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 Subset of Finger Millet Germplasm Using Geographical Origin and Data on 14 Quantitative Traits

Finger millet [Eleusine coracana (L.) Gaertn.] is an important cereal food crop in Africa and South Asia. It is a hardy crop that can be grown in very diverse environments from almost at sea level to about 2400 m.a.s.l. Finger millet has an excellent food value as its seeds contain protein ranging from 7 to 14% and are particularly rich in methionine amino acid, iron, and calcium. Despite all these merits, this crop has been neglected from the main stream of crop improvement research. One of the means to boost its production and productivity is to enhance utilization of finger millet germplasm to breed superior varieties. Keeping this objective in view, a core subset of finger millet germplasm (622 accessions) based on origin and data on 14 quantitative traits was developed from the entire global collection of 5940 accessions held in the genebank at ICRISAT, Patancheru, India. The comparison of means, variances, frequency distribution, Shannon-Weaver diversity index (H′) and phenotypic correlations indicated that the core subset represents the entire collection. These tests indicated that sampling was optimal and the diversity has been captured very well in the core subset. The correlation analysis indicated that panicle exsertion and longest finger length could be given lower priority in the future germplasm evaluation work of finger millet.     

Collection of Lupinus angustifolius L. Germplasm and Characterisation of Morphological and Molecular Diversity

Lupinus angustifolius L. is a Mediterranean species, domesticated in the 20th century, representing an important grain legume crop in Australia and other countries. This work is focused on the collection of wild germplasm and on the characterisation of morphological and molecular diversity of germplasm accessions. It reports the collection of 81 wild L. angustifolius accessions from the South and Centre of Portugal, available at the ‘Instituto Superior de Agronomia Gene Bank’, with subsequent morphological and molecular characterisation of a selection of these and other accessions. A multivariate analysis of morphological traits on 88 L. angustifolius accessions (including 59 wild Portuguese accessions, 15 cultivars and 14 breeding lines) showed a cline of variation on wild germplasm, with plants from Southern Portugal characterised by earlier flowering, higher vegetative development and larger seeds. AFLP and ISSR molecular markers grouped modern cultivars as sub-clusters within the wider diversity of wild germplasm, revealing the narrow pool of genetic diversity on which domesticated accessions are based. The importance of preserving, characterising and using wild genetic resources for L. angustifolius crop improvement is outlined by the results obtained.     

Analysis of the contribution of Mesoamerican and Andean gene pools to European common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) germplasm and strategies to establish a core collection

Common bean (Phaseolus vulgaris L.) was introduced in Europe from both Mesoamerican and Andean centres of origin. In this study, a collection including 544 accessions from all European regions showed that the Andean phaseolin types ‘T’ (45.6%) and ‘C’ (30.7%) prevailed over the Mesoamerican ones ‘S’ (23.7%), and accessions with cuboid seed shape (34.9%), maroon coat darker colour seed (44.3%), uniform seed colour (69.6%) were the most frequent. European accessions with phaseolin ‘S’ showed a significantly larger average seed size compared to those from America in the same phaseolin class while those presenting ‘T’ and ‘C’ phaseolin did not. This suggests that, during crop expansion in Europe, sampling or selection favoured the large-seeded races within the Mesoamerican ‘S’ gene pool or, possibly, introgression from Andean germplasm did occur. A core collection was developed using sampling approaches based on the information available in the genebank databases and on phaseolin patterns. Four sampling strategies were used: simple random sampling, and three random-stratified samplings, by logarithm of frequency of accessions by country, by European region, and by phaseolin pattern, respectively. Two sampling strategies resulted in core collections significantly different for phaseolin electrophoretic patterns from the whole collection. Stratification by phaseolin patterns increased the frequency of ‘S’ types (‘C’ type = 33%, ‘T’ type = 5.7% and ‘S’ type = 31.3%). The core collections were validated using seven seed characters, and no significant difference was observed in all strategies. This first developed European bean core collection will help to assess the contribution of the two American gene pools to the European germplasm and their relative importance for breeding purposes.     

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).     

