scholarly journals Enrichment of chickpea genetic resources collection monitored by microsatellites

2009 ◽  
Vol 45 (No. 1) ◽  
pp. 11-17 ◽  
Author(s):  
K. Jomová ◽  
M. Benková ◽  
J. Kraic
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Slovak Republic ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Microsatellite Analysis ◽  
Entire Collection ◽  
Single Fragment ◽  
New Germplasm ◽  
New Alleles

A set of 49 chickpea accessions maintained in the collection of the Genebank of the Slovak Republic was analyzed using microsatellite markers. The level of genetic diversity and the effectivity of new germplasm acquisition for the collection enrichment were evaluated. Five primer pairs used generated 50 different amplified alleles. Four of them, TA2, TA5, TR1, and TR7, containing a long TAA-tandem repeat, were polymorphic with 11–13 alleles per locus. A single fragment was obtained from all the accessions with the primer pair CATPER flanking a small microsatellite repetition in the mRNA sequence of chickpea cationic peroxidase. The genetic diversity was expressed as a diversity index (DI) and polymorphic information content (PIC) with values in the range from 0.885 to 0.904 and from 0.972 to 0.991, respectively. Recently acquired new germplasm contributed 13 new alleles to the entire collection, i.e. almost 70% of microsatellite diversity originated from the recently acquired accessions. Remarkable is also, that one accession carries a unique allel, not present in the remaining collection. Microsatellite analysis revealed the importance of collecting missions for the enrichment of collections of genetic resources.

scholarly journals Assessment of Genetic Diversity of Promising Castor Been (Ricinus communis L.) Genotypes in Nigeria

2019 ◽  
Vol 11 (3) ◽  
pp. 467-474
Author(s):  
Bolaji Zuluqurineen SALIHU ◽  
Olamide Ahmed FALUSI ◽  
Adeyinka Olufemi ADEPOJU ◽  
Ibrahim Wasiu AROLU ◽  
Oladipupo Yusuf DAUDU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Gene Diversity ◽  
Ricinus Communis ◽  
Polymorphic Information Content ◽  
Block Design ◽  
Genetic Material ◽  
Morphological Data ◽  
Research Attention ◽  
Ricinus Communis L

Castor oil plant (Ricinus communis L.) is an important oil crop with little research attention in Nigeria. In the present research, extent of genetic diversity among 20 Nigerian castor genotypes was determined using morphological descriptors and molecular markers. The genotypes were laid out on a randomized complete block design with three replicated plots. Molecular genotyping of the genotypes was carried out using genomic Simple Sequence Repeats (SSR). The genotypes revealed high divergence in seed colour, seed shape, seed mottle, seed caruncle and seed sizes. Seedling establishment varied from 70.18% (in Acc. 006) to 93.25% (Acc. 001) with average mean of 81.53%. Raceme length ranged from 15.90 cm to 29.54 cm with population mean of 20.80 cm. The highest seed yield (1222.98 kg/ha) was recorded in Acc. 001 and the least (611.46 kg/ha) was observed in Acc. 006. Seed oil content varied between 32.15% in Acc. 042 and 54.03% in Acc. 006. Agglomerative cluster dendrogram constructed from morphological data showed random distribution of the genotypes into three cluster groups irrespective of the sources/collection points. The genetic diversity based on SSR Marker Analysis revealed high average expected heterozygosity (0.74), Polymorphic information content (0.68), Nei’s gene diversity index (0.72) and Shannon's Information index (1.43). The dendrogram constructed from molecular data grouped the twenty genotypes into three groups at coefficient of 0.34. From these findings, it showed that the twenty genotypes evaluated are divergent in nature and they could serve as good genetic material for castor breeding in Nigeria.

Genetic diversity of old bread wheat germplasm from the Black Sea region evaluated by microsatellites and agronomic traits

2014 ◽  
Vol 13 (2) ◽  
pp. 119-130 ◽  
Author(s):  
Svetlana Landjeva ◽  
Ganka Ganeva ◽  
Viktor Korzun ◽  
Dean Palejev ◽  
Sabina Chebotar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bread Wheat ◽  
Black Sea ◽  
Agronomic Traits ◽  
Polymorphic Information Content ◽  
Group Differences ◽  
The Black Sea ◽  
Black Sea Region ◽  
Western Group ◽  
New Alleles

