Genetic Variability of Passion Fruit Multispecific Hybrids and Their Respective Wild Parents Determined by Microsatellite Markers

The Passiflora genus comprises more than 500 species that are used for food, industrial, ornamental, and pharmaceutical purposes. The sour passion fruit (P. edulis Sims) has low genetic variability for disease resistance, and the use of wild species in the cross-breeding basis is a promising alternative for introgression of resistance genes. The objective of this study was to characterize multispecific hybrids and wild materials with potential to be used as parents in passion fruit genetic breeding programs, using microsatellite markers. Genomic DNA from 33 accessions was extracted and analyzed using 23 microsatellite markers, which were used to estimate the genetic dissimilarities among accessions. The genetic dissimilarity matrices were used to perform clustering analysis by dendrogram using the Unweighted Pair-Group Method as grouping criterion and by graphic dispersion based on multidimensional scale, using the principal coordinates method. Genetic distances between accessions ranged from 0.067 to 1.00. The markers indicated genetic variability among the studied accessions and also the efficiency of the recurrent genome recovery within the backcross program. The genetic structure among the accessions shows the clustering tendency between the wild accessions of P. hatschbachii and P. quadrifaria and the accessions obtained by crossing these species. The same occurred for P. incarnata and P. edulis accessions. The knowledge generated by the molecular characterization provides information on the diversity of accessions and contributes to the work of breeders in the selection of parents.

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Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

Sustainability ◽

10.3390/su13126830 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6830

Author(s):

Murat Guney ◽

Salih Kafkas ◽

Hakan Keles ◽

Mozhgan Zarifikhosroshahi ◽

Muhammet Ali Gundesli ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Genetic Resources ◽

Juglans Regia ◽

Genetic Distances ◽

Mean Value ◽

Central Anatolia ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

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Genetic diversity in table grapes based on RAPD and microsatellite markers

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2011000900010 ◽

2011 ◽

Vol 46 (9) ◽

pp. 1035-1044 ◽

Cited By ~ 9

Author(s):

Patrícia Coelho de Souza Leão ◽

Sérgio Yoshimitsu Motoike

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genetic Relationships ◽

Similarity Index ◽

Genetic Distances ◽

Table Grape ◽

Group Method ◽

Molecular Characteristics ◽

Table Grapes ◽

Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

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

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.131.4.522 ◽

2006 ◽

Vol 131 (4) ◽

pp. 522-529 ◽

Cited By ~ 49

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.

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Genetic variability of Passiflora spp. from commercial fields in the Federal District, Brazil

Ciência Rural ◽

10.1590/s0103-84782011000600013 ◽

2011 ◽

Vol 41 (6) ◽

pp. 996-1002 ◽

Cited By ~ 6

Author(s):

Ana Paula Gomes de Castro ◽

Fábio Gelape Faleiro ◽

Daniel Diego Costa Carvalho ◽

Kenia Gracielle da Fonseca ◽

Marina de Fátima Vilela ◽

...

Keyword(s):

Genetic Variability ◽

Rapd Markers ◽

Federal District ◽

Genetic Distances ◽

Passion Fruit ◽

Binary Matrix ◽

Breeding Programs ◽

Wide Range ◽

Potential Success ◽

Sour Passion Fruit

This study aimed to characterize the genetic variability in commercial accessions of passion fruit from the Federal District, Brazil, by RAPD markers. Genetic analyses were done with leaf samples of 30 accessions. DNA samples were amplified by RAPD technique, and respective markers converted into a binary matrix, from which the genetic distances between the accessions were estimated. Clustering analyis based on genetic distances allowed to detect a wide range of genetic variabillity among the accessions of sour passion fruit, and to separate them from the two sweet passion fruit. The graphical positioning of 'BRS Ouro Vermelho' confirms its potential to improve the genetic variability of commercial varieties of sour passion fruit. Dispersal of genetic distances among commercial accessions of sour passion fruit supports evidence for different genetic origins of the materials planted in the Federal District. The verified genetic variability indicates the potential success of future breeding programs for this region.

