scholarly journals Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 890
Author(s):  
Zifeng Ouyang ◽  
Yimeng Wang ◽  
Tiantian Ma ◽  
Gisele Kanzana ◽  
Fan Wu ◽  
...  
Keyword(s):  
Group Method ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Important Data ◽  
Breeding Programs ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Medicinal Value ◽  
Genome Wide ◽  
Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

scholarly journals Detecting DNA Polymorphism and Genetic Diversity in a Wide Pistachio Germplasm: Comparison of AFLP, ISSR, and RAPD Markers

2006 ◽  
Vol 131 (4) ◽  
pp. 522-529 ◽  
Author(s):  
Salih Kafkas ◽  
Hakan Ozkan ◽  
Bekir Erol Ak ◽  
Izzet Acar ◽  
Halit Seyfettin Atli ◽  
...  
Keyword(s):  
Correlation Coefficients ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Data ◽  
Breeding Programs ◽  
Center Of Origin ◽  
Financial Investment ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
The Mediterranean

There are limited numbers of pistachio (Pistacia vera L.) cultivars in the world and their phenotypic appearance and productivity are variable. Understanding such variation would facilitate their use in cultivar breeding programs. Therefore, in this study, 69 pistachio cultivars and genotypes originating from seven countries were characterized by randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), and amplified fragment-length polymorphism (AFLP) markers. The results showed that all three marker systems were able to reveal variability between pistachio cultivars and genotypes. The correlation coefficients for genetic distances were statistically significant among all three molecular marker types. The correlation between RAPD and AFLP data was the highest (r = 0.73) and the value between RAPD and ISSR data was the lowest (r = 0.58). AFLP proved to be the best technique among them. ISSR and AFLP assays were reliable and produced reproducible bands. ISSR was preferred over RAPD, especially when financial investment and technical knowledge are limited. The constructed unweighted pair group method with arithmetic averages (UPGMA) dendrogram obtained from combined data separated the genotypes into two main clusters: one cluster (“Iranian”) included genotypes originating from Iran and the second cluster (“Mediterranean”) contained most other genotypes. The “Mediterranean” cluster further divided into three subclusters: one (“Siirt”) consisted of the cultivars Siirt and Hacireso with a few other selections; the second subcluster (“Turkish”) included Turkish cultivars; and the third subcluster contained Syrian, Italian, and the remaining cultivars. The closeness of the clusters was “Iranian” - “Siirt” - “Turkish”/“Syrian.” These findings reveal a new understanding in the diffusion of pistachio cultivation from its center of origin, the Iranian-Caspian region, via southeastern Turkey to Syria, the Mediterranean region of Europe, and northern Africa.

scholarly journals Genetic diversity and population structure of sugarcane (Saccharum spp.) accessions by means of microsatellites markers

2020 ◽  
Vol 42 ◽  
pp. e45088
Author(s):  
Hugo Zeni Neto ◽  
Luiz Gustavo da Mata Borsuk ◽  
Luiz Renato Frederico dos Santos ◽  
Henrique Sanches Angeli ◽  
Guilherme Souza Berton ◽  
...  
Keyword(s):  
Population Structure ◽  
Probabilistic Models ◽  
Similarity Coefficient ◽  
Group Method ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Pair Group ◽  
Industrial Yield ◽  
Degree Of Similarity ◽  
Simple Sequence

The success of sugarcane (Saccharum spp.) breeding programs depends on the choice of productive parent lines that have a high industrial yield and are genetically divergent. This study assessed the genetic divergence and population structure of sugarcane accessions that are the parents of the RB05 Series of the Sugarcane Breeding Program of Brazil. The DNA of 82 accessions was evaluated using 36 simple sequence repeat markers. The Jaccard similarity coefficient and Unweighted Pair Group Method with Arithmetic Mean clustering method were used to generate a cluster that was divided into 17 distinct groups derived from probabilistic models. The similarity coefficient used in both cases showed that the degree of similarity varied from 0.4716 (RB971551 x RB965586) to 0.9526 (RB936001 x SP89-1115), with a mean of 0.8536. This result demonstrates a high similarity between the 82 accessions and confirms Wright’s F statistic (0.125), which indicates moderate genetic variability. The less-similar crosses suggest that breeders seek a higher number of crosses using cultivar RB965586, highlighting the RB971551 x RB965586 and RB965586 x RB855511 crosses. The results demonstrate that crosses such as RB936001 x SP89-1115 and RB945954 x RB896342 should be avoided because of their high genetic similarity.