Old germplasm is an important genetic resource for enhancing modern crops with new alleles. In the present study, the genetic diversity of 52 historic varieties and landraces of bread wheat originated from the Western (Bulgaria) and Northeastern (Ukraine, Russia and Georgia) regions of the Black Sea basin was assessed based on microsatellite markers and agronomic characteristics. A set of 24 markers detected a total of 263 alleles at 25 microsatellite loci, with an average number of 10.5 alleles per locus and an average polymorphic information content (PIC) of 0.74. A total of 63 alleles at 22 loci were unique, being specific to a particular accession. Half of the alleles (132) were regionally specific, and the rest were common between the Western and Northeastern accessions. The latter group was characterized with greater total and private allelic richness, a higher number of unique alleles and a higher average PIC. The population was found to be very heterogeneous (average heterogeneity 41%), with the Northeastern pool (52.8%) being more diverse than the Western pool (30.9%). Most of the accessions of the Western group clustered together, and the rest were distributed among the subclusters of the Northeastern germplasm. Large inter-group differences in the frequencies of alleles ranging from 3.1 at Xgwm294-2A to 16.7 at Xgwm333-7B were observed. This variation might partly account for the differences in certain yield-related traits. The Northeastern accessions had significantly longer spikes with more number of spikelets. Some issues related to germplasm preservation in seed genebanks are discussed herein. The large molecular variation observed could be utilized by breeders for the selection of diverse parents, or by researchers for the production of mapping populations.

scholarly journals ANALYSIS OF GENETIC DIVERSITY IN TWELVE CULTIVARS OF PEA BASED ON MORPHOLOGICAL AND SIMPLE SEQUENCE REPEAT MARKERS

2018 ◽  
Vol 19 (2) ◽  
pp. 57
Author(s):  
Brijesh Kumar Singh ◽  
Monoj Sutradhar ◽  
Amit Kumar Singh ◽  
Ajay Kumar Singh ◽  
Rajendra Prakash Vyas
Keyword(s):  
Genetic Diversity ◽  
Total Variation ◽  
Simple Sequence Repeat ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Resolving Power ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Simple Sequence ◽  
Number Of Seeds

<p class="abstrakinggris"><span class="judul"><span>Pea</span></span><span class="judul"><em><span>(Pisum sativum </span></em></span><span class="judul"><span>L<em>.)</em></span></span><span class="judul"><span>is the second most important legume crop worldwide after chickpea</span></span><span class="judul"><span> (</span></span><span class="judul"><em><span>Cicer arietinum </span></em></span><span class="judul"><span>L</span></span><span class="judul"><span>.) </span></span><span class="judul"><span>and valuable resources for their genetic improvement. This study aimed to analyze genetic diversity of pea cultivars through morphological and molecular markers. The present investigation was carried out with 12 pea cultivars using 28 simple sequence repeat markers. A total of 60 polymorphic bands with an average of 2.31 bands per primer were obtained. The polymorphic information content, diversity index and resolving power were ranged from 0.50 to 0.33, 0.61 to 0.86 and 0.44 to 1.0 with an average of 0.46, 0.73 and 0.76, respectively. The 12 pea cultivars were grouped into 3 clusters obtained from cluster analysis with a Jaccardd’s similarity coefficient range of 0.47-0.78, indicating the sufficient genetic divergence among these cultivars of pea. The principal component analysis showed that first three principal components explained 86.97% of the total variation, suggesting the contribution of quantitative traits in genetic variability. The contribution of 32.59% for number of seeds per plant, stem circumference, number of pods per plant and number of seeds per pod in the PC1 leads to the conclusion that these traits contribute more to the total variation observed in the 12 pea cultivars and would make a good parental stock material. Overall, this SSR analysis complements morphological characters of initial selection of these pea germplasms for future breeding program.</span></span></p>

scholarly journals Utilization of Phytochemical and Molecular Diversity to Develop a Target-Oriented Core Collection in Tea Germplasm

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1667
Author(s):  
Do Yoon Hyun ◽  
Gwang-Yeon Gi ◽  
Raveendar Sebastin ◽  
Gyu-Taek Cho ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Diversity Index ◽  
Gene Diversity ◽  
Crop Improvement ◽  
Genetic Determinants ◽  
Phytochemical Variation ◽  
Entire Collection ◽  
Improvement Programs ◽  
Direct Use

Tea has received attention due to its phytochemicals. For the direct use of tea germplasm in breeding programs, a core collection that retains the genetic diversity and various phytochemicals in tea is needed. In this study, we evaluated the content of eight phytochemicals over two years and the genetic diversity through 33 SSR (simple sequence repeats) markers for 462 tea accessions (entire collection, ENC) and developed a target-oriented core collection (TOCC). Significant phytochemical variation was observed in the ENC between genotypes and years. The genetic diversity of ENC showed high levels of molecular variability. These results were incorporated into developing TOCCs. The TOCC showed a representation of the ENC, where the mean difference percentage, the variance difference percentage, the variable rate of coefficient of variance percentage, and the coincidence rate of range percentage were 7.88, 39.33, 120.79, and 97.43, respectively. The Shannon’s diversity index (I) and Nei’s gene diversity (H) of TOCC were higher than those of ENC. Furthermore, the accessions in TOCC were shown to be selected proportionally, thus accurately reflecting the distribution of the overall accessions for each phytochemical. This is the first report describing the development of a TOCC retaining the diversity of phytochemicals in tea germplasm. This TOCC will facilitate the identification of the genetic determinants of trait variability and the effective utilization of phytochemical diversity in crop improvement programs.

