Characterization Of Plant Genetic Resources Research Articles

Three-Way Multivariate Analysis for the Characterization of Plant Genetic Resources

Three-Way Multivariate Analysis for the Characterization of Plant Genetic Resources

Three-Way Multivariate Analysis for the Characterization of Plant Genetic Resources

Three-Way Multivariate Analysis for the Characterization of Plant Genetic Resources

Türkiye’deki maş fasulyesi [Vigna radiata (L.) Wilczek] genotiplerinin çıkış ve fide özellikleri yönünden karakterizasyonu

Amaç: Bu çalışmada amaç ülkemizden temin edilen maş fasulyesi genotipleri ve yurt dışından temin edilen çeşitlerinin çıkış ve fide özelliklerinde karakterizasyon yapılmasıdır.Yöntem ve Bulgular: Araştırmada Türkiye’nin farklı illerinden toplanan, 50 adet maş fasulyesi genotipi ile yurt dışından temin edilen 4 adet maş fasulyesi çeşidi kullanılmıştır. Çalışma, 2021 yılında Isparta Uygulamalı Bilimler Üniversitesi Ziraat Fakültesinde saksı denemesi şeklinde yürütülmüştür. Araştırma, Tesadüf Parselleri deneme desenine göre 3 tekerrürlü olarak kurulmuştur. Çalışmada çıkış oranı, kotiledon yaprakların uzunluğu ve genişliği, klorofil içeriği ve antosiyanin durumları belirlenmiştir. Genotiplerin çıkış oranı % 45 - 100, kotiledon yaprak uzunlukları 22.60 – 43.38 mm, kotiledon yaprak genişliği 7.42 - 4.92 mm, klorofil içeriği 26.70 - 37.70 arasında değişim göstermiş ve 48 adet genotipin gövdesinde antosiyanin tespit edilmiştir. Korelasyon analizi sonucunda en yüksek pozitif ve önemli ilişki kotiledon yaprak uzunluğu ile kotiledon yaprak genişliği (r=0.82) arasında saptanmıştır. Temel bileşen analizi sonucunda genotiplere ait toplam varyasyonun % 74.73’ünü tanımlayan 2 adet temel bileşen ekseni elde edilmiştir. Cluster analizi sonucunda maş fasulyesi genotiplerinin 4 grupta toplandıkları belirlenmiştir.Genel Yorum: Bitki genetik kaynaklarının fenotipik olarak karakterizasyonu bitki ıslahı ve yetiştiriciler için oldukça önemlidir. Maş fasulyesi genotiplerinde çıkış ve fide özelliklerinin geniş varyasyon gösterdiği çoklu karşılaştırma testleri ile de belirlenmiştir.Çalışmanın Önemi ve Etkisi: Araştırmadan elde edilen sonuçlara göre, genotiplerin çıkış ve fide özelliklerinde geniş bir varyasyon olduğu belirlenmiştir. Ülkemizdeki maş fasulyesi genotiplerinin fide ve çıkış özellikleri yönünden tanımlanması yapılarak hem mevcut varyasyon durumu ortaya çıkarılmış, hem de daha sonra maş fasulyesinde yapılacak agronomik ve morfolojik çalışmalara katkı sağlanmıştır.

Assessment of Genetic Diversity of Bambara Groundnut Accessions [Vigna subterranea (L) Verdcourt] in Sahelian Zone of Niger