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Genetic Variability Assay of Different Natural and Hatchery Populations of Rohu (Labeo rohita) in Bangladesh

International Journal of Life Sciences ◽

10.3126/ijls.v9i1.11923 ◽

2015 ◽

Vol 9 (1) ◽

pp. 30-36

Author(s):

Shikder Saiful Islam ◽

Md. Saifuddin Shah ◽

Foyez Ibn Shams ◽

Md. Rayhan Ali ◽

Md. Lifat Rahi

Keyword(s):

Genetic Variation ◽

Genetic Variability ◽

Labeo Rohita ◽

Genetic Distances ◽

Raw Material ◽

Group Method ◽

Pair Group ◽

Fish Samples ◽

Population Genetic Variation ◽

High Level

The level of genetic variation determines the genetic status and provides the raw material for selective improvement of a stock. Randomly amplified polymorphic DNA (RAPD) technique was used to assess the genetic variability of 7 different natural (2) and hatchery (5) populations of Indian Major Carp, Labeo rohita (Rohu) in Bangladsh. In total, 140 fish samples were collected (20 from each of the populations). Genomic DNA was extracted from the muscle tissue, and 5 different oligonucleotide primers were used which revealed 80% polymorphic DNA bands. The polymorphic loci proportions were 0.71, 0.75, 0.75, 0.85, 0.84, 0.86 and 0.89 for Ma-Fatema hatchery, Chowdhuri hatchery, Niribili hatchery, Sonali hatchery, Kapotakha hatchery, the Halda river and the Baluhor Baor populations respectively. The pair-wise population differentiation (FST) values indicated a high level of genetic variation between different populations. The Unweighted Pair Group Method of Arithmetic Mean (UPGMA) dendogram based on Nei’s genetic distances also revealed high level of inter-population genetic variation among the populations. The populations were segregated into two groups: the Halda River and Baluhar Baor hatchery in one group and Kapotakha, Ma-Fatema, Chowdhuri, Niribili and Sonali hatcheries in another group. Overall, RAPD results clearly indicate the reduced genetic quality of the hatchery seeds.DOI: http://dx.doi.org/10.3126/ijls.v9i1.11923 International Journal of Life Sciences Vol.9(1) 2015 30-36

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Genetic variability and homozygosity in a F4 castor bean population by microsatellite markers

Bragantia ◽

10.1590/1678-4499.536 ◽

2016 ◽

Vol 75 (3) ◽

pp. 307-313 ◽

Cited By ~ 2

Author(s):

Edna Lobo Machado ◽

Simone Alves Silva ◽

Luciel dos Santos Fernandes ◽

Helison Santos Brasileiro

Keyword(s):

Genetic Variability ◽

Microsatellite Markers ◽

Castor Bean ◽

Polymorphic Information Content ◽

Hierarchical Cluster ◽

Allele Frequencies ◽

Group Method ◽

Pair Group ◽

Expected Heterozygosity ◽

Genetic Dissimilarity

ABSTRACT The objectives of this study were to identify the genetic variability and estimate the level of homozygosity in a castor bean F4 population using microsatellite markers (SSR). To this end, it was performed the genotyping of the population through 53 pairs of SSR primers. Allele frequencies were estimated by number of alleles per locus, expected heterozygosity (He), observed heterozygosity (Ho) and polymorphic information content (PIC). An array of genetic dissimilarity was generated by Nei and Li index, and hierarchical cluster analysis was performed using the Unweighted Pair-Group Method Averages (UPGMA) method. Polymorphism was detected in a total of eight loci (15.09%) of the 53 evaluated, with the presence of two alleles per locus. Allele frequencies varied between 0.71 and 0.53, and the PIC, between 0.32 and 0.37. The average observed heterozygosity Ho (0.30) was lower than the expected heterozygosity He (0.47). Five dissimilar groups were formed, showing that there is genetic variability among the evaluated genotypes. The highest genetic dissimilarity was 0.708 and the lowest, 0.00. The percentages of homozygous genotypes varied from 25 to 75%. These results show that controlled selfing in castor bean raises the level of homozygosity, important for the breeding program.

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Preserving Biodiversity in Marginal Rural Areas: Assessment of Morphological and Genetic Variability of a Sicilian Common Bean Germplasm Collection

Plants ◽

10.3390/plants9080989 ◽

2020 ◽

Vol 9 (8) ◽

pp. 989

Author(s):

Maria Carola Fiore ◽

Francesco Maria Raimondo ◽

Francesco Mercati ◽

Ignazio Digangi ◽

Francesco Sunseri ◽

...

