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

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.

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Assessment of Genetic Diversity in Cultivated Tomato (Solanum Lycopersicum L.) Genotypes Using Rapd Primers

Journal of Horticultural Research ◽

10.2478/johr-2013-0012 ◽

2013 ◽

Vol 21 (1) ◽

pp. 83-89 ◽

Cited By ~ 5

Author(s):

Saida Sharifova ◽

Sabina Mehdiyeva ◽

Konstantinos Theodorikas ◽

Konstantinos Roubos

Keyword(s):

Genetic Diversity ◽

Rapd Analysis ◽

Diversity Index ◽

Random Amplified Polymorphic Dna ◽

Arithmetic Mean ◽

Similarity Coefficient ◽

Group Method ◽

Solanum Lycopersicum L ◽

Pair Group ◽

Upgma Cluster Analysis

Abstract Random Amplified Polymorphic DNA (RAPD) analysis was carried out on 19 Azerbaijan tomato genotypes, both cultivars and local populations. A total of 26 amplified products were revealed by 6 primers. The genetic similarity among evaluated genotypes ranged from 0.188 to 1.000. The lowest similarity was observed between cultivars ‘Azerbaijan’ and ‘Shakar’ (0.188), while the highest between ‘Elnur’ and ‘Garatag’ (1.000). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on Jaccard’s similarity coefficient divided genotypes into four main groups. The first group was the largest and consisted of 12 genotypes, while the fourth group was the smallest consisted of 1 genotype only. The most polymorphic primer was OPB-18 that presented a genetic diversity index of 0.823, while the least informative was primer OPG-17 with an index of 0.349. The average genetic diversity calculated from RAPD data was 0.665.

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Molecular Analysis of Genetic Diversity and Geographic Origin within an Ex Situ Germplasm Collection of Cherimoya by Using SSRs

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.132.3.357 ◽

2007 ◽

Vol 132 (3) ◽

pp. 357-367 ◽

Cited By ~ 12

Author(s):

P. Escribano ◽

M.A. Viruel ◽

J.I. Hormaza

Keyword(s):

Genetic Diversity ◽

Geographic Origin ◽

Germplasm Collection ◽

Ex Situ ◽

Group Method ◽

Pair Group ◽

Ssr Primers ◽

Upgma Cluster Analysis ◽

Ssr Loci ◽

Simple Sequence

Cherimoya (Annona cherimola Mill.) is an underused fruit crop with a clear niche for expansion in subtropical climates. In this study, 16 simple sequence repeat (SSR) loci were used to find molecular polymorphisms among 279 cherimoya accessions from a worldwide ex situ field germplasm collection. A total of 79 amplification fragments were amplified with 16 pairs of SSR primers, with an average of 4.9 bands/SSR. Mean expected and observed heterozygosities averaged 0.53 and 0.44, respectively. The total value for the probability of identity was 4.34 × 10−8. The SSRs studied resulted in 267 different fingerprinting profiles, of which 258 were unique genotypes; the rest were putative cases of synonymies or mislabeling errors. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis indicated the relationships among the analyzed accessions, showing some specific groups related to their geographical origins. Analysis of molecular variance (AMOVA) was performed to examine the distribution of genetic variation of the 148 accessions collected from putative cherimoya origin areas in Ecuador and Peru, showing that the major variations occurred within valleys in each country. The results confirmed the usefulness of microsatellites for identification of genetic diversity and geographic origin of cherimoya and are discussed in terms of their implications for ex situ conservation of cherimoya genetic resources.

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Genetic diversity and relationships in jute (Corchorus spp.) revealed by SSR markers

Bangladesh Journal of Botany ◽

10.3329/bjb.v38i2.5140 ◽

1970 ◽

Vol 38 (2) ◽

pp. 153-161 ◽

Cited By ~ 10

Author(s):

Saaimatul Huq ◽

Md Shahidul Islam ◽

Abu Ashraqur Sajib ◽

Nadim Ashraf ◽

Samiul Haque ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Marker ◽

Group Method ◽

Individual Plant ◽

Corchorus Olitorius ◽

Corchorus Capsularis ◽

Pair Group ◽

Ssr Primers ◽

Upgma Cluster Analysis

Characterization of sixteen jute genotypes, from Corchorus olitorius L. and Corchorus capsularis L. using jute specific SSR marker attained a high polymorphism value of 92.20%. A total of 171 different alleles were amplified by 27 primer pairs with a mean of 6.33 ± 2.04 alleles per locus. The genetic diversity was also relatively high (0.81 ± 0.06). The Un-weighted Pair-group Method with Arithmetic averages (UPGMA) cluster analysis of the 16 jute genotypes produced a dendogram, which was in concordance with known information. The study reinforces the utility of SSR primers for providing useful and high levels of markers for individual plant genotypes even with a narrow genetic base. Key words: Jute; Genetic diversity; SSR; Genotypes; Polymorphism DOI: 10.3329/bjb.v38i2.5140 Bangladesh J. Bot. 38(2): 153-161, 2009 (December)