The agro-morphological characterization of plant genetic resources is crucial to understand the phenotypic and genotypic relationships between different crop varieties. Bambara groundnut (Vigna subterranea) is a grain legume grown worldwide due to its high nutritional values, nitrogen-fixing ability, and drought tolerance. To assess the existing genotypic and phenotypic diversity within Bambara groundnut accessions and to estimate the genetic parameters guiding future varietal improvement programs, 22 Bambara groundnut accessions were characterized in the Sahelian zone of Niger. Thus, the coefficient of variation ranged from 2.42% to 48.25%, and 7 of the 22 parameters measured presented high coefficients of variation (CV˃20%). Yield had positive high correlation with shell weight (r=0.56), 100-seed weight (r=0.61), and seed weight (r=0.99). The highest GCV and PCV were observed in number of seeds per plant (PVC=35.05% and GCV=22.65%), hull weight (PVC=85.91% and GCV=25.51%) and dry biomass weight (PVC=36. 61% and GCV=23.66%), for a respective heritability and genetic gain of: (h2b=41.58%; GA=30.03%), (h2b=8.82%; GA=15.60%) and (h2b=41.76%; GA=31.49%). The highest heritability is observed in the number of leaves (92.40%) and the date of maturity (92.08%). Emergence date revealed high heritability and genetic gain (h2b=78.77% and GA=20%). Parameters with high heritability and genetic gain (h2b≥60% and GA≥20%), are the least influenced by the environment. So, direct selection for improvement of these traits may be beneficial. To authenticate genetic inequality, principal component analysis (PCA) and hierarchical ascending clustering (HAC) were performed. The results showed a great agro-morphological diversity divided into four different groups, for the studied characters. Group 3 (4 accessions) and group 1 (3 accessions) are the high yielding accessions, while group 4 (8 accessions) and group 2 (7 accessions) are the lower yielding accessions. ...................

Diversity Assessment and DNA-Based Fingerprinting of Sicilian Hazelnut (Corylus avellana L.) Germplasm.

The characterization of plant genetic resources is a precondition for genetic improvement and germplasm management. The increasing use of molecular markers for DNA-based genotype signature is crucial for variety identification and traceability in the food supply chain. We collected 75 Sicilian hazelnut accessions from private and public field collections, including widely grown varieties from the Nebrodi Mountains in north east Sicily (Italy). The germplasm was fingerprinted through nine standardized microsatellites (SSR) for hazelnut identification to evaluate the genetic diversity of the collected accessions, validating SSR discrimination power. We identified cases of homonymy and synonymy among acquisitions and the unique profiles. The genetic relationships illustrated by hierarchical clustering, structure, and discriminant analyses revealed a clear distinction between local and commercial varieties. The comparative genetic analysis also showed that the Nebrodi genotypes are significantly different from the Northern Italian, Iberian, and Turkish genotypes. These results highlight the need and urgency to preserve Nebrodi germplasm as a useful and valuable source for traits of interest employable for breeding. Our study demonstrates the usefulness of molecular marker analysis to select a reference germplasm collection of Sicilian hazelnut varieties and to implement certified plants’ production in the supply chain.

Applications of Biotechnology for Characterization of Plants and Pests as the Key Components of Plant Protection and Production Strategies: A Review

The second Sustainable Developmental Goals (SDG), among the seventeen SDG, is concerned with the pursuit of global food security and agricultural sustainability, which become the key to the success of the entire SDG. Whereas agricultural production and productivity are heavily threatened by the incidence of pests that inflict huge losses in various forms. This calls for prompt applications of biotechnology for the fast, accurate and reliable means for characterization of plant generic resources and pests as it is the pre-requisite and gateway for designing appropriate plant protection and production strategies. It is imperative that pests be identified properly so that judicious use of the literature can be made and sustainable management strategies can be implemented at the right stage. To this end, the application of biotechnology has made significant advances for reliable characterization of plant genetic resources as well as accurate diagnosis of pests, study of their genetic diversity and variability, detailed mechanisms of their transmission and evolutionary relationships. Accordingly, this review article covers the comprehensive account of the various molecular techniques, genome mapping and OMICS sciences utilized for characterization plants and pests that ultimately allow the detailed study of the biology and epidemiology of pests at any stage of their life cycle. The resulting data are eventually employed for enhancing successful implementation of sustainable plant protection and production strategies. In conclusion, the increasing projections of transboundary pests, environmental and abiotic factors together with the continuous scientific advancements and breakthroughs have made biotechnology to be an important engine of bioeconomy for generating invaluable products, processes and services.
 Int. J. Appl. Sci. Biotechnol. Vol 8(3): 247-288

Morphological characterization of Matisia cordata Bonpl. in a tropical dry forest from Antioquia, Colombia

