Study of allozyme diversity in guar [Cyamopsis tetragonoloba (L.) Taub.] germplasm

Guar [Cyamopsis tetragonoloba (L.) Taub.] is an important commercial crop of India, mainly cultivated in the northwestern part and neighboring areas of Pakistan. High morphological diversity is reported in guar. The present study attempts to analyze the genetic diversity in cultivated guar using allozyme polymorphism and compare it with reported morphological diversity. Accessions for the study were selected from a set of guar germplasm conserved at the National Bureau of Plant Genetic Resources, New Delhi. The morphological data of 108 selected accessions was subjected to UPGMA clustering. Fifty-five accessions were then picked randomly from the clusters generated. Tris-borate system (pH 8.3) was found to be most effective for detection of allozyme polymorphism in guar. Ten enzymes were selected for the study out of 18 systems tried, namely, malate dehydrogenase, malic enzyme, phosphogluco isomerase, glutamate oxaloacetate transaminase, esterase, peroxidase, alcohol dehydrogenase, glutamate dehydrogenase, glucose 6-phosphate dehydrogenase and shikimate dehydrogenase. A total of 20 loci were detected with 34 alleles. The number of polymorphic loci in different accessions was observed to be highly variable (0–9). An average of 1.27 allozyme per polymorphic locus was observed. The allele frequency data of the 55 accessions was used to determine genetic diversity parameters. The dendrogram generated on genetic distance showed three clusters in the distance range of 0–0.28. Most of the accessions were in the first clusters in a narrow distance range of 0–0.08. The second cluster consisted of improved varieties and accession from Pakistan. The third cluster of accessions was genetically more distant but there was no definite segregation of accessions according to the place of collection. The accessions from south west Rajasthan were scattered in all the three clusters showing higher variability in this region, also supported by higher morphological variation. The genetic distance was low among accessions of guar, indicating low diversity in India.     

A method for establishing a core collection of Saccharum officinarum L. germplasm based on quantitative-morphological data

A technique is proposed for establishing a representative core collection of S. officinarum accessions from the world collection of sugarcane germplasm maintained at the Sugarcane Breeding Institute-Research Centre, Cannanore, India. In the proposed method, the accessions were first sorted based on their relative contributions to the total variability by means of principal component scores based on a set of quantitative characters. Then, the cumulative proportion of their contributions to the total variance was computed. A logistic regression model was fitted to evaluate the functional relationship between the cumulative proportion of variance and the number of accessions. The size of the core set was decided as the inflection point on that fitted curve, i.e., the point beyond which the rate of increase in cumulative proportion of variability contributed by an accession began to decline. A method for eliminating entries with a high degree of similarity from the selected core set is also proposed.     

Identification of duplicates and fingerprinting of primary and secondary wild annual <Emphasis Type="Italic">Cicer</Emphasis> gene pools using AFLP markers

Wild annual Cicer gene pools contain valuable germplasm for chickpea improvement programs. Previous research showed that duplication might exist in accessions collected from these gene pools, which would hinder chickpea breeding and related research. AFLP (amplified fragment length polymorphism) markers were used to fingerprint the world collections of the primary and secondary gene pools including C. reticulatum Lad., C. bijugum K.H. Rech., C. judaicum Boiss. and C. pinnatifidum Jaub. et Sp. Duplicates were detected in a total of 24 accessions in both the gene pools, highlighting the necessity to fingerprint the germplasm. Genotypic difference was detected as gene pool specific, species specific and accession specific AFLP markers. These were developed into fingerprinting keys for accession identification between and within species and gene pools. Use of AFLP markers to detect duplicates and to identify accessions is a reliable method which will assist in the characterisation and use of wild annual Cicer germplasm in chickpea improvement programs. We recommend the procedure presented in this paper as a standard approach for the precise genetic identification and characterisation of future world collections of wild Cicer, to keep germplasm integrity and to benefit chickpea breeding and related research programs.     

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.     

