efficient utilisation of the material.     

Diversity in Indian sesame collection and stratification of germplasm accessions in different diversity groups

Sesame (Sesamum indicum L.) is one of the ancient oil crops, grown in India since over 5,000 years ago. Diversity in the Indian sesame collection (3,129 accessions), representing all eco-geographical regions, for a range of morphological and agronomic characters was studied. Wide variation in plant habit (plant height and branching pattern), pubescence of various plant parts (stem, leaf, corolla and capsule), flower colour and number of flowers per leaf axil, capsule characteristics (shape, size, number in the axil of a leaf and number of locules in a capsule), number of capsules per plant, number of seeds per capsule, mean seed weight, and yield per plant was recorded. A detailed multivariate analysis was performed on a set of 100 selected accessions representing different agro-ecological zones. The accessions were classified into 7 discrete clusters. The principal components analysis described the spatial relationship among the entities and confirmed groupings obtained through clustering. Based on the clustering pattern of 100 accessions, the entire collection was allocated to different clusters. Representation of various zones in 7 clusters gives us the opportunity to form distinct diversity groups making combined use of passport and characterisation data. These diversity groups would subsequently be used for sampling the accessions for building up a core collection of sesame, a project already operative at the NBPGR.     

Phenotypic diversity in the pigeonpea (<Emphasis Type="Italic">Cajanus cajan</Emphasis>) core collection

The pigeonpea core collection developed at ICRISAT genebank consists of 1,290 accessions from 53 countries. The core collection, which includes selected lines in extra early, early, medium and late maturity groups was evaluated for 18 qualitative and 16 quantitative characters during the 2004 rainy season, to assess the phenotypic diversity and determine the relative importance of different characters in evaluating pigeonpea germplasm accessions. The four maturity groups differed significantly for all characters under study. The medium maturity group showed significantly higher mean number of primary, secondary and tertiary branches, number of racemes, pod bearing length, pods per plant, shelling percent and plot seed yield. Late maturity group showed significantly higher mean for leaf size, plant height, pod length, seeds per pod and 100-seed weight, indicating this group as a good source of vegetable pigeonpea. Significant positive correlations were found between number of secondary branches and pods per plant in extra early group (r = 0.756), late maturity group (r = 0.776) and entire core (r = 0.728) and between number of racemes and pods per plant in all maturity groups and entire core. Principal coordinate and principal component analysis showed that seven qualitative and nine quantitative traits were important in explaining multivariate polymorphism. The Shannon–Weaver diversity index (H′) varied for different maturity groups and traits. Phenotypic diversity, averaged over all the 16 characters, increases from extra early group (0.36 ± 0.04) to late maturity group (0.42 ± 0.04) suggesting that medium and late maturity groups have greater diversity compared to extra early and early maturity groups.     

Development of Core Collection in Pigeonpea [<Emphasis Type="Italic">Cajanus cajan</Emphasis> (L.) Millspaugh] using Geographic and Qualitative Morphological Descriptors

Pigeonpea is an important pulse crop grown by smallholder farmers in the semi-arid tropics. Most of the pigeonpea cultivars grown to date are selections from the landraces, with a narrow genetic base. With the expansion of the crop to newer areas, problems of local importance are to be addressed. Hence, an economically feasible and faster germplasm evaluation mechanism, such as a core collection, is required. This article describes the development of core collection from 12,153 pigeonpea accessions collected from 56 countries and maintained at ICRISAT, Patancheru, India. The germplasm accessions from 56 countries were placed under 14 clusters based primarily on geographic origin. Data on 14 qualitative morphological traits were used for cluster formation by Ward’s method. From each cluster ≈10% accessions were randomly selected to constitute a core collection comprising 1290 accessions. Mean comparisons using Newman–Keuls test, variances’ comparisons by Levene’s test, and comparison of frequency distribution by χ²-test indicated that the core collection was similar to that of the entire collection for various traits and the genetic variability available in the entire collection is preserved in the core collection. The Shannon–Weaver diversity index for different traits was also similar for both entire and core collection. All the important phenotypic associations between different traits available in the entire collection were preserved in the core collection. The core collection constituted in the present study facilitates identification of useful traits economically and expeditiously for use in pigeonpea improvement.     