Characterization of plant genetic resources is the first step to conserve plant diversity. Morphoagronomic characterization is a method that requires a selection of sensible descriptors, which are characteristics that define a phenotype. Sapodilla (Matisia cordata Bonpl.) is a plant genetic resource and is an important part of the agricultural tradition of the nearby western of Antioquia (Colombia). However, the lack of scientific information about this species shows that it is an underutilized fruit. The local community, in its traditional knowledge, recognizes two phenotypes of sapodilla: Creole and Ecuadorian. The phenotypic diversity of 100 trees of M. cordata was evaluated from 28 morphoagronomic descriptors. The Gower distance and UPGMA method were used to determine the diversity and make the dendrogram, respectively. The Bayes methodology was used to obtain the highest posterior density intervals of 95% probability and compare both phenotypes. Trees of the Creole phenotype had elliptical crown and acute shaped fruits, whereas the Ecuadorian phenotype presented a pyramidal crown and diverse fruit shapes. The Creole phenotype had stems with larger diameter at chest height (28.8 cm), more knots (10 cm), smaller leaves (25 cm), lighter fruits (301 g), larger peduncles (15.6 mm), smaller (40 mm) and lighter seeds (30 g), and an epicarp and a darker pulp than the Ecuadorian phenotype. The farmers’ local knowledge was partially confirmed since most of the descriptors coincided with the local perception, except descriptors of color and flavor of the pulp.

CHARACTERIZATION OF POMEGRANATE CULTIVARS IN PALM GROVES OF THE OUED RIGH VALLEY (SOUTH-EASTERN ALGERIA)

Varietal recognition is a key step for good management of genetic diversity. Indeed, the morphological description of certain organs, such as the leaves, flowers, fruits and seeds, allow a more or less rapid and reliable identification of the varieties or cultivars. The culture of the pomegranate tree is very known in the valley of Oued Righ in the Algerian Southern, and it constitutes the main fruit species with a number of trees of 27.77 % of total number. The pomegranate tree is found in more than 84% of the farms of the region and its production is complementary of that of the dates. Unfortunately, no study has been realized on the characterization and the valorization of this species. To know and identify the varieties or the existing cultivars, we have undertaken a work of characterization of clones cultivated in the valley of Oued Righ. The plant material constituted by 13 clones of pomegranate tree stemming from various farms. The method of work consists in taking 20 fruits by tree for physico-chemical analyses in the laboratory. The results of analyses on sample of 13 clones described five cultivars, among which some present acceptable characters of fruit from a caliber point of view, contents in sugars and acidity. It shows that the naming of cultivars by the farmers based only on the acid taste of fruits "Hamad" or sweetened "Hlou" is not scientific and remain insufficient. Our results confirm the usefulness of morphological descriptors in the characterization of plant genetic resources. However, more clarification can be achieved by the undeniable contribution of molecular markers.

Usage of microsatellite markers for characterization of polyploids: a case study in reference to hexaploid bamboo species

Abstract Microsatellite markers are most valuable tools for characterization of plant genetic resources or population genetic analysis. Since they are codominant and allelic markers, utilizing them in polyploid species remained doubtful. In such cases, microsatellite markers are usually analyzed by treating them as dominant marker. In the current study, it has been showed that despite of losing the advantage of co-dominance, microsatellite markers are still powerful tool for genotyping of polyploid species because of availability of large number of reproducible alleles per locus. It has been studied by genotyping of nineteen sub populations of Dendrocalamus hamiltonii (hexaploid bamboo species) with seventeen polymorphic SSR primer pairs. Among these, ten primers gave typical banding pattern of microsatellite marker as expected in diploid species but rest seven gave unusual pattern i.e. more than two bands per locus per genotype. In such case genotyping data are generally analyzed by considering as dominant markers. Given these facts, data were analyzed in both ways as dominant and codominant. All the seventeen primer were first scored as non-allelic data and analyzed; later ten primer pairs giving standard banding pattern were analyzed as allelic data and the results were compared. The UPGMA clustering and genetic structure showed that results obtained with both the data sets were very similar, and therefore the SSR marker could be utilized to characterize polyploid species by considering them as dominant marker. The study is highly useful to widen the scope of SSR markers applications and beneficial to the researchers dealing with polyploid species.

