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.

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

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.

scholarly journals SSR Markers Reveal the Genetic Diversity of Asian Cercis Taxa at the U.S. National Arboretum

HortScience ◽  
2017 ◽  
Vol 52 (4) ◽  
pp. 498-502 ◽  
Author(s):  
Chandra S. Thammina ◽  
David L. Kidwell-Slak ◽  
Stefan Lura ◽  
Margaret R. Pooler
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
The United States ◽  
Group Method ◽  
Cercis Canadensis ◽  
Landscape Plant ◽  
Pair Group ◽  
Upgma Cluster Analysis ◽  
Eastern Redbud ◽  
The U.S

The redbud (Cercis L. species) is a popular landscape plant grown widely in the United States. There are more than 20 cultivars of eastern redbud (Cercis canadensis L.) and at least three cultivars of Asian taxa (primarily Cercis chinensis Bunge) in the trade. The U.S. National Arboretum (USNA) has a diverse collection of Cercis germplasm collected in North America and Asia. Fourteen genomic simple sequence repeat (genomic-SSR) markers were used to analyze the genetic diversity of 53 accessions of Asian Cercis taxa from our collection, including C. chinensis, Cercis chingii Chun, Cercis gigantea ined., Cercis glabra Pamp., Cercis racemosa Oliv., and Cercis yunnanensis Hu and W. C. Cheng. SSR markers detected an average of 5.7 alleles per locus with a range of two to nine alleles. A dendrogram was generated by unweighted pair group method with arithmetic mean (UPGMA) cluster analysis using the Jaccard similarity coefficient. Four major clusters were identified. Accessions tended to group by taxa or provenance, but with some notable exceptions caused either by misidentification or nomenclatural confusion in the species. This information will be used for collection management and for making decisions in the breeding program to maximize genetic diversity of cultivated Cercis.

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 Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 143
Author(s):  
Lei Zhu ◽  
Huayu Zhu ◽  
Yanman Li ◽  
Yong Wang ◽  
Xiangbin Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Group Method ◽  
Motif Length ◽  
Pair Group ◽  
Ssr Loci ◽  
Ssr Frequency ◽  
Basic And Applied Research ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.

Use of expressed sequence tag microsatellite markers for exploring genetic diversity in lentil and related wild species

2016 ◽  
Vol 154 (7) ◽  
pp. 1254-1269 ◽  
Author(s):  
A. SINGH ◽  
H. K. DIKSHIT ◽  
D. SINGH ◽  
N. JAIN ◽  
M. ASKI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Wild Species ◽  
Expressed Sequence Tag ◽  
Group Method ◽  
Comparative Genomic ◽  
Pair Group ◽  
Ssr Loci ◽  
Related Wild Species ◽  
Expressed Sequence

SUMMARYExpressed sequence tag-simple sequence repeat (EST-SSR) markers were used to analyse genetic diversity among three Lens species. The SSR loci amplified successfully in wild species, with 94·82% transferability in Lens culinaris subsp. orientalis, 95·4% in Lens nigricans, 98·81% in L. culinaris subsp. odemensis, 94·82% in L. culinaris subsp. tomentosus and 96·55% in Lens ervoides. Ninety-nine alleles (average 3·41 alleles/locus) were detected by 29 SSR markers. Based on the unweighted pair group method with arithmetic mean cluster analysis, all the genotypes were grouped into three clusters at a similarity level of 0·30. The diversity analysis indicated no species-specific clustering of the wild and cultivated species. Wild species L. nigricans and L. culinaris subsp. odemensis, L. culinaris subsp. orientalis and L. ervoides were grouped in Cluster I, whereas the Mediterranean land races of L. culinaris subsp. culinaris and L. culinaris subsp. tomentosus formed a separate group in Cluster II A. Cluster II B comprised L. ervoides, L. culinaris subsp. orientalis and L. culinaris subsp. culinaris. Clusters II C, II D and II F included cultivated Indian lentil genotypes. Cluster II E comprised Indian and Mediterranean germplasm lines. Cluster II F included three early maturing germplasm lines, whereas Cluster III included only two germplasm lines. The functional annotation of SSR-containing unigenes revealed that a majority of genes were involved in an important transport-related function or were a component of metabolic pathways. A high level of polymorphism of EST-SSRs and their transferability to related wild species indicated that these markers could be used for molecular screening, map construction, comparative genomic studies and marker-assisted selection.