Keyword(s):

Common Bean ◽

Rural Areas ◽

Germplasm Collection ◽

Genetic Distances ◽

Ex Situ ◽

Group Method ◽

Gene Pools ◽

Mountain Areas ◽

Pair Group ◽

Principal Coordinates

The historical cultivation of common bean (Phaseolus vulgaris L.) has resulted in the development of local populations/cultivars in restricted Italian rural areas. Many common bean landraces, still cultivated in small mountain areas from Sicily, have become outdated and endangered due to the commercial varieties spreading. These accessions are poorly known but often represent a genetic heritage to be preserved and enhanced. The ex situ conservation of fifty-seven Sicilian common bean landraces was carried out at the “Living Plants Germplasm Bank” at Ucria (Messina, Italy), founded by the Nebrodi Regional Park, together with the “Sicilian Plant Germplasm Repository” of University of Palermo (SPGR/PA). To assess the germplasm genetic diversity, nineteen morphological traits and eight Simple Sequence Repeats (SSRs) were used. Genetic distances among landraces were calculated to construct a clustering tree by using unweighted pair group method arithmetic (UPGMA). Seed germplasm diversity of Sicilian common bean varied from 80.7% to 93.3%, based on six seed descriptors and six leaf, flower, and pod descriptors, respectively, while cluster genetic analysis depicted a clear separation among all the 57 landraces. Principal coordinates (PCoA) and STRUCTURE analyses showed a prevalent rate of admixture between Mesoamerican and Andean gene pools in Sicilian common bean collection, confirming its heterogeneity. The observed high level of diversity evidenced the needs to adopt accurate criterion to plan a definitive ex situ germplasm collection to share agrobiodiversity with local farmers and to avoid any further loss of genetic resources in rural and protected areas.

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Genetic divergence of Heliconiaceae species in the Central West Brazil region

Agronomía Colombiana ◽

10.15446/agron.colomb.v35n3.67661 ◽

2017 ◽

Vol 35 (3) ◽

pp. 285-292

Author(s):

Cintia Graciele Da Silva ◽

Edneia Zullian Dalbosco ◽

Petterson Baptista Da Luz ◽

Willian Krause ◽

Vivian Loges ◽

...

Keyword(s):

Genetic Variability ◽

Genetic Divergence ◽

Quantitative Traits ◽

Group Method ◽

Clustering Methods ◽

Breeding Programs ◽

Mato Grosso ◽

Relative Contribution ◽

Pair Group ◽

Inflorescence Length

The purpose of this study was to describe morphological traits and estimate genetic divergence and parameters between accessions of the genus Heliconia sp. from different municipalities in the state of Mato Grosso, Brazil. A set of 25 traits, 15 quantitative and 10 qualitative were evaluated. The genetic divergence was estimated based on Mahalanobis' distance, with the clustering methods known as Unweighted Pair Group Method using Arithmetic Averages (UPGMA). Genetic variability was observed for all assessed quantitative traits and the accessions were grouped in different classes. The traits with highest relative contribution to variability were longevity of flower stems and inflorescence length. The results indicated the existence of genetic variability among accessions of the Heliconiasp. germplasm bank, which can be used in breeding programs.

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

Plants ◽

10.3390/plants10050890 ◽

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.

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Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000400007 ◽

2000 ◽

Vol 23 (4) ◽

pp. 739-743 ◽

Cited By ~ 1

Author(s):

Mariana Pires de Campos Telles ◽

José Alexandre Felizola Diniz-Filho

Keyword(s):

Stochastic Process ◽

Genetic Divergence ◽

Isolation By Distance ◽

Genetic Distances ◽

Small Sample ◽

Group Method ◽

Gene Frequencies ◽

Exponential Relationship ◽

Local Populations ◽

Pair Group

An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a relatively small number of local populations, the correlogram profiles varied considerably, with Manhattan distances greater than those defined by other simulation studies. This method allows one to establish a range of correlogram profiles under the same stochastic process of spatial divergence, thereby avoiding the use of unnecessary explanations of genetic divergence based on other microevolutionary processes.

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