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 Morphometric and Genetic Variation in Three Populations of Indian Salmon (Polydactylus plebeius)

2013 ◽  
Vol 5 (3) ◽  
pp. 275-281
Author(s):  
Ramakrishnan THIRUMARAISELVI ◽  
Muthusamy THANGARAJ ◽  
Vellaichamy RAMANADEVI
Keyword(s):  
Univariate Analysis ◽  
Arithmetic Mean ◽  
Group Method ◽  
Morphometric Character ◽  
Clear Pattern ◽  
Arbitrary Primers ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Morphometric Analyses ◽  
The Status

Morphometric character analyses and RAPD was used to discriminate and ratify the status of three populations of Indian salmon, Polydactylus plebeius along the coromandel coast of India. Morphometric analyses showed a clear pattern of differentiation between the stocks and revealed the discreteness of two groups, southern stock (Pazhayar) and northern stock (Cuddalore). The univariate analysis of variance showed significant differences between means of the samples for most morphometric descriptors. A total of 1077 scorable bands were produced using all ten arbitrary primers in three populations. An un-weighted pair-group method with arithmetic mean (UPGMA) dendrogram was constructed based on genetic values to show the genetic relationship among the three populations. The genetic diversity (H) of P. plebeius in Cuddalore was more (0.0733 ± 0.0648) than Pazhayar (0.0609 ± 0.0416) and Vellar (0.0613 ± 0.0344) populations. All the three populations had significantly (p

scholarly journals Multivariate analysis of ‘bacuri’ reproductive and vegetative morphology

2016 ◽  
Vol 7 (2) ◽  
pp. 232 ◽  
Author(s):  
Isis Gomes de Brito Souza ◽  
Valdomiro Aurélio Barbosa de Souza ◽  
Kaesel Jackson Damasceno e Silva ◽  
Paulo Sarmanho da Costa Lima
Keyword(s):  
Phenotypic Variability ◽  
Germplasm Collection ◽  
Tree Breeding ◽  
Arithmetic Mean ◽  
Group Method ◽  
Phenotypic Variance ◽  
Breeding Programs ◽  
Fruit Length ◽  
Pair Group ◽  
Fruit Tree Breeding

The objective of this study was to characterize sixteen genotypes of P. insignis available in the Embrapa Meio-Norte germplasm collection (Teresina, Piauí, Brazil) with respect to 33 morphological traits relating to leaves, flowers, branches, fruits and seeds. Phenotypic variance among genotypes was estimated using the Mahalanobis distance technique and the unweighted pair group method with arithmetic mean analysis (UPGMA). The method of Singh (1981) was used to determine which of the traits contributed most to diversity within genotypes. The occurrence of phenotypic variability among P. insignis genotypes indicated that it would be possible to achieve positive gains with selection. The most distant genotypes were BGB 16 and BGB 48, while crosses between genotype BGB 48 and genotypes BGB 32 and BGB 56 offers the greatest potential as parental types for this fruit tree breeding programs . The flesh content, ovary and fruit length , ratio between fruit length and diameter were the characters that most contributed to diversity among the studied genotypes.

scholarly journals Genetic Variability of 21 Tea Genotypes [Camellia sinensis (L.) O. Kuntze] Based on RAPD Markers

2018 ◽  
Vol 5 (2) ◽  
pp. 77
Author(s):  
Budi Martono ◽  
Syafaruddin Syafaruddin
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Similarity ◽  
Binary Data ◽  
Rapd Markers ◽  
Group Method ◽  
Breeding Programs ◽  
Pair Group ◽  
Monomorphic Band ◽  
And Cluster Analysis