Revealing Genetic Diversity, Population Structure and Cultivar-Specific SSR Alleles in Pistachio Using SSR Markers

2021 ◽  
Author(s):  
Harun Karcı ◽  
Aibibula Paizila ◽  
Murat Güney ◽  
Mederbek Zhaanbaev ◽  
Salih Kafkas
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Large Scale ◽  
Germplasm Collection ◽  
Mean Value ◽  
Group Method ◽  
Arithmetic Average ◽  
Genic Ssr ◽  
Pair Group ◽  
Average Analysis

Abstract Pistachio (Pistacia vera L.) is the only cultivated species in Pistacia genus and one of the most important nut crop in terms of production. Pistachio cultivars have significant level of variation in their phenotypic appearance and productivity. Understanding the genetic diversity between pistachio cultivars could facilitate breeding programs. Simple sequence repeat (SSR) markers are powerful tools in genetic diversity and germplasm collection studies. However, published information about the characterization of large scale pistachio cultivar germplasm with adequate number of SSR markers is limited. In this study, sixty-six pistachio cultivars and genotypes originated from six different countries were characterized and fingerprinted by 74 genomic and 18 genic SSR markers. SSR analysis identified 576 alleles for all 66 cultivars and genotypes. The number of alleles per locus ranged from 2 to 20 (CUPOhBa1592) alleles with a mean value of six alleles per locus. The polymorphism information content (PIC) values ranged from 0.07 (CUPVEST2939) to 0.87 (CUPSiOh2460) with a mean PIC value of 0.58. The pistachio cultivars and genotypes were divided into five clusters according to Structure and UPGMA (Unweighted Pair Group Method with Arithmetic Average) analysis. Total of 61 cultivar specific alleles were detected in 34 cultivars, among them three primers (CUPOhBa1592, CUPBaPa1606 and CUPOhBa2127) produced more than four cultivar-specific loci therefore very promising for cultivar identification, fingerprinting and breeding studies in pistachio.

Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 731-737 ◽  
Author(s):  
N A Barkley ◽  
M L Newman ◽  
M L Wang ◽  
M W Hotchkiss ◽  
G A Pederson
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Phylogenetic Relationships ◽  
Expressed Sequence Tag ◽  
Genetic Distances ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Expressed Sequence ◽  
Simple Sequence

Polymorphic expressed sequence tag - simple sequence repeat (EST-SSR) markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number of alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pairwise combinations and assessing differences in character data. The resulting dendrograms (unweighted pair group method with arithmetic means (UPGMA) and parsimony) clustered the accessions into 2 main clades, which corresponded to accessions characterized morphologically as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their current taxonomic classification. These markers were also beneficial in identifying contaminated and (or) misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera.Key words: bamboo germplasm, genetic diversity, phylogeny.

scholarly journals Caracterização de acessos de pimentas do Amazonas

2015 ◽  
Vol 33 (3) ◽  
pp. 290-298 ◽  
Author(s):  
Lucifrancy V Costa ◽  
Jânia LS Bentes ◽  
Maria TG Lopes ◽  
Silfran RM Alves ◽  
Januário M Viana Júnior
Keyword(s):  
Genetic Resources ◽  
Plant Genetic Resources ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
International Plant ◽  
Unweighted Pair Group Method

