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.

scholarly journals Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing

2007 ◽  
Vol 89 (2) ◽  
pp. 93-106 ◽  
Author(s):  
NOELLE A. BARKLEY ◽  
ROB E. DEAN ◽  
ROY N. PITTMAN ◽  
MING L. WANG ◽  
CORLEY C. HOLBROOK ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Data Set ◽  
Mini Core Collection ◽  
Genomic Ssr ◽  
Cultivated Peanut ◽  
The Mean ◽  
Wild Accessions ◽  
Almost All

SummaryThirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15·4 alleles per locus. The mean polymorphic information content (PIC) score was 0·687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10·1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.

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 Genetic Diversity Analysis of Soybean [Glycine max (L.) Merrill.] Germplasms in Bangladesh Using SSR Markers

2021 ◽  
Vol 13 (2) ◽  
pp. 1
Author(s):  
M. K. Khatun ◽  
M. A. Haque ◽  
M. A. Malek ◽  
M. H. Rashid ◽  
S. Islam ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Mean Value ◽  
Ammonium Bromide ◽  
Diversity Analysis ◽  
Dna Ladder ◽  
Genetic Diversity Analysis ◽  
Soybean Genotypes ◽  
The Mean

The purpose of the present study was to investigate the genetic diversity and molecular characterization of 50 soybean genotypes in Bangladesh with 20 SSR markers. Genomic DNA was isolated by modified standard cetyl tri-methyl ammonium bromide (CTAB) extraction protocol and alleles were amplified by polymerase chain reaction (PCR). Allele sizes were estimated in comparison with 50 bp DNA ladder. The software NTSYSpc version 2.2 and POPGENE version 1.31 were utilized for molecular data analysis and preparation of dendrogram. Polymorphic Information Content (PIC) values varied from 0.53 (Satt664) to 0.98 (Satt009, Satt330 and Satt522) with the mean value 0.897 and expected heterozygosity varied from 0.4059 (Satt685) to 0.1246 (Satt664) with the mean value 0.244. The dendrogram analysis depicted that the 50 genotypes were grouped in four (4) major clusters. The most diverse genotypes were SBG-1, PM-78-6-3-13, BS-3 and AGS-31, which suggest that the simple sequence repeat (SSR) markers are very efficient for genetic diversity analysis. The similarity matrix revealed the diversity among genotypes. The diverse genetic materials obtained from the present study on genetic diversity of soybean genotypes in Bangladesh may be utilized in the future breeding programme.

scholarly journals Genetic Diversity of Puerto Rican Farmer-held Papaya (Carica papaya) Using SSR Markers

HortScience ◽  
2018 ◽  
Vol 53 (8) ◽  
pp. 1109-1114 ◽  
Author(s):  
Dianiris Luciano-Rosario ◽  
Luis A. Cruz-Saavedra ◽  
Dimuth Siritunga
Keyword(s):  
Genetic Diversity ◽  
Puerto Rico ◽  
Genetic Resources ◽  
Puerto Rican ◽  
Ssr Markers ◽  
Carica Papaya ◽  
Plant Genetic Resources ◽  
Group Method ◽  
Department Of Agriculture ◽  
Pair Group

Native to Central America, papaya (Carica papaya) is one of the most cultivated fruit crops in the tropical areas of the world. Genetic diversity analyses are an important aspect of conservation of plant genetic resources. In the island of Puerto Rico, where papaya has been consumed for centuries, knowledge on the genetic diversity of papaya is lacking. Therefore, 162 papaya accessions were evaluated using 23 simple sequence repeat (SSR) markers. Of these accessions, 139 were farmer-held samples from Puerto Rico, 13 were U.S. Department of Agriculture (USDA) repository samples, and 10 were commercial varieties. A total of 214 alleles were identified with a mean observed heterozygosity (Ho) of 0.219. Inbreeding coefficient (F) was 0.565, and when evaluating the population structure of these accessions, 2 groups (k = 2) were identified. Unweighted pair group method with arithmetic mean (UPGMA) dendrogram showed no geographical organization within the unknown Puerto Rican samples. This assessment provides an extensive record of the genetic diversity of papaya in Puerto Rico which can contribute to breeding strategies and to the conservation of papaya genetic resources in the Caribbean.

