scholarly journals Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 487
Author(s):  
Trinity P. Hamm ◽  
Marcin Nowicki ◽  
Sarah L. Boggess ◽  
William E. Klingeman ◽  
Denita Hadziabdic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Diversity Index ◽  
Molecular Tools ◽  
Closely Related Species ◽  
Future Studies ◽  
Expected Heterozygosity ◽  
Large Genus ◽  
Simple Sequence

The Viburnum genus is of particular interest to horticulturalists, phylogeneticists, and biogeographers. Despite its popularity, there are few existing molecular markers to investigate genetic diversity in this large genus, which includes over 160 species. There are also few polymorphic molecular tools that can delineate closely related species within the genus. Viburnum farreri, a member of the Solenotinus subclade and one of the centers of diversity for Viburnum, was selected for DNA sequencing and development of genomic simple sequence repeats (gSSRs). In this study, 15 polymorphic gSSRs were developed and characterized for a collection of 19 V. farreri samples. Number of alleles per locus ranged from two- to- eight and nine loci had four or more alleles. Observed heterozygosity ranged from 0 to 0.84 and expected heterozygosity ranged from 0.10 to 0.80 for the 15 loci. Shannon diversity index values across these loci ranged from 0.21 to 1.62. The markers developed in this study add to the existing molecular toolkit for the genus and will be used in future studies investigating cross-transferability, genetic variation, and species and cultivar delimitation in the Viburnum genus and closely allied genera in the Adoxaceae and Caprifoliaceae.

Molecular characterization of almond accessions from the island of La Palma (Canary Islands, Spain) using SSR markers

2014 ◽  
Vol 12 (3) ◽  
pp. 323-329 ◽  
Author(s):  
Guillermo Padilla ◽  
Rafel Socias i Company ◽  
Amando Ordás
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Average Value ◽  
La Palma ◽  
Expected Heterozygosity ◽  
Commercial Cultivars ◽  
Soft Shell ◽  
Genetic Profiles ◽  
Simple Sequence

In this study, 15 simple sequence repeat (SSR) markers were used for genetic diversity analysis of 45 almond accessions, which included 25 local cultivars from La Palma Island and three other commercial cultivars. A total of 110 amplification fragments were produced, with an average value of 7.9 alleles per locus. Twelve of the SSR markers can be considered as highly informative, with values of expected heterozygosity and power of discrimination above 0.5 and 0.8, respectively. Due to cases of synonymy and homonymy, 37 different genetic profiles were obtained, with the homonymy of the soft-shell varieties known as ‘Mollar’ being the most significant. Cluster analysis identified four groups within the accessions. One of these groups exclusively consisted of the two commercial cultivars ‘Guara’ and ‘Ferraduel’. The other commercial cultivar used in the study, ‘Desmayo Largueta’, was in a cluster with three cultivars from the same locality. The analysis of molecular variance revealed that the within-localities component accounts for most of the total variation, suggesting that La Palma almond cultivars did not originate independently in different parts of the island. The results of the study reveal the genetic singularity of La Palma almond cultivars and the genetic diversity among them.

scholarly journals Evaluation of the Genetic Variation of Cowpea Landraces (Vigna unguiculata) from Western Cameroon Using Qualitative Traits

2017 ◽  
Vol 9 (4) ◽  
pp. 508-514 ◽  
Author(s):  
Toscani NGOMPE-DEFFO ◽  
Eric Bertrand KOUAM ◽  
Honoré BEYEGUE-DJONKO ◽  
Mariette ANOUMAA
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Growth Habit ◽  
Diversity Index ◽  
Diversity Indices ◽  
Crop Species ◽  
Qualitative Trait ◽  
Qualitative Traits ◽  
Leaf Hairiness

Characterization of the genetic diversity and analysis of the genetic relationship between accessions of a crop species is a key step in breeding superior cultivars. The main objective of the hereby study was to determine the genetic variation between 30 cowpea accessions collected throughout the eight divisions of the Western Region of Cameroon using qualitative traits. Phenotypic variation of these accessions was evaluated using diversity indices and cluster analyses. A total of twenty qualitative traits were used for the study. Fifteen of them (75%) were polymorphic, displaying each at least two phenotypic classes. The monomorphic characters were growth pattern, leaf color, leaf hairiness, plant hairiness and pod hairiness, each with only one phenotypic class. Results showed a relatively significant level of genetic diversity among the studied cowpea accessions. Overall, the average of the observed and effective number of phenotypic classes per qualitative trait were Na = 2.350 and Ne = 1.828 respectively. The Nei’s genetic diversity and the Shannon weaver diversity index were He = 0.369, ranging from zero (monomorphic trait) to 0.655 (growth habit) and H’ = 0.609, ranging from zero (monomorphic trait) to 0.996 (seed crowding), respectively. The dendrogram constructed from the twenty qualitative traits revealed 05 accessions clusters with the number of accessions in each cluster varying from one to eleven. Information obtained from this study is likely be useful for future cowpea breeding program.