Morphological patterns in a world collection of <Emphasis Type="Italic">Cleome gynandra</Emphasis>

Cleome gynandra L. is a leafy vegetable native to sub-Saharan Africa and Asia and cultivated on dry areas. The plant plays an important role in the food and nutrition security of local communities. The objective of this study was to illustrate variation and diversity in the Cleome collection held at the World Vegetable Center. In total, 242 accessions were cultivated and morphologically characterized and analyzed. The gynophore and filament, both important organs of the flower, played a key role in taxonomical identification. High morphological variation was detected in traits including plant height, pod length, leaf size, flower color, and earliness. Distinct morphological differentiation was detected between Asian and African accessions. On average, the African accessions were larger, less uniform and later in flowering and seed maturation than the Asian accessions. The results were used to establish a core collection of 49 Cleome accessions. Gaps in the current collection were detected. High within-accessions diversity challenges the existing ex situ conservation system; to maintain diversity, seed should be collected from a large number of plants, both during the collection mission and in ex situ regeneration. The results are relevant for germplasm collection strategies and regeneration protocols for good genebank practices.     

Sampling a Core Collection of Island Cotton (Gossypium barbadense L.) Based on the Genotypic Values of Fiber Traits

A genetic model, including effects of environments, genotypes, and genotype by environment interaction, was employed to analyze five fiber traits of Island cotton (Gossypium barbadense L.). Genotypic values of 304 accessions were predicted by the adjusted unbiased prediction (AUP). Genetic similarities between different accessions were measured by Mahalanobis distances based on genotypic values. Appropriate sampling strategies, linkage rules in stepwise clustering, and sampling proportion were evaluated. To form a core collection of Island cotton, 60 accessions were sampled by the deviation sampling strategy combined with single linkage rule of hierarchical clustering. The genetic variation and structure captured by the core collection were examined in means, variances, ranges and coefficients of variation, correlation coefficients of quantitative traits, and the accessions distribution plotted by first two principal components between two collections. It was showed that the initial collection was well represented by the core collection for exploiting the Island cotton germplasm. These authors contributed equally to this work.     

Patterns of Phenotypic Variation in a Germplasm Collection of Carthamus tinctorius L. from the Middle East

Phenotypic diversity was assessed for quantitative and qualitative traits in a salt-tolerant subset of the international safflower (Carthamus tinctorius L.) germplasm collection originating from 11 countries in three regions (Central Asia, Southwest Asia and Africa) of the Middle East. Phenotypically, the germplasm, among and within regions, was highly variable, especially for rosette- and yield-related traits. Frequency of desirable variants of seven agronomically important traits ranged from 14% for long rosette period to 50% for no or few spines. Level of population differentiation was high for number of capitula per plant (30%), whereas most traits partitioned their diversity (82–87%) within populations. Region-specific nonrandom associations among sets of qualitative traits and the existence of broad morphological and phenotypic diversity in this germplasm were supported by the large number of log-linear models needed to describe qualitative trait associations, the high number of principal components needed to account for total variability, and the low discriminatory power of phenotypic traits among germplasm from regions and countries in the Middle East. These results suggest that adaptation of the species to the wide spatial and temporal variation in the Middle East resulted in a multitude of ecotypes and in enormous amount of local variation. A multivariate selection criterion for high biological and seed yield, long rosette period and no or few spines identified five accessions from Southwest Asia that can be introduced into subsistence farming systems as a multipurpose crop under saline agriculture.     

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).     

