scholarly journals Assessing the Genetic Diversity of Chrysanthemum Cultivars with Microsatellites

2013 ◽  
Vol 138 (6) ◽  
pp. 479-486 ◽  
Author(s):  
Yuan Zhang ◽  
Chen Wang ◽  
HongZheng Ma ◽  
SiLan Dai
Keyword(s):  
Genetic Diversity ◽  
Magnetic Beads ◽  
Genomic Library ◽  
Gene Diversity ◽  
Sustainable Use ◽  
Morphological Characteristics ◽  
Breeding Programs ◽  
Genetic Studies ◽  
Mean Values ◽  
Cultivar Classification

The morphological characteristics of chrysanthemum (Chrysanthemum ×morifolium) are rich in variation. However, as a result of the aneuploid polyploidy of the chrysanthemum genome and the lack of proper tools, the genomic information of this crop is limited. Development of microsatellite markers has been an increasing trend in crop genetic studies because of the applicability of these markers in breeding programs. In this study, we reported the development of a simple sequence repeat in chrysanthemums using a magnetic beads enrichment method. An enriched genomic library with AC and GT microsatellite motifs was constructed, and 53 positive clones were detected by a colony polymerase chain reaction (PCR) technique. Of these clones, 35 showed high-quality sequences, and 35 primer pairs were designed accordingly. Twenty-six (74.29%) of the 35 primer pairs revealed polymorphisms on a set of 40 chrysanthemum cultivars. There were 172 alleles amplified over 26 loci with an average of 6.615 alleles per locus. The mean values of gene diversity corrected for the sample size and the inbreeding coefficient were 0.609 and 0.119 over 26 loci, respectively, which indicated that the majority of the microsatellite loci is highly informative. Cluster analysis based on 26 polymorphic loci demonstrated that the selected cultivars were clustered according to geographical origin. This study shows the isolation efficiency of the magnetic beads technique; the abundance of microsatellites in chrysanthemum; and the potential application for the cultivar classification, the studies on genetic diversity, and molecular breeding of chrysanthemums, which is beneficial to promoting the conservation and sustainable use of this crop.

Highly polymorphic microsatellite markers in Chamaecyparis obtusa

2001 ◽  
Vol 31 (12) ◽  
pp. 2248-2251 ◽  
Author(s):  
Y Nakao ◽  
H Iwata ◽  
A Matsumoto ◽  
Y Tsumura ◽  
N Tomaru
Keyword(s):  
Microsatellite Loci ◽  
Magnetic Beads ◽  
Genomic Library ◽  
Gene Diversity ◽  
Pcr Amplification ◽  
Chamaecyparis Obtusa ◽  
Mendelian Inheritance ◽  
Average Gene Diversity ◽  
Polymorphic Microsatellite ◽  
Average Gene

Nine microsatellite loci in hinoki, Chamaecyparis obtusa (Sieb. et Zucc.) Endl., were identified and characterized. A genomic library, developed using enrichment with magnetic beads, was screened to identify microsatellite repeats (CT/AG). The microsatellite loci, where the alleles were segregated, displayed codominant Mendelian inheritance. Genetic analysis of 16 plus trees and two unrelated individuals of Chamaecyparis obtusa revealed that all loci were highly polymorphic, with an average of 10.3 alleles per locus, and an average gene diversity of 0.77. The applicability of these microsatellite loci was also tested in other species of the Cupressaceae and in Cryptomeria japonica (L.f.) D. Don (Taxodiaceae, a family closely related to Cupressaceae). Polymerase chain reaction (PCR) amplification was successful for about half of the loci of the species in the genus Chamaecyparis. However, the PCR amplification patterns of the 11 species of Cupressaceae showed no clear correlations with their molecular phylogeny. The highly polymorphic microsatellite loci in Chamaecyparis obtusa, identified here, will be useful in studies of hinoki breeding and population genetics.

scholarly journals Genetic diversity among tropical maize inbred lines as revealed by SSR markers

2020 ◽  
pp. 2010-2019
Author(s):  
Maizura Abu Sin ◽  
Ghizan Saleh ◽  
Nur Ashikin Psyquay Abdullah ◽  
Pedram Kashiani
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Inbred Lines ◽  
Hybrid Breeding ◽  
Heterotic Groups ◽  
Breeding Programs ◽  
Maize Inbred Lines