scholarly journals Characterization of Genetic Diversity of Stone Fruit Rootstocks Used in Chile by Means of Microsatellite Markers

2012 ◽  
Vol 137 (5) ◽  
pp. 302-310 ◽  
Author(s):  
María José Arismendi ◽  
Patricio Hinrichsen ◽  
Ruben Almada ◽  
Paula Pimentel ◽  
Manuel Pinto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Stone Fruit ◽  
Identification System ◽  
Expected Heterozygosity ◽  
Commercially Important ◽  
Taxonomic Groups ◽  
Simple Sequence

Stone fruit (Prunus L.) production in Chile covers ≈43,000 ha and includes a wide variety of soils and climates requiring a large diversity of rootstocks. The most commercially important rootstock cultivars are 26 genotypes from three different taxonomic groups belonging to the subgenera Amygdalus (L.) Benth. Hook. (peach group), Prunus Focke [= Prunophora (Neck.)] Focke (plum group), and Cerasus (Adans.) Focke (cherry group) with eight, seven, and 10 individuals, respectively. To determine their genetic diversity, characterization by microsatellite markers [simple sequence repeat (SSR)] was conducted. Of a total of 20 SSR markers evaluated, 12 generated amplified products that were consistent in the three taxonomic groups. The number of alleles per marker ranged from 18 for PSM-3 to four in CPPCT-002. Clustering analysis, by both traditional hierarchical and model-based approaches, indicate that all genotypes are clustered in their respective taxonomic groups, including the interspecific hybrids. Genetic diversity, measured as the average distances (expected heterozygosity) between individuals in the same cluster, was higher in Cerasus (0.78) followed by Prunus (0.72) and Amygdalus (0.64). Total number of alleles observed was 133, of which 14, 33, and 35 from six, 10, and 10 loci were unique for the peach, plum, and cherry rootstock groups, respectively. Alleles shared among peach/plum, plum/cherry, and peach/cherry rootstock genotypes were 13, 14, and 18 from nine, seven, and seven loci, respectively. Only six alleles from five loci were common to the three taxonomic groups. In addition, to develop a rootstock identification system based on SSR markers, a minimum set of three markers (PMS-3, BPPCT-037, and BPPCT-036) able to differentiate the 26 genotypes was identified. This study is the first step toward establishing a stone fruit rootstock breeding program in Chile.

ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

2021 ◽  
Author(s):  
Lalit Arya ◽  
Ramya Kossery Narayanan ◽  
Anjali Kak ◽  
Chitra Devi Pandey ◽  
Manjusha Verma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Morinda Citrifolia ◽  
Species Differentiation ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

Genetic Diversity and Characterization of a Core Collection of Malus Germplasm Using Simple Sequence Repeats (SSRs)

2011 ◽  
Vol 30 (4) ◽  
pp. 827-837 ◽  
Author(s):  
Sarah M. Potts ◽  
Yuepeng Han ◽  
M. Awais Khan ◽  
Mosbah M. Kushad ◽  
A. Lane Rayburn ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Core Collection ◽  
Simple Sequence

scholarly journals Polymorphic microsatellites of analysis in cultivars of taro

2012 ◽  
Vol 30 (1) ◽  
pp. 106-111 ◽  
Author(s):  
Raquel SC Nunes ◽  
Fernanda R Pinhati ◽  
Luciana P Golinelli ◽  
Tiyoko Nair H Rebouças ◽  
Vânia Margaret F Paschoalin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Varieties ◽  
Mato Grosso ◽  
Espírito Santo ◽  
Polymorphic Microsatellites ◽  
Espirito Santo ◽  
Microsatellite Alleles ◽  
Mato Grosso Do Sul ◽  
Simple Sequence