Genetic diversity and intra-specific phylogeny of Triticum turgidum L. subsp. dicoccon (Schrank) Thell. revealed by RFLPs and SSRs

Today, emmer wheat, T. turgidum subsp. dicoccon, widely grown in the past is a candidate crop for sustainable agriculture in Italy. As part of a research project aimed at the enhanced use of the hulled wheat germplasm, molecular characterization was carried out to understand the genetic structure of the crop and to identify accessions of interest. A collection of 194 accessions was analyzed with 15 microsatellite loci (SSRs), while only a sample of 38 accessions was tested with 19 RFLP probes. The marker loci were selected on the basis of their independent genomic distribution. Genetic distances and allelic frequencies were calculated for each marker class. The genetic relationships were visualized with dendrograms. RFLP loci were, on average, less polymorphic than SSRs. An average Dice's genetic distance of 0.22 for RFLPs vs 0.38 for SSRs was detected, while an expected average heterozygosity per locus of 0.23 for RFLPs vs 0.26 for SSRs was also estimated. With a least number of 10 loci per marker class it was possible to identify each genotype. The most diverse accessions had different geographic origins. Germplasms from Italy and Ethiopia appear to belong to a more primitive genepool, given that a group of accessions from these countries were genetically differentiated from a Russian-Iranian group.     

Analysis of Genetic Diversity Among Saccharum spontaneum L. From Four Geographical Regions of India, Using Molecular Markers

Saccharum spontaneum L. a wild relative of sugarcane is the most variable and diverse among the Saccharum species. This species had been successfully exploited in sugarcane improvement programmes since 1915 and most of the present day commercial varieties are derivatives of interspecific hybrids involving S. spontaneum. The S. spontaneum germplasm available today in the World collections is diverse and represent different geographical groups. In the present investigation, an attempt was made to characterize 40 S. spontaneum clones collected from 4 different geographical areas in India using 20 random, 2 ISSR and 2 telomere primers. Of the 491 bands generated by these primers 83.9% were polymorphic. The genetic diversity estimated based on these markers was found to be moderate (48.9%). The pair-wise genetic distance between the accessions ranged from 29.8 to 60.0. The accessions from Arunachal Pradesh were found to be the most diverse, while Tamil Nadu accessions showed relatively less diversity. Diversity between Tamil Nadu and Kerala collections was found to be low, while the diversity between the Orissa group and the rest was found to be high. The collections from Mayurbanj and Cuttack regions of Orissa were found to be distinct. Arunachal Pradesh accessions, being more diverse, are a potential source for exploitation in sugarcane breeding programmes.     

Allelic Size Standards and Reference Genotypes to Unify International Cocoa (Theobroma cacao L.) Microsatellite Data

Standardisation of microsatellite allele profiles between laboratories is of fundamental importance to the transferability of genetic fingerprint data and the identification of clonal individuals held at multiple sites. Here we describe two methods of standardisation applied to the microsatellite fingerprinting of 429 Theobroma cacao L. trees representing 345 accessions held in the worlds largest Cocoa Intermediate Quarantine facility: the use of a partial allelic ladder through the production of 46 cloned and sequenced allelic standards (AJ748464 to AJ48509), and the use of standard genotypes selected to display a diverse allelic range. Until now a lack of accurate and transferable identification information has impeded efforts to genetically improve the cocoa crop. To address this need, a global initiative to fingerprint all international cocoa germplasm collections using a common set of 15 microsatellite markers is in progress. Data reported here have been deposited with the International Cocoa Germplasm Database and form the basis of a searchable resource for clonal identification. To our knowledge, this is the first quarantine facility to be completely genotyped using microsatellite markers for the purpose of quality control and clonal identification. Implications of the results for retrospective tracking of labelling errors are briefly explored.     

Temporal variation of diversity in Italian durum wheat germplasm

The aim of this work is to analyse the temporal change of genetic diversity in Italian durum wheat germplasm. The germplasm deployed in this study (158 accessions), belonging to 5 different historical classes, was characterised for its microsatellite and gliadin markers. The level of genetic diversity (He), based on gliadin and SSR markers results – on average – greater in indigenous landraces present in Italy before 1915, with the exception of pure line material which had been selected from landraces (showing highest level of heterozigosity for gliadin markers). Genotypes obtained from crosses or mutagenesis (referring to the 1950–1960 period) along with those resulting from crosses between CIMMYT lines and old materials (1970s and beyond) were also genetically more diverse. Forty-nine percent of indigenous landraces were genetically heterogeneous. Nine out of 53 landrace accessions were able to capture 4 different SSR private alleles. It is speculated that the reduction of allele richness is an indicator of the genetic erosion of the pre-breeding germplasm and it is pointed out that the implementation of appropriate methods of genetic conservation of this germplasm is a priority for breeding and food safety.     