Genetic diversity and phenotypic superiority are important attributes of parental inbred lines for use in hybrid breeding programs. In this study, genetic diversity among 30 maize (Zea mays L.) inbred lines comprising of 28 introductions from the International Maize and Wheat Improvement Center (CIMMYT), one from Indonesia and a locally developed, were evaluated using 100 simple sequence repeat (SSR) markers, as early screening for potential parents of hybrid varieties. All markers were polymorphic, with a total of 550 unique alleles detected on the 100 loci from the 30 inbred lines. Allelic richness ranged from 2 to 13 per locus, with an average of 5.50 alleles (na). Number of effective alleles (ne) was 3.75 per locus, indicating their high effectiveness in revealing diversity among inbred lines. Average polymorphic information content (PIC) was 0.624, with values ranging from 0.178 to 0.874, indicating high informativeness of the markers. High gene diversity was observed on Chromosomes 8 and 4, with high number of effective alleles, indicating their potential usefulness for QTL analysis. The UPGMA dendrogram constructed identified four heterotic groups within a similarity index of 0.350, indicating that these markers were able to group the inbred lines. The three-dimensional PCoA plot also supports the dendrogram grouping, indicating that these two methods complement each other. Inbred lines in different heterotic groups have originated from different backgrounds and population sources. Information on genetic diversity among the maize inbred lines are useful in developing strategies exploiting heterosis in breeding programs

scholarly journals Unraveling genetic variations of Dalbergia latifolia (Fabaceae) from Yogyakarta and Lombok Island, Indonesia

2020 ◽  
Vol 21 (2) ◽  
Author(s):  
Kusumadewi S. Yulita ◽  
TIKA D. ATIKAH ◽  
WITA WARDANI ◽  
SUSILA
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Sustainable Use ◽  
Iucn Red List ◽  
Genetic Variations ◽  
Timber Species ◽  
Population Genetic Analysis ◽  
Medium Level ◽  
Individual Trees ◽  
Lombok Island

Abstract. Yulita KS, Atikah TD, Wardani W, Susila. 2020. Unraveling genetic variations of Dalbergia latifolia (Fabaceae) from Yogyakarta and Lombok Island, Indonesia. Biodiversitas 21: 833-841. Dalbergia latifolia Roxb. (Fabaceae) or sonokeling is a timber species extracted for its beautiful heartwood used mainly for musical instruments. D. latifolia was listed in Appendix 2 of CITES since 1997, and the demand for its timber is increasing. The species is considered vulnerable (VU A1cd ver 2.3) to extinction according to the IUCN Red List, while cultivations were mainly done from a root cutting. To anticipate the further loss of population size while maintaining sustainable use of the species, it is essential to evaluate the genetic diversity since the genetic diversity level could serve as an indicator of plant adaptability to its environment. This present study was the first to report the genetic diversity of five populations of D. latifolia from Yogyakarta and Lombok Island, West Nusa Tenggara, Indonesia. Ten combinations of Sequence Random Amplified Polymorphism (SRAP) primers were used to amplify 48 samples of D. latifolia from five populations in Yogyakarta and Lombok Island. The 137 SRAP loci were used for a cluster, and population genetic analysis, with mean NPL, was of 13.6/locus, PLP of 56.18%, H of 0.16, and PIC for all population was of 0.28. The lowest gene diversity (H = 0.11) was observed in population WL 1 of Lombok Island, while the highest (H = 0.20) was recorded for population KP of Yogyakarta. The Yogyakarta and Lombok populations were genetically structured at a medium level (Gst = 0.27), with low genetic distance (0.0310-0.1281), and a moderate level of variation observed among individual trees (ca. 0.5 coefficient similarity). The results of this present study were expected to provide necessary information on further research of D. latifolia from Indonesia to support the sustainable use of D. latifolia in Indonesia and the preservation of this species.

scholarly journals An RNA Sequencing Transcriptome Analysis and Development of EST-SSR Markers in Chinese Hawthorn through Illumina Sequencing

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 82 ◽  
Author(s):  
Suliya Ma ◽  
Wenxuan Dong ◽  
Tong Lyu ◽  
Yingmin Lyu
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Low Cost ◽  
Polymorphism Analysis ◽  
Diversity Analysis ◽  
Large Set ◽  
Mean Values ◽  
Genetic Diversity Analysis ◽  
Geographical Regions