Identification of elite Indian sugarcane varieties through DNA fingerprinting using genic microsatellite markers

Sugarcane is one of the important crops for sustainable economy and global energy security with high phenotypic polymorphism. Precise identification and characterization of plant genetic resources is one of the most essential aspects for breeding programs. Sugarcane popular hybrid varieties and genetic stocks routinely being used as a parent in hybridization program were included in the study. Molecular cataloguing was accomplished using a set of 70 primer pairs, of which ~ 39% were found to be robust polymorphic and unique in all the genotypes used. The number of DNA bands amplified by expressed sequenced tags derived simple sequence repeat (EST-SSR) primers ranged from 1 to 10 with an average of 5 bands per primer pair and their fragment size ranged between 50 and 1690 bp. Polymorphism information content (PIC) values were ranged from 0.17 to 1.00 with an average of 0.58. Unique DNA fingerprints of thirteen elite sugarcane varieties were generated with 27 polymorphic sugarcane specific EST-SSR markers. Analyses of DNA profiles produced by microsatellite markers showed the unique bands specific for individual variety. Generated DNA profiles would facilitate accurate variety identification in the perspective of protection of the breeder’s intellectual property rights, farmer’s rights and their purity testing. In addition, developed reliable DNA fingerprinting system will be able to track a potent parent genotype for breeding programs. The identified genotype specific and unique EST-SSR markers will be valuable for conservation and management of sugarcane genetic resources.

Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP.

SummaryGBS-SNP-CROP is a bioinformatics pipeline originally developed to support the cost-effective genome-wide characterization of plant genetic resources through paired-end genotyping-by-sequencing (GBS), particularly in the absence of a reference genome. Since its 2016 release, the pipeline’s functionality has greatly expanded, its computational efficiency has improved, and its applicability to a broad set of genomic studies for both plants and animals has been demonstrated. This note details the suite of improvements to date, as realized in GBS-SNP-CROP v.4.0, with specific attention paid to a new integrated metric that facilitates reliable variant identification despite the complications of homologs. Using the new de novo GBS read simulator GBS-Pacecar, also introduced in this note, results show an improvement in overall pipeline accuracy from 66% (v.1.0) to 84% (v.4.0), with a time saving of ∼70%. Both GBS-SNP-CROP versions significantly outperform TASSEL-UNEAK; and v.4.0 resolves the issue of non-overlapping variant calls observed between UNEAK and v.1.0.Availability and implementationGBS-SNP-CROP source code and user manual are available at https://github.com/halelab/GBS-SNP-CROP. The GBS read simulator GBS-Pacecar is available at https://github.com/halelab/GBS-Pacecar.Supplementary information Supplementary data are available at Bioinformatics online.

Characterization and evaluation data of some leguminous plants stored in National Genebank

Characterization of plant genetic resources is the major description of germplazm for breeding. Their morpho-agronomic, biochemistry and molecular evoluation also plays an important role for creation new valuable varieties. With the support of information technologies it can be more effective collection, conservation and use of characterization and evluation data as a database format. So, for this purpose there were created characterization databases on leguminous plants within the structure of Central Databases System. As we mentioned above characterizing of each sample with more traits is very important for the breeding issues. We have tried to achieve it in our research also. For characterization and evaluation data we used international plant descriptors prepared by ICARDA (International Center of Agriculture in Dry Areas), FAO and Bioversity International . It was created the leguminous plants (bean, cow pea, chickpea, horse bean, grass pea) databases by proper database management systems within the structure of Central Database (CDB) on PGR of Azerbaijan based on MS FoxPro. Evaluated samples were taken from the National Genebank collection by proper crop groups.