No Brasil é encontrada ampla variabilidade de pimentas do gênero Capsicum sendo a Amazônia um importante centro de diversidade. Informações a respeito da diversidade em coleção de germoplasma servem, entre outros objetivos, para dar suporte aos programas de melhoramento de espécies cultivadas. O presente trabalho teve como objetivos caracterizar morfologicamente e estimar a diversidade genética entre 40 acessos de pimentas coletadas no Amazonas, pertencentes à coleção da Universidade Federal do Amazonas. Foram utilizados descritores morfológicos recomendados pelo IPGRI (International Plant Genetic Resources Institute) para o gênero Capsicum e análise sensorial para pungência e aroma. Utilizando 17 descritores, identificados como essenciais, foi calculada a similaridade genética entre os acessos por meio do coeficiente de similaridade geral de Gower. Para o agrupamento dos acessos foi utilizado o método hierárquico das médias das distâncias UPGMA (Unweighted Pair-Group Method Using an Arithmetic Average) e a representação gráfica da similaridade entre eles feita pelo método de Análise de Coordenadas Principais (PCO). Três espécies foram identificadas, sendo 35 de C. chinense um de C. baccatum e quatro acessos de C. frutescens. Houve variabilidade fenotípica principalmente nas características de frutos que mostraram diferenças quanto ao tamanho, formato, coloração e pungência. Foram identificadas duas pimenteiras do morfotipo murupi, duas dedo de moça, quatro malagueta, sete olho de peixe, 13 pimentas de cheiro e 12 pimentas curabiá. As análises de agrupamento e dispersão gráfica foram concordantes em agrupar os acessos com pequena distância genética. Os acessos estudados apresentaram ampla variabilidade entre e dentro das espécies identificadas.

scholarly journals Genetic Diversity of Carpetgrass Germplasm Based on Simple Sequence Repeat Markers

HortScience ◽  
2015 ◽  
Vol 50 (6) ◽  
pp. 797-800
Author(s):  
Xiaoli Wang ◽  
Zhiyong Wang ◽  
Li Liao ◽  
Xinyi Zhang ◽  
Changjun Bai
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Warm Season ◽  
Group Method ◽  
Sequence Repeat ◽  
Marker Assisted Breeding ◽  
Arithmetic Means ◽  
Pair Group ◽  
Simple Sequence

Carpetgrass [Axonopus compressus (Sw.) Beauv.] is an important warm-season perennial turfgrass that is widely used in tropical and subtropical areas. The genetic diversity of 63 carpetgrass accessions in China was studied using simple sequence repeat (SSR) markers. Fourteen SSR primer combinations generated a total of 49 distinct bands, 48 (97.96%) of which were polymorphic. The number of observed alleles ranged from 2 to 6, with an average of 3.5. Coefficients of genetic similarity among the accessions ranged from 0.24 to 0.98. Unweighted pair-group method with arithmetic means (UPGMA) clustered the 63 accessions into three groups, and not all samples from the same region belonged to the same group. SSR markers will promote marker-assisted breeding and the assessment of genetic diversity in wild germplasm resources of carpetgrass.

scholarly journals Genetic Diversity and Population Structure of Japanese Plum-Type (Hybrids of P. salicina) Accessions Assessed by SSR Markers

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1748
Author(s):  
Brenda I. Guerrero ◽  
M. Engracia Guerra ◽  
Sara Herrera ◽  
Patricia Irisarri ◽  
Ana Pina ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Group Method ◽  
Japanese Plum ◽  
Pair Group ◽  
Prunus Salicina ◽  
Wide Range ◽  
High Level ◽  
Informative Content

Japanese plum (Prunus salicina Lindl.) is widely distributed in temperate zones across the world. Since its introduction to USA in the late 19th century, this species has been hybridized with up to 15 different diploid Prunus species. This high level of introgression has resulted in a wide range of traits and agronomic behaviors among currently grown cultivars. In this work, 161 Japanese plum-type accessions were genotyped using a set of eight Simple Sequence Repeats (SSR) markers to assess the current genetic diversity and population structure. A total of 104 alleles were detected, with an average of 13 alleles per locus. The overall Polymorphic Informative Content (PIC) value of SSR markers was 0.75, which indicates that these SSR markers are highly polymorphic. The Unweighted Pair Group Method with Arithmetic (UPGMA) dendrogram and the seven groups inferred by Discriminant Analysis of Principal Components (DAPC) revealed a strong correlation of the population structure to the parentage background of the accessions, supported by a moderate but highly significant genetic differentiation. The results reported herein provide useful information for breeders and for the preservation of germplasm resources.

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