Variation among Spanish faba beans cultivars: taxonomic and evolutionary implications

Summary Univariate and multivariate analysis were used to examine phenotypic variability within a Spanish faba bean germplasm collection maintained at the Centro de Investigación y Desarrollo Agrario, Córdoba, Spain.The analysis of 158 Spanish faba bean accessions and 12 quantitative traits indicated highly significant differences among botanical groups for 8 characters and among geographic regions for 10 characters. An east to west clinal pattern of variation for some characters was detected.In order to identify the main characters which account for the major variation, the same collection was subjected to principal component analysis for 12 quantitative traits. Reproductive and plant height characters appeared to be the major sources of diversity.To determine the importance of both geographic and botanical variation among the Spanish cultivars, discriminant analysis was applied. According to these analyses, plant height, height of the lowest pod-bearing node, pod length and 100 seed weight, were important traits discriminating among different geographic regions. The main character discriminating among botanical groups was the 100 seed weight.Our results fit in a pattern in which both agroecological and anthropological causes could have played a role in the observed variation. This analysis can help plant breeders in choosing the most favorable accessions in plant breeding.     

Phenotypic variation within a fenugreek (<Emphasis Type="Italic">Trigonella foenum-graecum</Emphasis> L.) germplasm collection. II. Cultivar selection based on traits associated with seed yield

Fenugreek (Trigonella foenum-graecum L.) is a minor crop in the Wimmera region of south-eastern Australia. Limited studies have been in the past and these have been on few accessions. This paper describes the use of quantitative and qualitative analyses to determine the main traits associated with seed yield of fenugreek and to identify accessions suitable for commercial production. Phenotypic correlation analysis and simple graphical analysis on a population of fenugreek accessions grown in 1998 and 1999 were used to determine important traits associated with yield. Traits important for yield were early vigour, growth habit, flowering date, end of flowering date, biomass at late flowering and harvest index. Yield per plant and seed weight were also important. Other traits considered important for commercial success included machine harvestability, and bacterial blight resistance. Four accessions (A150118, A150147, A150265, and A150292) were selected as cultivars for commercial release. Although all originating from latitudes >30°, the accession were from different locations and were highly diverse in plant type and phenotypic characteristics. This diversity could be exploited in future breeding programs.     

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.     

Chinese Cornus officinalis: genetic resources, genetic diversity and core collection

Cornus officinalis is plant species that is widely used in traditional Chinese medicine. To help the efficient utilization and conservation of this species, the genetic diversity of 73 germplasm resources collected from Zhejiang, Henan and Shaanxi provinces in China were used in a primary core collection. The germplasm resources were classified nine types and the analysis of morphological traits and chemical components showed wide variations among the germplasm types. The primary core collection of C. officinalis was evaluated by using 18 inter-simple sequence repeat (ISSR) markers and a mini core collection was developed based on three strategies on construction of a core germplasm resources. The ISSR results showed that a total of 233 alleles were identified in these 73 accessions, the genetic diversity (P?=?91.02%, H?=?0.293, I?=?0.446) revealed with an average of 2 alleles per locus. The genetic diversity index analysis suggested that there is a great richness and uniqueness of genetic variation in this primary core collection. Cluster analysis by UPGMA and STRUCTURE placed the 73-germplasm resources into four linkage clusters. Almost all samples from one sampling location were clustered together. Compared to the RS and SW strategy, the LDSS strategy proved to be more representative in the core collection of C. officinalis. Finally, a mini core collections by LDSS, composed of 18 accessions (24.66% of the primary core collection), let more than 94.85% of polymorphic loci remained, 97.55% of the observed number of alleles and 99.28% of the effective number of alleles of the mini core collection, respectively. The Nei’s gene diversity and Shannon’s Information index of core collection were 0.294 and 0.443, respectively. Taken all together, the results indicated that mini core collections constructed by the LDSS strategy represented their primary core collections and provided a rational framework for intensive surveys of natural variation in C. officinalis genetic resources.