<em>Knowing the genetic diversity in the tea germplasms collection is one of important conditions for assembling new superior varieties. Information of genetic diversity can be obtained through analysis using RAPD molecular markers. The study aimed to determine the genetic diversity of 21 tea genotypes based on RAPD markers. The research was conducted in Integrated Laboratory, Seameo Biotrop, Bogor, from July to September 2013. Genomic DNA was isolated from 21 tea genotypes leaf samples, then amplified with primer OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08. Electrophoresis result was converted into binary data. The genetic similarity and cluster analysis calculation was done using NTSYS-pc version 2.10. In this research, 50 polymorphic bands (94,34%) and 3 monomorphic band (5,66%) were obtained. Cluster analysis based on Nei's genetic distance using the unweighted pair-group method with arithmatic (UPGMA) divided 21 tea genotypes into two groups at a genetic similarity value of 0,48. Group 1 consisted of 20 tea genotypes, while the second group comprised only a one genotype (Sin 27). The range of genetic similarity matrix was between 28%–92%, the lowest genetic similarity (28%) was found between GMB 4 and Sin 27 genotypes, while the highest (92%) was found between AS 2 and AS 1 genotypes. The information obtained can be utilized in breeding programs with the support of agronomic characters as well as in the conservation of tea germplasm.</em>

scholarly journals GENETIC DIVERSITY OF Brassica rapa GERMPLASM OF KHYBER PAKHTUNKHWA PAKISTAN REVEALED BY MOLECULAR MARKERS

2019 ◽  
Vol 18 (6) ◽  
pp. 57-65
Author(s):  
Naushad Ali ◽  
Sardar Ali ◽  
Naqib Ullah Khan ◽  
Sohail Ahmad Jan ◽  
Malik Ashiq Rabbani ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Ssr Markers ◽  
Brassica Rapa ◽  
Arithmetic Mean ◽  
Group Method ◽  
Khyber Pakhtunkhwa ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Ssr Primers ◽  
Simple Sequence

A total of 96 indigenous Brassica rapa accessions were collected from different locations of Khyber Pakhtunkhwa, Pakistan. Simple Sequence Repeats (SSR) markers were used to identify the most diverse genotypes among the collected lots. Twenty six (26) different SSR primers were used for (genetic) variability among collected genotypes. These primers were selected from literature based on their previous results. These primers produced 135 scorable bands of which 75 were polymorphic, with an average of 55.5% polymorphic loci, and reflected the broader genetic background of the collected genotypes. An average 2.88 polymorphic bands with an average PIC value of 0.49 was recorded. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) divided all genotypes into three main groups. Group one contained three clusters, while group two and three had four and two clusters each. Based on the UPGMA dendrogram, genotypes collected from Kohat, Bannu, Swat and Haripur showed considerable amount of variation. From the present study, it is concluded that SSR markers can be proved as the best tool for the genetic variability of other local and exotic B. rapa genotypes.

An assessment of genetic diversity in Desmodium sumichrastii (Fabaceae) of central Mexico

2006 ◽  
Vol 84 (5) ◽  
pp. 876-882 ◽  
Author(s):  
Brenda Y. Bedolla-Garcia ◽  
Sabina I. Lara-Cabrera
Keyword(s):  
Genetic Distances ◽  
Similarity Coefficient ◽  
Group Method ◽  
Central Mexico ◽  
Diverse Populations ◽  
Randomly Amplified Polymorphic Dna ◽  
Eastern Asia ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Neighboring State

The genus Desmodium contains ca. 450 species, distributed in Eastern Asia, Mexico, and Brazil, with 40 endemic species in Mexico, including Desmodium sumichrastii (Schinder) Standley. Randomly amplified polymorphic DNA (RAPD) variation was used to assess genetic variation within and among five populations of D. sumichrastii from west-central Mexico, constituting the first assessment in the tribe Desmodieae. Ninety percent of all bands were polymorphic for the 10 decamer RAPD primers used. Sixty-one percent of the variation was within populations, and 39% was among them. This pattern of higher variation within than among populations is unusual, but can be attributed to ethological characteristics of pollinators. The unweighted pair-group method with arithmetic averages (UPGMA) dendrogram based on Nei's genetic distances plots populations from Jalisco together, whereas populations from Aguililla in the neighboring state of Michoacan are separated and next to the San Miguel del Monte population (also in Michoacan). However, the dendrogram based on Dice's similarity coefficient calculated for all individuals separately groups the populations from Aguililla. We also found a significant correlation between genetic and geographic distances, which is in agreement with Dice's UPGMA dendrogram, where closer populations are more genetically similar. Interestingly the most diverse populations are located within a Biosphere Preserve, and the least diverse populations are located in heavily disturbed sites.