Genetic differentiation of bottle gourd [Lagenaria siceraria (Molina) Standl.] landraces assessed by fruit qualitative traits and simple sequence repeat markers

Phenotypic and genotypic characterization of plant genetic resources is fundamental for breeding and strategic conservation. This study assessed the genetic diversity present in bottle gourd landraces using 10 fruit qualitative traits and 11 simple sequence repeat (SSR) markers. Thirty six South African bottle gourd landraces collected from various geographic locations were used for the study. Phenotypic diversity was estimated using Shannon-Weaver diversity indices, principal component and cluster analyses. Phenotypic diversity index was 0.98, showing high genetic diversity among bottle gourd landraces. Principal component analysis identified four PCs which contributed for 75.3% of the total phenotypic variation. Presence or absence of fruit neck, fruit shape, degree of neck bending and fruit neck length positively correlated with PC1, which accounted for 37.6% of the total variation. Primary fruit colour and fruit texture highly correlated with PC2 which accounted for 15.78% of the total variation. Number of alleles varied from 3 to 9 with a mean of 6 per SSR locus. Number of effective alleles ranged from 1.99 to 6.72 with a mean of 3.75. Expected heterozygosity values ranged from 0.5 to 0.87 with a mean of 0.71 with polymorphic information content varying from 0.5 to 0.85 and a mean of 0.7. Qualitative traits and SSR markers analyses had significant correlation (r=0.15, P=0.02) in clustering the landraces. The present study revealed that fruit qualitative traits are useful attributes in bottle gourd breeding and genetic analysis.

Caracterização agro-morfológica de acessos de feijão-frade (Vigna unguiculata): bases para o melhoramento

The morphological characterization of plant genetic resources is essential for the knowledge of phenotypic variation and relationships among genotypes. This information could be useful in the development of plant breeding programs. Cowpea is a grain legume cultivate worldwide due to its high nutritional values, nitrogen-fixing ability and adaptation to drought. A collection of 27 Portuguese cowpea accessions and 5 references were characterized by morphological and agronomic parameters, using six qualitative and eleven quantitative parameters. All accessions presented determinate growth and normal pods. Most of the accessions had erect growth habit (96.87%), white flowers (87.50%) and cream seeds (84.38%). The earliest accessions reached flowering at 77 days and the latest at 119 days after sowing. Concerning production traits, in average, the number of pods per plant ranged from 8.08 to 31.50 pods, the 100 seeds weight varied from 11.80 g to 30.85 g, and the total production from 40.96 g.m-2 to 153.65 g.m-2. In conclusion, a high variability was observed in this cowpea collection, which may be indicative of the potential for its incorporation in cowpea breeding programs. Since some of the morphological characteristics are influenced by environmental conditions, it will be very important to complement this study with a molecular characterization.

Evaluation of Morphological and Agronomical Characterization of Turkish Pepper Accessions

Collection and characterization of plant genetic resources and assessment of genetic variation plays a fundamental role in plant breeding programs. Pepper is an important crop in many countries and Turkey is fourth in world pepper production. A large number of cultivars and landraces are grown in commercial production in Turkey. Morphological traits of Turkish pepper accessions were evaluated and genetic variation in the population was assessed for further breeding. Principal component (PC) analysis indicated that 75.46% of total variation was accounted for on 10 PC axes and the first three axes were used in principal coordinate analysis for qualitative traits. The clustering pattern and principal coordinates revealed no relationship between geographic origin and geographic diversity in examined populations. There was considerable morphologic variation assessed among pepper genotypes likely due to introduction of diverse pepper genetic material to Turkey and continuing local selection. The large diversity indicates that pepper germplasm is a good source for use in breeding programs to develop improved local pepper populations through breeding that are adapted to local environmental conditions. Farmers prefer to use landraces due to their agronomic traits and resistance to some stress conditions. Some genotypes exhibited variation in plant growth habit, branching habit, and agronomic properties of fruit that makes them suitable either for processing or fresh consumption.

The genetic diversity associated with seed proteins in a collection of Spanish underground vetches (Vicia sativa L. subsp. amphicarpa (Dorthes) Asch. et Graebn.)

The characterization of plant genetic resources is the first step towards improving their use. The Spanish Plant Genetic Resources Centre, which belongs to the National Institute for Agricultural and Food Technology Research (CRF-INIA), conserves accessions of wild underground vetches collected in Spain. In the present work, 26 underground vetch accessions were characterized in terms of their seed storage proteins (separated by SDS-PAGE) as a means of assessing the genetic variation of these plants and their agronomic value. Vicia sativa cv. Vereda was used as control. A total of 54 bands were detected, of which 49 were polymorphic. Fifty eight different electrophoretic patterns were observed in total. Protein bands were scored in terms of their presence (1) or absence (0) for all the seeds studied, and two matrices constructed, one with all the bands present in each accession, the other with the different patterns for each accession. Dendrograms based on the Jaccard similarity index and the UPGMA clustering method were produced from these matrices, and the degree of genetic variation between and within accessions was calculated. The groups obtained were compared with the chromosome number for each accession. The results reflect the great diversity of underground vetch seed storage proteins. The aerial and underground seeds of 16 accessions were then analysed separately. In some cases, the aerial and underground flowers of the same plant produced different proteins.