Exploring the Genetic Diversity of Some Squash (Cucurbita Maxima L.) Germplasm Using Morphological and Molecular Markers in Erzincan

2021 ◽  
Author(s):  
HALIL IBRAHIM OZTURK ◽  
Veysel Dönderalp ◽  
Hüseyin Bulut ◽  
Recep Korkut ◽  
Arash HOSSEINPOUR ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Ssr Markers ◽  
Molecular Level ◽  
Polymorphic Information Content ◽  
Plant Genetic Resources ◽  
Molecular Characteristics ◽  
Cucurbita Maxima ◽  
High Genetic Diversity ◽  
The Mean

Abstract Background Plant genetic resources constitute the most valuable assets of countries. It is of great importance to determine the genetic variation among these resources and to use the data in breeding studies. Cucurbita maxima species in the cucurbitaceae family have high genetic diversity, but its genetic diversity at the molecular level is inadequately characterized. Methods and Results To determine the genetic diversity among genotypes of Cucurbita maxima species of squash, which is widely grown in Erzincan, 14 different squash genotypes collected were examined based on the morphological parameters and molecular characteristics. SSR (Simple sequence repeat) markers were used to determine genetic diversity at the molecular level. The analysis of morphological characterization within genotypes showed a wide variability in morphological traits of plant, flower, fruit, and leaf. Seven SSR markers yielded a total of 23 polymorphic bands, the number of alleles per marker ranged from 2 to 5, and the mean number of alleles was 3.286. Polymorphic information content (PIC) ranged from 0.00 (GMT-M61) to 0.202 (GMT-P25), and the mean PIC value per marker was 0.130. Cluster analysis using Nei's genetic distance determined that 14 genotypes were divided into 3 major groups. Conclusions The SSR markers used were effective in distinguish among similar winter squash or pumpkin and therefore can be beneficial for consideration of Cucurbita maxima species diversity, screening of genetic resources and their selection.

Genetic diversity of selected accessions for seed protein among pigeonpea minicore collection

2016 ◽  
Author(s):  
L. G. Jaggal ◽  
B. R. Patil ◽  
P. M. Naik ◽  
K. Priya
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Core Collection ◽  
Seed Protein ◽  
Polymorphic Information Content ◽  
Efficient System ◽  
Major Allele Frequency ◽  
Entire Collection ◽  
Major Allele ◽  
Simple Sequence

Protein is an important part of our diet and legumes viz., pigeonpea, chickpea, groundnut, cowpea, blackgram, greengram, etc are very rich source of protein. Among them, pigeonpea consists of about 20 to 22% of seed protein. Minicore collection set is consisted of approximately 10 % of core collection and 1% of entire collection with lot of diversity present in it. Nitrogen content of pigeonpea minicore collection set was estimated using Micro-Kjeldhal method and was ranged from 9.82 to 21.45 %. Based on per cent seed protein, twelve accessions of high and twelve accessions of low seed protein were selected for molecular characterization using 23 simple sequence repeat (SSR) markers. The PowerMarker result depicted that, among twenty three amplified markers, twenty markers generated polymorphism with mean polymorphic information content (PIC), major allele frequency (MAF) and genetic diversity of 0.479, 0.589 and 0.525 respectively. Based on molecular characterization, the dendrogram was constructed using DARwin 5.0 software distinguished the selected accessions of both high and low seed protein separately into different clusters showing diversity The results illustrate the potential of marker systems to distinguish the content of seed protein in pulses crop at genus level. Use of these markers also offers an efficient system for the assessment of genetic diversity within minicore set of pigeonpea.