Chinese hawthorn (Crataegus pinnatifida) is an important ornamental and economic horticultural plant. However, the lack of molecular markers has limited the development and utilization of hawthorn germplasm resources. Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) allow precise and effective cultivar characterization and are routinely used for genetic diversity analysis. Thus, we first reported the development of polymorphic EST-SSR markers in C. pinnatifida with perfect repeats using Illumina RNA-Seq technique. In total, we investigated 14,364 unigenes, from which 5091 EST-SSR loci were mined. Di-nucleotides (2012, 39.52%) were the most abundant SSRs, followed by mono- (1989, 39.07%), and tri-nucleotides (1024, 20.11%). On the basis of these EST-SSRs, a total of 300 primer pairs were designed and used for polymorphism analysis in 70 accessions collected from different geographical regions of China. Of 239 (79.67%) pairs of primer-generated amplification products, 163 (54.33%) pairs of primers showed polymorphism. Finally, 33 primers with high polymorphism were selected for genetic diversity analysis and tested on 70 individuals with low-cost fluorescence-labeled M13 primers using capillary electrophoresis genotyping platform. A total of 108 alleles were amplified by 33 SSR markers, with the number of alleles (Na) ranging from 2 to 14 per locus (mean: 4.939), and the effective number of alleles (Ne) ranging from 1.258 to 3.214 (mean: 2.221). The mean values of gene diversity (He), observed heterozygosity (Ho), and polymorphism information content (PIC) were 0.524 (range 0.205–0.689), 0.709 (range 0.132–1.000), and 0.450 (range 0.184–0.642), respectively. Furthermore, the dendrogram constructed based on the EST-SSR separated the cultivars into two main clusters. In sum, our study was the first comprehensive study on the development and analysis of a large set of SSR markers in hawthorn. The results suggested that the use of NGS techniques for SSR development represented a powerful tool for genetic studies. Additionally, fluorescence-labeled M13 markers proved to be a valuable method for genotyping. All of these EST-SSR markers have agronomic potential and constitute a scientific basis for future studies on the identification, classification, and innovation of hawthorn germplasms.

scholarly journals GENETIC DIVERSITY INAUS RICE LANDRACES OF BANGLADESH USING SSR MARKERS

2017 ◽  
Vol 30 (1) ◽  
pp. 11-20 ◽  
Author(s):  
M. Khalequzzaman ◽  
M. Z. Islam ◽  
M. A. Siddique ◽  
M. F. R. K. Prince ◽  
E. S. M. H. Rashid ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Three Dimensional ◽  
Group Method ◽  
Breeding Programs ◽  
Arithmetic Average ◽  
Pair Group ◽  
Rice Landraces ◽  
Conservation Genetic ◽  
Maximum Selection

Assessment of genetic diversity is essential for germplasm characterization, utilization and conservation. Genetic diversity of 31 Aus rice landraces of Bangladesh was assessed using 36 SSR (simple sequence repeats) markers. A total of 141 alleles were detectedand the number of alleles per locus ranged from two (RM1216, RM145, RM282, RM293, RM567and RM496) to 10 alleles (RM304), with an average of 3.92. The gene diversity varied from 0.06 (RM145) to 0.80 (RM304) with an average of 0.54 and the PIC values ranged from 0.06 (RM145) to 0.78 (RM304), with an average of 0.48.PIC value revealed that RM304 was the best marker for characterizing the studied Aus rice genotypes. The dendrogram from unweighted pair-group method with arithmetic average clustering of markers classified the genotypes into five major groups with a coefficient of 0.49. Two and three-dimensional graphical views of Principal Coordinate Analysis (PCA) revealed that the genotypes Hashikalmi, Chaina, Puitraaijang, Saithsail, Kuchmuch, Kalodhan, Ausdhan and Itcriewere found far away from the centroid of the cluster and can be selected as parents for further breeding programs.The results provided some useful implications for establishment of sovereignty of Bangladeshi rice gene pool. This information will provide maximum selection of diverse parents, background selection during backcross breeding programs and assist in broadening germplasm-based rice breeding programs in future.

scholarly journals Breeding potential and genetic diversity of "Híbrido do Timor" coffee evaluated by molecular markers

2010 ◽  
Vol 10 (4) ◽  
pp. 298-304 ◽  
Author(s):  
Tesfahun Alemu Setotaw ◽  
Eveline Teixeira Caixeta ◽  
Guilherme Ferreira Pena ◽  
Eunize Maciel Zambolim ◽  
Antonio Alves Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Markers ◽  
Genetic Structure ◽  
Gene Diversity ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Potential Use

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon's information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed.

Microsatellite analysis of genetic diversity in four populations of Populus tremuloides in Quebec

2003 ◽  
Vol 81 (4) ◽  
pp. 360-367 ◽  
Author(s):  
Janet Wyman ◽  
Anne Bruneau ◽  
M -Francine Tremblay
Keyword(s):  
Genetic Diversity ◽  
Populus Tremuloides ◽  
Gene Diversity ◽  
Morphological Characteristics ◽  
Dna Fingerprint ◽  
Morphological Identification ◽  
Infinite Allele Model ◽  
Clone Size ◽  
Stepwise Mutation ◽  
Individual Potential