Conservation of Billbergia zebrina genetic resources: AFLP polymorphism of in vitro regenerated genotypes

2011 ◽  
Vol 10 (1) ◽  
pp. 20-23 ◽  
Author(s):  
Lirio L. Dal Vesco ◽  
Valdir M. Stefenon ◽  
Leocir J. Welter ◽  
Neusa Steiner ◽  
Miguel P. Guerra
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Gene Diversity ◽  
Plant Genetic Resources ◽  
Natural Populations ◽  
Shannon Index ◽  
Aflp Markers ◽  
High Genetic Diversity ◽  
Index Of Diversity

Biotechnological techniques comprise useful tools for the conservation of endangered plant genetic resources. In the present work, polymorphism and usefulness of amplified fragment length polymorphism (AFLP) markers in assessing the genetic diversity in populations of Billbergia zebrina were investigated in nodular cultures and adult plants of the species. AFLP markers revealed moderate-to-high genetic diversity based on the estimations of Nei's gene diversity (mean He = 0.28), Shannon index of diversity (mean HS = 0.48) and the number of polymorphic fragments (mean of 56.17 polymorphic fragments over six primer pairs). In comparison to published studies of population genetics performed in other bromeliad species, the present study suggests that natural populations of B. zebrina likely maintain high levels of genetic diversity, an important feature towards conservation of plant genetic resources. The results obtained reveal that AFLP markers comprise a powerful tool in order to assess the levels of genetic diversity in natural populations of this endangered species. Integrating AFLP markers with in vitro propagation techniques is understood as an adequate strategy for conservation programmes of this species.

scholarly journals Genetic Diversity of Torch Ginger (Etlingera elatior) Germplasm Revealed by ISSR and SSR Markers

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Nor Asiah Ismail ◽  
M. Y. Rafii ◽  
T. M. M. Mahmud ◽  
M. M. Hanafi ◽  
Gous Miah
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Germplasm Collection ◽  
Peninsular Malaysia ◽  
Molecular Characteristics ◽  
Etlingera Elatior

Fifty-seven accessions of torch ginger (Etlingera elatior) collected from seven states in Peninsular Malaysia were evaluated for their molecular characteristics using ISSR and SSR markers to assess the pattern of genetic diversity and association among the characteristics. Diversity study through molecular characterization showed that high variability existed among the 57 torch ginger accessions. ISSR and SSR molecular markers revealed the presence of high genetic variability among the torch ginger accessions. The combination of different molecular markers offered reliable and convincing information about the genetic diversity of torch ginger germplasm. This study found that SSR marker was more informative compared to ISSR marker in determination of gene diversity, polymorphic information content (PIC), and heterozygosity in this population. SSR also revealed high ability in evaluating diversity levels, genetic structure, and relationships of torch ginger due to their codominance and rich allelic diversity. High level of genetic diversity discovered by SSR markers showed the effectiveness of this marker to detect the polymorphism in this germplasm collection.

scholarly journals Assessment of genetic diversity among wild populations of the striped catfish (Pangasianodon hypophthalmus) by 20 novel microsatellite markers

2021 ◽  
Vol 63 (7) ◽  
pp. 37-41
Author(s):  
Van Sang Nguyen ◽  
◽  
Minh Thanh Nguyen ◽  
Hoang Thong Nguyen ◽  
Hoang Gia Linh Tran ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Draft Genome ◽  
Null Alleles ◽  
Wild Populations ◽  
High Genetic Diversity ◽  
Pangasianodon Hypophthalmus ◽  
Striped Catfish ◽  
The Mean