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Assessment of genetic diversity in 35 Pisum sativum accessions using microsatellite markers

Canadian Journal of Plant Science ◽

10.4141/cjps2011-261 ◽

2012 ◽

Vol 92 (6) ◽

pp. 1075-1081 ◽

Cited By ~ 11

Author(s):

Sajjad Ahmad ◽

Manjit Singh ◽

Neil Dylan Lamb-Palmer ◽

Mark Lefsrud ◽

Jaswinder Singh

Keyword(s):

Genetic Diversity ◽

Pisum Sativum ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Group Method ◽

Gene Pools ◽

Breeding Lines ◽

High Performing ◽

Pair Group ◽

Upgma Cluster Analysis

Ahmad, S., Singh, M., Lamb-Palmer, N. D., Lefsrud, M. and Singh, J. 2012. Assessment of genetic diversity in 35 Pisum sativum accessions using microsatellite markers. Can. J. Plant Sci. 92: 1075–1081. Field pea is an important Canadian pulse crop and therefore developing high-performing cultivars is critical for Canadian pea growers. Information about genetic diversity is a key component for the creation of novel and desirable germplasm to develop elite pea breeding lines. The objective of the present study is to assess genetic diversity in 35 diverse Pisum accessions using 15 polymorphic microsatellites located on different pea chromosomes. Microsatellites were found to be polymorphic, amplifying a total of 41 alleles and were able to differentiate all 35 Pisum genotypes. These markers were scored by their polymorphic information content (PIC), ranging from 0.055 (AA206) to 0.660 (AB72) with an average of 0.460, and by their discriminating power (D), which varied from 0.057 (AA206) to 0.679 (AB 72) with an average of 0.475. Genetic similarity values ranged from 0.074 (between Maple pea NZ and Line 45760) to 0.875 (between Galena and Dakota) with an average of 0.336. Unweighted pair group method with arithmetic averages (UPGMA) cluster analysis grouped the 35 pea accessions into two major clusters and eight sub-clusters. The majority of Canadian and European genotypes were grouped separately, suggesting both these groups are from genetically distinct gene pools. The genetically diverse groups identified in this study can be used to derive parental lines for pea breeding.

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

Horticulturae ◽

10.3390/horticulturae7060143 ◽

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.

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Genetic Diversity of Puerto Rican Farmer-held Papaya (Carica papaya) Using SSR Markers

HortScience ◽

10.21273/hortsci12943-18 ◽

2018 ◽

Vol 53 (8) ◽

pp. 1109-1114 ◽

Cited By ~ 1

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.

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

The Journal of Agricultural Science ◽

10.1017/s0021859615001252 ◽

2016 ◽

Vol 154 (7) ◽

pp. 1254-1269 ◽

Cited By ~ 1

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.

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

10.21203/rs.3.rs-1104578/v1 ◽

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.

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

Genome ◽

10.1139/g05-022 ◽

2005 ◽

Vol 48 (4) ◽

pp. 731-737 ◽

Cited By ~ 28

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.

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Genetic Diversity and Relationships in Malus sp. Germplasm Collections as Determined by Randomly Amplified Polymorphic DNA

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.126.3.318 ◽

2001 ◽

Vol 126 (3) ◽

pp. 318-328 ◽

Cited By ~ 15

Author(s):

Nnadozie C. Oraguzie ◽

Sue E. Gardiner ◽

Heather C.M. Basset ◽

Mirko Stefanati ◽

Rod D. Ball ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Random Amplified Polymorphic Dna ◽

Group Method ◽

Scatter Plot ◽

Arithmetic Average ◽

Germplasm Collections ◽

Food Research ◽

Pair Group ◽

Upgma Cluster Analysis

Four subsets of apple (Malus Mill.) germplasm representing modern and old cultivars from the repository and apple genetics population of the Horticulture and Food Research Institute of New Zealand Limited were used in this study. A total of 155 genotypes randomly chosen from the four subsets were analyzed for random amplified polymorphic DNA (RAPD) variation. Nine decamer primers generated a total of 43 fragments, 42 of which were polymorphic across the 155 genotypes. Pairwise distances were calculated between germplasm subsets using the distance metric algorithm in S-PLUS, and used to examine intra-and inter-subset variance components by analysis of molecular variation (AMOVAR). A phenogram based on unweighted pair group method with arithmetic average (UPGMA) cluster analysis was constructed from the pairwise distances and a scatter plot was generated from principal coordinate analysis. The AMOVAR showed that most of the variation in the germplasm (94.6%) was found within subsets, suggesting that there is significant variation among the germplasm. The grouping of genotypes based on the phenogram and scatter plot generally did not reflect the pedigree or provenance of the genotypes. It is possible that more RAPD markers are needed for determining genetic relationships in apple germplasm. Nevertheless, the variation observed in the study suggests that the current practice of sublining populations in the first generation to control inbreeding may not be necessary in subsequent generations. If these results are confirmed by fully informative molecular markers, germplasm managers should reassess the structure of their genetics populations. There may be a need to combine sublines in order to capture the maximum genetic diversity available and to streamline breeding efforts.

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