Marker-assisted sampling of the cultivated Andean potato Solanum phureja collection using RAPD markers

The potato crop originated in the Andean highlands where numerous farmer's varieties and non-cultivated wild species exist. An Andean potato collection is held in trust at the International Potato Center (CIP) to preserve the biodiversity of this crop and ensure the supply of germplasm for potato improvement worldwide. A core collection representing the biodiversity of the Andean potato germplasm is under construction using morphological, molecular, and geographic data. One of the eight cultivated potato species, Solanum phureja, has been genotyped using the RAPD technique. A protocol suitable for large germplasm collection genotyping has been developed to process numerous samples at reasonable costs. From 106 RAPD primers evaluated, we have selected 12 primers yielding 102 polymorphic markers, which unambiguously discriminated all 128 accessions but 2 that are possible duplicates. The S. phureja germplasm collected throughout the Andean countries appears to have a homogeneous genetic constitution. There was no clear geographic pattern as indicated by cluster analysis of the RAPD data. A sub-group of 20 accessions has been identified on the basis of the marker data and selected to maximize molecular (RAPD) variance and polymorphism. The probability of capturing equal amounts of marker polymorphism in this sub-group of 20 accessions by random sampling is less than 40%. This set accessions represents our first group of accessions that may constitute a core of the S. phureja collection. This tentative core will be challenged for diversity content by alternate markers and agronomic traits. Hence, the methodology for sampling less than 10% of the base collection, proposed for core collections by Brown (1989), can be based on molecular marker data provided cost-efficient fingerprints are developed.     

Patterns of diversity in pigeonpea (<Emphasis Type="Italic">Cajanus cajan</Emphasis> (L.) Millsp.) germplasm collected from different elevations in Kenya

Pigeonpea germplasm accessions collected from low (<500 m), medium (501–1000 m), high (1001–1500 m) and very high elevation zones (>1500 m) of Kenya were evaluated for 15 agronomic traits and seed protein content at ICRISAT, Patancheru, India. There were significant differences (P < 0.001) among elevation zones for the number of primary and secondary branches, days to 75% maturity, pod length, seeds per pod, 100-seed weight and seed yield. Mean values indicated that the accessions from low elevation zone were significantly different from those collected in higher elevation zones for early flowering and maturity, number of primary branches, pod length, number of pods per plant, seeds per pod, 100-seed weight, seed yield and harvest index. None of the accessions collected in Kenya belonged to extra early (<80 days to 50% flowering) and early (80–100 days to 50% flowering) maturity groups, as defined by time to flowering at Patancheru, India. Mean diversity index based on all characters indicated that accessions from the low elevation zone are more diverse than those from the higher elevation zones. Frequency distribution for trait extremes indicated that the accessions from the low elevation zone were early to flower and mature, short statured, produced more primary and secondary branches with high pod bearing length, long pods, more pods per plant, more seeds per pod, a high seed yield and harvest index. Accessions from the very high elevation zone were late flowering, with a large number of tertiary branches, large seeds and a high shelling percentage and could be a source for cold tolerance and the breeding of vegetable types. Results suggest that the elevation of collection sites is therefore a very important determinant of variation patterns of pigeonpea in Kenya.     

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.     

Genetic Analysis of Egyptian Date (<Emphasis Type="Italic">Phoenix dactylifera</Emphasis> L.) Accessions Using AFLP Markers

Forty-seven samples of date palm (Phoenix dactylifera L.) collected from eight locations in Egypt were studied using four sets of amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. These samples belonged to 21 named accessions and 9 of unknown pedigrees. A total of 350 bands were scored and 233 (66.6%) were polymorphic. Twenty-seven Egyptian accessions and ‘Medjool’and ‘Deglet Noor’accessions from California could beclassified into the major cluster. This major cluster may represent a major group of date palm germplasm in North Africa. There were four other clusters, each containing one or two accessions. The variety ‘Halawy’and one accession of unknown provenance were most likely from hybridization between two clusters. Six groups of accessions of which had the same names, revealed similar but not identical AFLP profiles suggesting these accessions might derive from seedlings rather thanthrough clonal offshoot propagation.     

Diversity among landraces of Indian snapmelon (<Emphasis Type="Italic">Cucumis melo</Emphasis> var. <Emphasis Type="Italic">momordica</Emphasis>)