Genetic diversity of winter wheat in Shaanxi province, China, and other common wheat germplasm pools

Cultivated Chinese wheat germplasm has been a valuable genetic resourcein international plant breeding. Landraces endemic to China are a geneticresource that is distinct from other wheat germplasm. Patterns of geneticdiversity among cultivated Chinese accessions and relationship to othergermplasm pools are unknown, despite the proven value and potential novelty. Theobjective of this work was to determine the level of genetic diversity withinimproved Chinese germplasm in the context of several other wheat germplasmpools. We analyzed a set of improved accessions cultivated from the 1940s to the1990s in Shaanxi province, China, using six simple sequence repeat (SSR) primerpairs and 30 restriction fragment length polymorphism - probe enzymecombinations (RFLP-PEC) previously used to characterize 21 geographically basedgermplasm pools. Shaanxi germplasm consists of three groups based on foreignintroductions from Italy, Australia, Denmark, and Russia. There was a decreasein genetic diversity among Shaanxi accessions cultivated in the 1970s and 1980sto the 1990s, and accession classifications based on primary decade ofcultivation were found to be significantly undifferentiated. The analysis of themean genetic distance among 22 geographically based pools of germplasm suggestsseveral regions are significantly undifferentiated. A vast majority of the totalamount of variation was found within pools; therefore, pools appear to belargely differentiated based on small differences in band relative frequency andfew if any unique bands. Previous studies have identified some Chinese landracepools as morphologically and genetically unique. The Shaanxi pool does not havethe same unique morphological or genetic features, nor is it more similar to thelandrace pools than other improved germplasm pools.     

Physico-chemical characterisation of yam (Dioscorea alata L.) tubers from Vanuatu

The objectives of this study were: (1) to analyse the physico-chemical characteristics of 48 Dioscorea alata varieties representing a core sample of the Vanuatu national germplasm collection; (2) to relate those characteristics with the varieties eating quality; and (3) to assess the possibility of selecting varieties according to their chemotype. Overall, 331 accessions were collected from 15 different islands of Vanuatu, planted in an ex situ germplasm collection and described during 3 years. The 48 varieties included in the core sample were selected according to their island of origin, eating quality, tuber shape, tuber flesh colour and morphotype. Analyses of their tubers were made for percentage dry matter, starch, amylose, lipids, minerals, proteins, sugars and gelatinisation temperature range. Significant variation exists for each of these characteristics except for gelatinisation temperature. Varieties with good eating quality are characterised with high dry matter, starch and amylose contents. Chemotypes appear to be genetically controlled and further screening of germplasm and/or breeding will have to take into consideration these characteristics, important for farmers’ adoption.     

Genetic diversity of wild soybean (<Emphasis Type="Italic">Glycine soja</Emphasis> Sieb. et Zucc.) and Japanese cultivated soybeans [<Emphasis Type="Italic">G. max</Emphasis> (L.) Merr.] based on microsatellite (SSR) analysis and the selection of a core collection

Wild soybeans, Glycine soja, are a source of genetic variation to improve soybeans. To improve the efficiency evaluation of conserved germplasm a core or mini-core collection approach that maximizes allelic diversity in a proportion of the whole collection has frequently been advocated. The genetic diversity of a wild soybean collection (1,305 accessions) plus Japanese cultivated soybeans (53 accessions) were analyzed at 20 SSR marker loci. Higher levels of allelic diversity were found in wild soybeans (28 alleles per locus) than Japanese cultivated soybean (five alleles per locus). The genetic distance between wild soybeans from different regions reflected their proximity. Accessions from Russia consisted of a diverse array of alleles resulting in accessions being spread further apart in a PCA plot than accessions from other regions. Accessions of wild soybean from Korea included many rare alleles and thus had a high representation in the core collection. The two core collections developed here, traditional and mini, consisted of 192 accessions with 97% of the allelic diversity (14% of the whole collection) and 53 accessions with 62.4% of the allelic diversity (5% of the whole collection), respectively.     

Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP

Sweet potato (Ipomoea batatas L.) is the fifth most important crop in the developing countries after rice, wheat, maize and cassava. The amplified fragment length polymorphism (AFLP) method was used to study the genetic diversity and relationships of sweet potato accessions in the germplasm collection of Sokoine University of Agriculture, Morogoro and Sugarcane Research Institute, Kibaha, Tanzania. AFLP analysis of 97 sweet potato accessions using ten primer combinations gave a total of 202 clear polymorphic bands. Each one of the 97 sweet potato accessions could be distinguished based on these primer combinations. Estimates of genetic similarities were obtained by the Dice coefficient, and a final dendrogram was constructed with the un-weight pair-group method using arithmetic average. AFLP-based genetic similarity varied from 0.388 to 0.941, with a mean of 0.709. Cluster analysis using genetic similarity divided the accessions into two main groups suggesting that there are genetic relationships among the accessions. Principal Coordinate analysis confirmed the pattern of the cluster analysis. Analysis of molecular variance revealed greater variation within regions (96.19%) than among regions (3.81%). The results from the AFLP analysis revealed a relatively low genetic diversity among the germplasm accessions and the genetic distances between regions were low. A maximally diverse subset of 13 accessions capturing 97% of the molecular markers diversity was identified. We were able to detect duplicates accessions in the germplasm collection using the highly polymorphic markers obtained by AFLP, which were found to be an efficient tool to characterize the genetic diversity and relationships of sweet potato accessions in the germplasm collection in Tanzania.     

Determining Sources of Diversity in Cultivated and Wild <Emphasis Type="Italic">Lablab purpureus</Emphasis> Related to Provenance of Germplasm by using Amplified Fragment Length Polymorphism

To improve understanding of diversity of Lablab purpureus and establish relationships among 103 germplasm accessions collected from diverse geographic origins, amplified fragment length polymorphism markers were used. Four primer sets selected out of 16 produced 289 clear, repeatable polymorphisms. UPGMA analysis of similarity data clustered the accessions according to their subspecific taxonomic organization, i.e., subsp. purpureus and subsp. uncinatus, as well as to cultivated and wild forms. The well-represented landraces from Africa and Asia, belonging predominantly to subsp. purpureus, displayed moderate genetic diversity. Wild forms from Africa showed far greater levels of diversity that would justify taxonomic re-assessment of the wild subsp. uncinatus. The molecular analysis identified forms that were collected in the wild in India but were genetically placed intermediate between wild and cultivated forms. As these plant types did not exist among the African accessions, it is suggested that they might represent escapes from early attempts of domestication. These results support the suggested pathway of domestication and distribution of L. purpureus from Africa to Asia. Additional members to a previously published core collection of the species are proposed.     

Evaluating landraces of bread wheat <Emphasis Type="Italic">Triticum aestivum</Emphasis> L. for tolerance to aluminium under low pH conditions

Bread wheat (Triticum aestivum L.) landraces held within ex situ collections offer a valuable and largely unexplored genetic resource for wheat improvement programs. To maximise full utilisation of such collections the evaluation of landrace accessions for traits of interest is required. In this study, 250 accessions from 21 countries were screened sequentially for tolerance to aluminium (Al) using haematoxylin staining of root tips and by root regrowth measurement. The staining test indicated tolerance in 35 accessions, with an intermediate response to Al exhibited in a further 21 accessions. Of the 35 accessions classified as tolerant, 33 also exhibited increased root length following exposure to Al. The tolerant genotypes originated from Bulgaria, Croatia, India, Italy, Nepal, Spain, Tunisia, and Turkey. AFLP analysis of the 35 tolerant accessions indicated that these represent diverse genetic backgrounds. These accessions form a valuable set of germplasm for the study of Al tolerance and may be of benefit to breeding programs for expanding the diversity of the gene pool from which tolerant cultivars are developed.     

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.     

Germplasm Sources for Improvement of Forage Quality in Lotus corniculatus L. and L. uliginosus Schkuhr (Fabaceae)

Extensive germplasm resources are present in collections of Lotus corniculatus and L. uliginosus, two forage species that are valuable in situations where other legumes are not persistent. Naturalised populations in many regions are the primary gene pool for genetic improvement of these species and interspecific hybrids are an important source of variation for agronomic and forage quality traits. Although previous research has provided evidence that selection for optimal levels of condensed tannins and herbage productivity are feasible breeding objectives, less is known about correlations of condensed tannin with other parameters of nutritive value. A germplasm collection of 38 accessions in both species from 9 geographic regions was used as a data base to determine these correlations. Forage of each accession was sampled in two successive years from a field site in south-eastern Australia and analysed for condensed tannin, in vitro digestible dry matter, nitrogen, acid detergent fibre and neutral detergent fibre. In both species condensed tannin was negatively correlated with in vitro digestible dry matter and nitrogen. This result helped to identify potentially valuable accessions with low condensed tannin (<4% of dry weight) and high in vitro digestible dry matter (>70%). One of these was an interspecific hybrid of L. uliginosus and L. corniculatus, confirming the view that interspecific hybridization would be a valuable avenue for improvement of agronomic and forage quality characters in Lotus species.     

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.