scholarly journals Assessment of genetic diversity and variety identification based on developed retrotransposon-based insertion polymorphism (RBIP) markers in sweet potato (Ipomoea batatas (L.) Lam.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yusha Meng ◽  
Wenjin Su ◽  
Yanping Ma ◽  
Lei Liu ◽  
Xingguo Gu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Sweet Potato ◽  
Variety Identification ◽  
Group Method ◽  
Insertion Polymorphism ◽  
Ltr Retrotransposon ◽  
Germplasm Resources ◽  
Ltr Retrotransposons ◽  
Diversity Assessment

AbstractSweet potato, a dicotyledonous and perennial plant, is the third tuber/root crop species behind potato and cassava in terms of production. Long terminal repeat (LTR) retrotransposons are highly abundant in sweet potato, contributing to genetic diversity. Retrotransposon-based insertion polymorphism (RBIP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there have been no transposon marker-based genetic diversity analyses of sweet potato. Here, we reported a structure-based analysis of the sweet potato genome, a total of 21555 LTR retrotransposons, which belonged to the main LTR-retrotransposon subfamilies Ty3-gypsy and Ty1-copia were identified. After searching and selecting using Hidden Markov Models (HMMs), 1616 LTR retrotransposon sequences containing at least two models were screened. A total of 48 RBIP primers were synthesized based on the high copy numbers of conserved LTR sequences. Fifty-six amplicons with an average polymorphism of 91.07% were generated in 105 sweet potato germplasm resources based on RBIP markers. A Unweighted Pair Group Method with Arithmatic Mean (UPGMA) dendrogram, a model-based genetic structure and principal component analysis divided the sweet potato germplasms into 3 groups containing 8, 53, and 44 germplasms. All the three analyses produced significant groupwise consensus. However, almost all the germplasms contained only one primary locus. The analysis of molecular variance (AMOVA) among the groups indicated higher intergroup genetic variation (53%) than intrapopulation genetic variation. In addition, long-term self-retention may cause some germplasm resources to exhibit variable segregation. These results suggest that these sweet potato germplasms are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the utility of RBIP markers for determining the intraspecies variability of sweet potato and have the potential to be used as core primer pairs for variety identification, genetic diversity assessment and linkage map construction. The results could provide a good theoretical reference and guidance for germplasm research and breeding.

scholarly journals Assessment of Genetic Relationships among Cultivated and Wild Pistachios (Pistacia vera L.) using Molecular Markers

2019 ◽  
Vol 27 (1) ◽  
pp. 37-46 ◽  
Author(s):  
Mohammad Aref Pourian ◽  
Davood Bakhshi ◽  
Ali Aalami ◽  
Hossein Hokmabadi
Keyword(s):  
Genetic Relationships ◽  
Genetic Erosion ◽  
Inter Simple Sequence Repeat ◽  
Group Method ◽  
Pistacia Vera ◽  
Wild Type ◽  
Persian Empire ◽  
Breeding Programs ◽  
Mean Values ◽  
Pair Group

Abstract Iran is one of the main diversity centers and origins of pistachios in the world. Pistachio cultivation spread first within the ancient Persian Empire and then moved gradually westward. Knowledge of the genetic relationships among wild and cultivated varieties of pistachio is important for the efficient utilization of the available germplasm resources. Three molecular marker strategies, namely, inter-simple sequence repeat (ISSR), inter-retrotransposon amplified polymorphism (IRAP), and retrotransposon microsatellite amplified polymorphism (REMAP), were used to study the genetic relationships among 35 pistachio accessions including 15 wild-type genotypes of Pistacia vera and 20 important cultivars from Iran. According to the results, high levels of polymorphism were observed for all three marker systems. REMAP and IRAP techniques had the higher mean values of genetic relationships parameters than ISSR technique. The results from this study showed that the 5′LTR2, Sukkula, Sukkula + UBC855, and 5′LTR2 + UBC811 primers were the most informative and could be used to evaluate the genetic relationships of pistachios accessions. Cluster analysis using the unweighted pair group method with arithmetic mean (UPGMA) properly separated the accessions and divided them into four main groups. The presence of most cultivated genotypes in a group indicates genetic erosion of cultivated pistachio in Iran. Wild-type genotypes of P. vera are located in different clusters indicating the high diversity of the genotypes. The results provide useful genetic information about wild pistachios in northeastern of Iran and indicate that the use of wild pistachios in breeding programs could be useful for generating new genotypes with interesting characters.

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