Diversity among 36 snapmelon landraces, collected from 2 agro-ecological regions of India (9 agro-climatic sub-regions), was assayed using RAPD primers, morphological traits of plant habit and fruit, 2 yield-associated traits, pest and disease resistance and biochemical composition (TSS, ascorbic acid, titrable acidity). Typical differences among accessions were observed in plant and fruit characteristics and snapmelon germplasm with high titrable acidity and possessing resistance to downy mildew, Cucumber mosaic virus, Zucchini yellow mosaic virus, Papaya ringspot virus, Aphis gossypii and Meloidogyne incognita was noticed in the collection. RAPD based grouping analysis revealed that Indian snapmelon was rich in genetic variation and region and sub-region approach should be followed across India for acquisition of additional melon landraces. Accessions of var. agrestis and var. momordica clustered together and there was a separate cluster of the accessions of var. reticulatus. Comparative analysis of the genetic variability among Indian snapmelons and an array of previously characterized reference accessions of melon from Spain, Israel, Korea, Japan, Maldives, Iraq, Pakistan and India using SSRs showed that Indian snapmelon germplasm contained a high degree of unique genetic variability which was needed to be preserved to broaden the genetic base of melon germplasm available with the scientific community. N. P. S. Dhillon and Ranjana contributed equally to this work and are considered the first authors.     

Molecular Markers for the Classification of Switchgrass (Panicum virgatum L.) Germplasm and to Assess Genetic Diversity in Three Synthetic Switchgrass Populations

Information regarding the amount of genetic diversity is necessary to enhance the effectiveness of breeding programs and germplasm conservation efforts. Genetic variation between 21 switchgrass genotypes randomly selected from two lowland (‘Alamo’ and ‘Kanlow’) and one upland (‘Summer’) synthetic cultivars were estimated using restriction fragment length polymorphism (RFLP) markers. Comparison of 85 RFLP loci revealed 92% polymorphism between at least two genotypes from the upland and lowland ecotypes. Within ecotypes, the upland genotypes showed higher polymorphism than lowland genotypes (64% vs. 56%). ‘Kanlow’ had a lower percent of polymorphic loci than ‘Alamo’ (52% vs. 60%). Jaccard distances revealed higher genetic diversity between upland and lowland ecotypes than between genotypes within each ecotype. Hierarchical cluster analysis using Ward's minimum variance grouped the genotypes into two major clusters, one representing the upland group and the other the lowland group. Phylogenetic analysis of chloroplast non-coding region trnL (UAA) intron sequences from 34 switchgrass accessions (6 upland cultivars, 2 lowland cultivars, and 26 accessions of unknown affiliation) produced a neighbor-joining dendrogram comprised of two major clusters with 99% bootstrap support. All accessions grouped in the same cluster with the lowland cultivars (‘Alamo’ and ‘Kanlow’) had a deletion of 49 nucleotides. Phenotypic identification of greenhouse-grown plants showed that all accessions with the deletion are of the lowland type. The deletion in trnL (UAA) sequences appears to be specific to lowland accessions and should be useful as a DNA marker for the classification of upland and lowland germplasm.     

Genetic Diversity in Tef [<Emphasis Type="Italic">Eragrostis tef</Emphasis> (Zucc.) Trotter] Germplasm

One hundred and forty-four heterogeneous tef germplasm accessions collected from 10 major tef growing areas in Ethiopia were evaluated for 18 quantitative traits in a simple lattice design, at Holetta and Ginchi, in 2001 main growing season to study the genetic diversity in tef. The combined analysis of variance revealed the presence of significant variation among germplasm accessions for all traits studied. Cluster analysis revealed the overlapping of the germplasm accessions from different origin and the accessions were grouped into eight distinct clusters of 1–78. Generalized distance square confirmed the presence of significant genetic distance between clusters. In principal component (Prin) analysis, the first four principal components with latent root values above one accounted for about 80.6% of the variability existing among the germplasm accessions. Prin1 constituted about 55% of the variability mainly from almost equal contribution of 10 quantitative traits, indicating that most of the traits are equally important in tef diversity. In this study, the regions and altitudes of origin were not found to have a substantial effect on the genetic diversity in tef germplasm. Diversity within the regions was found to be significant and, hence, an opportunity for exploitation in tef improvement.     

Rice Diversity Collection,Conservation and Management in Northeastern India

Rice is the principal crop of northeastern region of India, where a considerable range of diversity exists. The germplasm collection has also unfold the occurrence of large number of rice landraces in the region. Between 1985 and 2002, a total 2639 accessions of rice germplasms including their wild relatives have been collected. Most of these germplasm material have been conserved in the National Gene Bank, New Delhi following their necessary characterization and evaluation. With the establishment of the Regional Gene Bank Module with medium-term storage facilities (6–7°C with 40–45% relative humidity) at Barapani, Meghalaya, the rice germplasm conservation (ex situ) have been initiated in the region.