Taro (Colocasia esculenta) is a tuberous plant belonging to the Araceae family whose tuber is the 14th most consumed food crop in the world. Characterized as an unconventional vegetable, taro is grown in Brazil as a subsistence crop, but in recent years began to gain commercial importance, especially in the states of Espirito Santo, Minas Gerais and Rio de Janeiro. To avoid loss of genetic diversity of the local varieties traditionally grown in Brazil a core collection for taro germplasm has been developed by the Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural do estado do Espirito Santo (Incaper). The aim of this study was to perform a molecular characterization of the seven regional core collections. Genetic diversity of the cultivars was investigated by using SSR (Simple Sequence Repeats) polymorphisms, in seven loci (Xuqtem55, Xuqtem73, Xuqtem84, Xuqtem88, Xuqtem91, Xuqtem97 and Xuqtem110). Genetic diversity of the cultivars, based on the seven microsatellite alleles, was evaluated by using the software GelCompar II, showed that the loci Xuqtem73, Xuqtem88 and Xuqtem110 were the most informative, featuring 7, 10 and 8 alleles, respectively, a percentage of cultivars with polymorphic alleles of 85, 57 and 100% and identical PIC of 0.91. Based on Xuqtem110 locus analysis, the seven cultivars were grouped in two clusters. Chinês Regional Incaper cultivar was originated from Chinês cultivar which originated the São Bento cultivar, corroborating previous results. Macaquinho and Chinês cultivars were shown to be the primitive ones originating the allelic collections found in the states of Mato Grosso do Sul and Espirito Santo.

scholarly journals Genetic analysis of silver-fir populations in the Beskids

2011 ◽  
Vol 72 (2) ◽  
pp. 115-119 ◽  
Author(s):  
Leon Mejnartowicz
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Abies Alba ◽  
Genetic Distances ◽  
Silver Fir ◽  
Geographical Distance ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (<em>Abies alba</em>): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (<em>I</em> = <em>0.42</em>), percentage of polymorphic loci <em>(%PoL </em>= <em>64.29</em>) and number of rare alleles (<em>NoRa </em>= <em>5</em>). Besides, the BM population has the highest observed heterozygosity (<em>Ho </em>= <em>0.291</em>), which exceeds the expected heterozygosity (<em>He </em>= <em>0.254</em>), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of <em>He </em>= <em>0.262 </em>and <em>Ho </em>= <em>0.264</em>.

Assessment of Genetic Diversity of Rheum species (Endangered Medicinal Herb of Indian Himalayan Region) using Molecular Markers

2021 ◽  
Vol 16 (11) ◽  
pp. 147-154
Author(s):  
Anjali Uniyal ◽  
Akhilesh Kumar ◽  
Sweta Upadhyay ◽  
Vijay Kumar ◽  
Sanjay Gupta
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Fragment Length Polymorphism ◽  
Dna Polymorphisms ◽  
Inter Simple Sequence Repeats ◽  
Pharmaceutical Industries ◽  
Endangered Medicinal Herb ◽  
Identification And Characterization ◽  
Simple Sequence

The Rheum species are important medicinal plants that are facing extinction due to their unplanned development and overexploitation by pharmaceutical industries. DNA polymorphisms are not prone to environmental modifications, thus they are widely used for the identification and characterization of plants. The use of different molecular markers has enabled the researchers for the valuation of genetic variability and diversity in its natural zone of distribution. The conventional approach may take several years to yield this information. For the estimation of molecular and genetic variations in geographical zone of distribution, various molecular markers technique are available like RAPD (Randomly Amplified Polymorphic DNA), RFLP (Restriction fragment length polymorphism), ISSR (Inter-Simple Sequence Repeats), SSR and AFLP. The uses of different molecular markers for the study of genetic diversity have been discussed in the review.

Schistosome genetic diversity: the implications of population structure as detected with microsatellite markers

Parasitology ◽  
2002 ◽  
Vol 125 (7) ◽  
pp. S51-S59 ◽  
Author(s):  
J. CURTIS ◽  
R. E. SORENSEN ◽  
D. J. MINCHELLA
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Microsatellite Markers ◽  
Natural Populations ◽  
Mitochondrial Marker ◽  
Tropical Regions ◽  
Blood Flukes

Blood flukes in the genus Schistosoma are important human parasites in tropical regions. A substantial amount of genetic diversity has been described in populations of these parasites using molecular markers. We first consider the extent of genetic variation found in Schistosoma mansoni and some factors that may be contributing to this variation. Recently, though, attempts have been made to analyze not only the genetic diversity but how that diversity is partitioned within natural populations of schistosomes. Studies with non-allelic molecular markers (e.g. RAPDs and mtVNTRs) have indicated that schistosome populations exhibit varying levels of gene flow among component subpopulations. The recent characterization of microsatellite markers for S. mansoni provided an opportunity to study schistosome population structure within a population of schistosomes from a single Brazilian village using allelic markers. Whereas the detection of population structure depends strongly on the type of analysis with a mitochondrial marker, analyses with a set of seven microsatellite loci consistently revealed moderate genetic differentiation when village boroughs were used to define parasite subpopulations and greater subdivision when human hosts defined subpopulations. Finally, we discuss the implications that such strong population structure might have on schistosome epidemiology.

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