The striped catfish, Pangasianodon hypophthalmus, is one of the most economically important aquaculture species in Vietnam. This study developed 26 novel microsatellite markers from the draft genome of the striped catfish to assess the genetic diversity of three wild populations of the striped catfish (Bien Ho, Cuu Long, and Kratie) for establishing the breeding program. The study exhibited that 6 out of 26 loci had significantly high null allele frequency and deviated from Hardy - Weinberg equilibrium; thus, they were eliminated for further analysis. Across 20 loci without null alleles, a total of 255 different alleles was identified, ranging from 7 to 21 alleles per locus, with many unique alleles for each population. The results based on 20 loci revealed the mean polymorphic information content PIC=0.783; the mean observed heterozygosity Ho=0.809; the mean expected heterozygosity He=0.812; inbreeding coefficient Fis=-0.0147 (Fis<0). The results indicated that the striped catfish populations have high genetic diversity and are suitable for selective breeding. The Analysis of Molecular Variance (AMOVA) and comparison of genetic distances showed significant genetic differentiation among three populations while the Kratie population was distant from the others.

Molecular characterization of the Latvian apple (Malus) genetic resource collection based on SSR markers and scab resistance gene Vf analysis

2011 ◽  
Vol 9 (2) ◽  
pp. 189-192 ◽  
Author(s):  
Gunars Lacis ◽  
Irita Kota ◽  
Laila Ikase ◽  
Dainis Rungis
Keyword(s):  
Genetic Resources ◽  
Resistance Gene ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Plant Genetic Resources ◽  
Sustainable Use ◽  
Scab Resistance ◽  
High Genetic Diversity ◽  
Resource Collection ◽  
Ssr Loci

Apple cultivars are an integral part of the Latvian State Program for Preservation and Sustainable Use of Genetic Resources for Food and Agriculture. Latvian apple (n = 109) cultivars of local origin, nominated as National Plant Genetic Resources, were analyzed with eight simple sequence repeat (SSR) markers recommended by the European Cooperative Programme for Plant Genetic Resources (ECPGR) Malus/Pyrus working group and a marker for scab resistance gene (Vf). All SSR loci exhibited a high level of polymorphism – 12 to 39 alleles, 18.75 in average, with high observed heterozygosity (Ho) ranging from 0.64 to 0.89 and a mean of 0.78. The gene diversity (polymorphism information content value) varied from 0.79 to 0.90, with an average of 0.86. All cultivars could be distinguished with the tested set of SSR loci, with a high frequency of rare (38%) or unique (26%) alleles. For the Vf gene, all three possible genotypes (VfVf, Vfvf and vfvf) were detected for 1, 6 and 102 varieties, respectively. The analyzed germplasm showed high genetic diversity, particularly landraces, while the modern cultivars clustered mainly into two groups. Cluster analysis did not reveal a clear pattern with well-defined groups, but confirmed some relationships based on known or putative pedigrees, as well as suggesting the possible parentage of some cultivars.

scholarly journals Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1643
Author(s):  
Didas Kimaro ◽  
Rob Melis ◽  
Julia Sibiya ◽  
Hussein Shimelis ◽  
Admire Shayanowako
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Polymorphic Information Content ◽  
Geographic Origin ◽  
Germplasm Collection ◽  
Fixation Index ◽  
Population Structure Analysis ◽  
The Mean

Understanding the genetic diversity present amongst crop genotypes is an efficient utilization of germplasm for genetic improvement. The present study was aimed at evaluating genetic diversity and population structure of 48 pigeonpea genotypes from four populations collected from diverse sources. The 48 pigeonpea entries were genotyped using 33 simple sequence repeat (SSR) markers that are polymorphic to assess molecular genetic diversity and genetic relatedness. The informative marker combinations revealed a total of 155 alleles at 33 loci, with an average of 4.78 alleles detected per marker with the mean polymorphic information content (PIC) value of 0.46. Population structure analysis using model based revealed that the germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 53.3% of genetic variation existed within individuals. Relatively low population differentiation was recorded amongst the test populations indicated by the mean fixation index (Fst) value of 0.032. The Tanzanian pigeonpea germplasm collection was grouped into three major clusters. The clustering pattern revealed a lack of relationship between geographic origin and genetic diversity. This study provides a foundation for the selection of parental material for genetic improvement.

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