Genetic diversity studies of alfalfa germplasm (Medicago sativa L. subsp. sativa) of United States origin using microsatellite analysis

2017 ◽  
Author(s):  
Shuying Yin ◽  
Yanrong Wang ◽  
Zhibiao Nan
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Polymorphic Information Content ◽  
The United States ◽  
Microsatellite Analysis ◽  
Information Index ◽  
Diversity Studies ◽  
Two Populations

This study aimed to understand the genetic diversity and population structure of alfalfa germplasm from the United States. In this study, the population structure and genetic diversity of six alfalfa cultivars of United States origin were investigated by microsatellite analysis with 40 individuals per cultivar. A total of 312 discernible alleles were amplified from the whole genome with an average of 31.2 alleles per locus. The average values of polymorphic information content and Shannon’s information index were 0.928 and 0.133, respectively, showing high levels of genetic diversity. Two populations were identified by STRUCTURE software with principal coordinate analysis and neighbour-joining clustering. Analysis of molecular variance analysis (AMOVA) revealed that the majority of genetic variation was within cultivars (96.42%) rather than between cultivars (3.58%). In conclusion, analyses of genetic diversity and population structure may be useful for the genetic analysis and utilization of genetic variation in alfalfa breeding.

Genetic diversity of mungbean (Vigna radiata L.) germplasm in Indonesia

2014 ◽  
Vol 12 (S1) ◽  
pp. S91-S94 ◽  
Author(s):  
Puji Lestari ◽  
Sue Kyung Kim ◽  
Reflinur ◽  
Yang Jae Kang ◽  
Nurwita Dewi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Vigna Radiata ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Conservation Strategy ◽  
Low Genetic Diversity ◽  
Breeding Programmes ◽  
The Mean ◽  
Simple Sequence

Despite widespread mungbean [Vigna radiata (L.) Wilczek] consumption in Indonesia, few molecular studies have been carried out on accessions and available data are minimal. In this study, we used 30 newly developed simple sequence repeat (SSR) markers designed from the mapped sequence scaffolds of the Korean Sunhwanokdu and Gyeonggijaerae 5 mungbean genomes. These markers were used to examine loci in 83 mungbean accessions collected from diverse geographical areas in Indonesia. A total of 107 alleles were detected among the accessions with 29 polymorphic markers. However, the mean of polymorphic information content (0.33) value and diversity index (0.38) value was indicative of low genetic diversity in this germplasm. The mungbean population structure was not clearly differentiated and the number of subpopulations was unclear. Neighbour-joining tree analysis revealed that the genetic cluster did not reflect the geographical origin of the accessions. Interestingly, the most agriculturally improved varieties were genetically similar to some landraces from one of the main mungbean-producing regions. These newly developed SSR markers could be useful for detecting genetic variability as a basis for establishing a conservation strategy for mungbean germplasm with the aim of enhancing Indonesian breeding programmes.

scholarly journals Implementation of a limited set of SSR markers for screening of genetic variability in Latvian and Swedish sour cherry (Prunus cerasus L.) genetic resources collections

2011 ◽  
Vol 65 (1-2) ◽  
pp. 21-28
Author(s):  
Gunārs Lācis ◽  
Isaak Rashal ◽  
Viktor Trajkovski
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Resources ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Polymorphic Information Content ◽  
Sour Cherry ◽  
Prunus Cerasus ◽  
Discrimination Power ◽  
Ssr Loci

Implementation of a limited set of SSR markers for screening of genetic variability in Latvian and Swedish sour cherry (Prunus cerasusL.) genetic resources collectionsForty-one sour cherry (Prunus cerasusL.) accessions were evaluated using three SSR markers to characterise genetic diversity in the sour cherry genetic resource collections at the Latvia State Institute of Fruit-Growing (LIFG), Dobele, Latvia and the Division of Horticultural Genetics and Plant Breeding at Balsgård, Department of Crop Sciences, Swedish University of Agricultural Sciences (SLU-Balsgård), Sweden, and to test the usability and reliability of a small set of SSR markers for preliminary characterisation of sour cherry germplasm collections. The SSR loci were highly polymorphic with 7-14 alleles per locus. Heterozygosity and Polymorphic Information Content values ranged from 0.750 to 1.000 and 0.748-0.899, respectively, while discrimination power per locus varied from 0.716 to 0.965. Five to thirty genotypes were found in the sour cherry collections for the three tested SSR loci. The combined discrimination power of all loci was effectively 0.994 and 0.999 for the LIFG and SLU-Balsgård collections, respectively. The SSRs used were able to uniquely identify all accessions in the analysed genetic resources collections. The genotype data allowed estimation of genetic diversity and genetic characterisation of accessions in the collections. Genetic similarity analysis showed higher genetic similarity among the Baltic and Scandinavian sour cherry varieties, than between Baltic and Eastern European varieties.

scholarly journals Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1121
Author(s):  
Hela Chikh-Rouhou ◽  
Najla Mezghani ◽  
Sameh Mnasri ◽  
Neila Mezghani ◽  
Ana Garcés-Claver
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phenotypic Diversity ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Molecular Data ◽  
Mantel Test ◽  
Phenotypic Traits ◽  
Genetic Diversity And Structure

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into fivegroups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.

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