To determine overall genetic variability in aspen (Populus tremuloides Michx.) along the clay belt of northwestern Quebec, four populations were sampled at the transition zone between mixed-wood and conifer-dominated forests using a hierarchical strategy. Our objectives were (i) to estimate gene diversity among and within populations using microsatellite markers and (ii) to examine whether clonal structuring in aspen could be detected. For each population, three stands at least 1 km apart were sampled. Within each stand, five putative clones were sampled with a distance of 50 m between each clone. To examine potential genetic diversity within clones, for three of the putative clones sampled per stand, the three trees closest to this individual (potential ramets) were also sampled. All samples were analysed at four microsatellite loci. Measures of genetic variation all indicated that most of the variation occurred within rather than among the populations. Rst, based on a stepwise mutation model, was 0.0409, slightly higher than Fst, which was based on infinite allele model (0.0323). Within each stand, DNA fingerprint of five putative clones allowed the differentiation of genetically distinct individuals within these putative clones, and from 1.62 to 2.2 times more genetically distinct individuals were identified than by morphological identification. In the present study there was no correlation between the mean distance of the potential ramet to the central trunk (potential ramets were often within 2–3 m of the central trunk) and the possibility of the central trunk and ramet sharing the same genotype. The number of unique genotypes for the three putative clones sampled per stand varied from 11 genotypes per 15 samples to 14 per 15 samples. Consequently, it was not possible to identify clones by either distance from a given central trunk or morphological characteristics. Thus, after stand disturbance, suckers from different genotypes are likely to be closely mixed.Key words: genetic diversity, Populus tremuloides, microsatellites, clone size.

scholarly journals Genetic Diversity of Arabica Coffee (Coffea arabicaL.) in Nicaragua as Estimated by Simple Sequence Repeat Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Mulatu Geleta ◽  
Isabel Herrera ◽  
Arnulfo Monzón ◽  
Tomas Bryngelsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Simple Sequence Repeat ◽  
Significant Contribution ◽  
Gene Diversity ◽  
Ex Situ ◽  
Sequence Repeat ◽  
Breeding Programs ◽  
Arabica Coffee ◽  
Simple Sequence

Coffea arabicaL. (arabica coffee), the only tetraploid species in the genusCoffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT) and the within-population gene diversity (HS) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13;P<0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved throughex situconservation of a low number of populations from each variety.

scholarly journals Study genetic diversity in maize inbreds and improved hybrid vigor in hybrids produce to determine commercial hybrids in Iraq

2015 ◽  
Vol 5 (3) ◽  
pp. 728-731
Author(s):  
Ziyad A. Abed
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Field Experiments ◽  
Random Amplified Polymorphic Dna ◽  
Hybrid Vigor ◽  
Breeding Programs ◽  
Genetic Studies ◽  
Maize Inbreds ◽  
High Level

 A field experiments was conducted in greenhouse to determinate the genetic diversity among 7 genotypes from maize(4 inbreds and 3hybrids) by using molecular markers with Random Amplified polymorphic DNA(RAPD),that shown high level of polymorphism among genotypes of maize ,where the percentage of polymorphism ranged from(66%) and (83.33%) the highest number of polymorphism band (16) and size fragment ranged between (3800 bp) with the primer ( Bnlg 1185 ) and the lowest 180 with the primer( Bnlg 1464).The genetic distance value ranged between (0.3451) and (0.6534) ,where the lowest genic distance between (k1 and k2),while the highest genetic distance between(k4) and (k3xk4).In this study RAPD markers were shown to be powerful to detect genetic diversity and provided us high polymorphism values within genotypes of maize ,also we can conclude for useful those primers for genetic studies in plant breeding programs for developing synthetic cultivars or improved inbreds of maize. 

scholarly journals Genetic diversity in soybean genotypes with resistance to Heterodera glycines

2011 ◽  
Vol 11 (4) ◽  
pp. 304-312 ◽  
Author(s):  
Éder Matsuo ◽  
Tuneo Sediyama ◽  
Cosme Damião Cruz ◽  
Rosângela D'Arc de Lima Oliveira ◽  
Rita de Cássia Teixeira Oliveira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Morphological Characteristics ◽  
Optimization Method ◽  
Genotypic Differences ◽  
Performance Tests ◽  
Breeding Programs ◽  
Soybean Genotypes ◽  
Superior Genotypes

The purpose of this study was to analyze the genetic diversity among soybean genotypes inoculated with Heterodera glycines race 3. The experiments were conducted in a greenhouse. In two performance tests of morphological characteristics and resistance to the pathogen, 27 soybean genotypes were assessed. The coefficient of genotypic determination was estimated by the method of analysis of variance and the genetic diversity analyzed based on dendrograms and optimization method. The estimated coefficients of determination indicated a predominantly genetic origin of the genotypic differences in the traits. The genetic variability was maintained in the superior genotypes, which can be used in breeding programs for resistance to soybean cyst nematode.

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