Data analysis for molecular characterization of plant genetic resources

Characterizations of plant genetic resources based on molecular markers have been increased in the last years. Studies using a broad range of markers applied on hundreds of plant species are the theoretical basis for inferring genetic diversity to propose both breeding and conservation strategies. Despite increased importance of molecular characterization in plant genetic resources, there is scarce information about analysis of this type of data. To fill this gap of information, this review discuss the rationale behind analyses achieved to study genetic relationship among accessions (within and between groups) and to identify accession, and also discuss the adequacy of some analyses and/or parameters for specific purposes. Genetic diversity within groups may be either quantified for the whole group (parameters to choose will depend on type of marker), or quantified and visualized for the relationships among individuals. Quantification parameters will be chosen depending on type of marker, reproduction mode and relatedness of individuals. Visualization is achieved by hierarchical and non-hierarchical methods. Genetic diversity between groups should be quantified either by analysis of molecular variance, or Nei’s parameters, or Wright’s F-statistics. Efficiency of accession identification can be evaluated by maximal probability of identical match by chance and number of resolved genotypes.

Random amplified polymorphic DNA (RAPD) variation in Fagopyrum tataricum Gaertn. accessions from China and the Himalayan region

The diversity among 52 landraces and cultivars of tartary buckwheat (Fagopyrum tataricum Gaertn.) and one accession of its wild ancestor, F. tataricum ssp. potanini Batalin, from diverse geographic origins was examined using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) markers. Eighteen primers produced a total of 240 fragments, of which 153 (63.75%) were monomorphic and 87 (36.25%) polymorphic bands. UPGMA-based pairwise Jaccard’s coefficient of similarity was used to deduce the relationships among 53 genetically diverse accessions. The similarity between cultivated tartary buckwheat accessions ranged from 0.61 to 1.00. Four distinct clusters were formed which corresponded well with the geographic distribution of the tartary buckwheat. Nepalese accessions showed maximum diversity followed by Chinese accessions. Tartary buckwheat accessions from the Himalayan region of northwestern India revealed a narrow gene pool. The wild buckwheat accession did not group with any of the three cultivated tartary buckwheat groups, and formed its own single-entry group. Genetic similarity (0.59) of Chinese buckwheat accessions with the wild ancestor reaffirmed that cultivated tartary buckwheat originated in the Yunnan province of northwestern China. Consistent with some earlier reports, our study demonstrated the usefulness of the RAPD technique for the characterization of plant genetic resources and assessment of diversity between species.

DNA contents inPaspalum spp. determined by flow cytometry

DNA contents in nuclei isolated from 81 accessions ofPaspalum, representing 35 species, was determined by laser flow cytometry. Nuclei were isolated by chopping leaf base tissue in Tris/HCl buffer containing 1 % Triton X-100 and fixed in EtOH. Fixation, or no fixation, of nuclei in 70% or 95% EtOH did not affect estimates of DNA contents in DAPI-stained nuclei. DNA contents, among the species examined, varied approximately four-fold (1.02 – 3.86 pg/2C nucleus). Coefficients of variation ranged from less than 1% to approximately 5% and did not increase following fixation. Variation in DNA contents between plants within accessions was less than 0.1%. Significant differences in DNA contents estimates within and between species were detected. Data presented suggested that DNA content is a useful descriptor for characterization of plant genetic resources. The occurrence of significant levels of variation within and betweenPaspalum species indicates that estimates of DNA contents may be useful for characterization and identification ofPaspalum cytotypes. In addition, the identification and maintenance of variability for DNA contents withinPaspalum spp. might be useful as a means to capture genomic adaptations to ecological variation.