Genetic relationships within the Cucurbitaceae as assessed by consensus chloroplast simple sequence repeats (ccSSR) marker and sequence analyses

2003 ◽  
Vol 81 (8) ◽  
pp. 814-832 ◽  
Author(s):  
Sang-Min Chung ◽  
Deena S Decker-Walters ◽  
Jack E Staub
Keyword(s):  
Simple Sequence Repeats ◽  
Genetic Relationships ◽  
Morphological Data ◽  
Insertion And Deletion ◽  
Nicotiana Tabacum L ◽  
The Family ◽  
Pcr Products ◽  
Species Comparisons ◽  
Sequence Substitution ◽  
Simple Sequence

To investigate genetic relationships in Benincaseae (19 accessions), Cucurbiteae (1), Joliffieae (2), Melothrieae (2), and Sicyeae (3) tribes of the family Cucurbitaceae, consensus chloroplast simple sequence repeats (ccSSR) primer pairs obtained from tobacco (Nicotiana tabacum L.) chloroplast DNA were used. Variation in the length and putative sequence substitution events of polymerase chain reaction (PCR) products were analyzed. Sequencing of four fragments (ccSSR-1, -7, -8, and -19) revealed that convergence in fragment length occurs in more distant species comparisons. In ccSSR-1 and -8, the same fragment lengths occurred as the result of different insertion and deletion events. Nevertheless, the examination of a large number of ccSSR fragments suggested that this apparent homoplasy could be overshadowed by evolutionary relationships among taxa. This hypothesis is supported by the relative degree of positive congruence of taxon groupings after cluster and principal components analyses performed on both base pair length and sequence substitution data. Moreover, these analyses support previous biochemical and morphological data indicating that distinct lineages exist within the Benincaseae. Likewise, data support the hypotheses that the genus Benincasa is descended from an ancient African ancestor and that the progenitor of the New World Sicyeae tribe shares a common ancestor with the genus Luffa of the Old World Benincaseae.Key words: Benincaseae, chloroplast, consensus, homoplasy, microsatellite, simple sequence repeats.

Species delimitation in Capparis spinosa group (Capparaceae) in Iran: Multivariate morphometric analysis and ISSR markers

Phytotaxa ◽  
2020 ◽  
Vol 456 (1) ◽  
pp. 1-26
Author(s):  
MARYAM AHMADI ◽  
HOJJATOLLAH SAEIDI ◽  
MANSOUR MIRTADZADINI
Keyword(s):  
Genetic Relationships ◽  
Taxonomic Status ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Morphological Data ◽  
Genetic Affinity ◽  
Intermediate Phenotypes ◽  
Subspecies Level ◽  
Capparis Spinosa ◽  
Simple Sequence

Multivariate morphometric approach (using PCA mix and CDA) and Inter-Simple Sequence Repeat Markers (ISSR) were used to characterize the patterns of morphological and genetic relationships of Capparis spinosa group in Iran. The morphological data analyses revealed that this complex could be divided into three main groups. C. spinosa subsp. cartilaginea and C. spinosa subsp. spinosa var. mucronifolia were reliably delineated by morphological data, but C. spinosa subsp. spinosa var. parviflora, C. spinosa subsp. spinosa var. herbacea, C. spinosa subsp. spinosa var. canescens, C. spinosa subsp. spinosa var. aegyptia and their intermediate phenotypes were overlapped. The results of ISSR data were different from morphological analyses and var. parviflora exhibited a close genetic affinity to var. mucronifolia rather than the other varieties of sub. spinosa. The results of this study revealed that subsp. cartilaginea should be recognized at species level. In case of var. parviflora, we propose subspecies level for this variety. Further investigation is needed to reveal the taxonomic status of var. mucronifolia.

scholarly journals Development and Application of Genic Simple Sequence Repeat Markers from the Transcriptome of Loquat

2014 ◽  
Vol 139 (5) ◽  
pp. 507-517 ◽  
Author(s):  
Xiaoying Li ◽  
Hongxia Xu ◽  
Jianjun Feng ◽  
Junwei Chen
Keyword(s):  
Large Scale ◽  
Trinucleotide Repeat ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Eriobotrya Japonica ◽  
Pcr Products ◽  
Ssr Loci ◽  
Trait Locus ◽  
High Level ◽  
Simple Sequence

Deep transcriptome sequencing allows for the acquisition of large-scale microsatellite information, and it is especially useful for genetic diversity analysis and mapping in plants without reference genome sequences. In this study, a total of 14,004 simple sequence repeats (SSRs) were mined from 10,511 unigenes screening of 63,608 nonredundant transcriptome unigenes in loquat (Eriobotrya japonica) with a frequency of 22 SSR loci distributed over 100 unigenes. Dinucleotide and trinucleotide repeat SSRs were dominant, accounting for 20.62%, and 42.1% of the total, respectively. Seventy primer pairs were designed from partial SSRs and used for polymerase chain reaction (PCR) amplification. Of these primer pairs, 54 exhibited amplification and 33 were polymorphic. The number of alleles at these loci ranged from two to 17, and the polymorphism information content values ranged from 0.24 to 0.89. We tested the transferability of 33 SSR polymorphic primer pairs in apple and pear, and the transferability rates in these two species were 90.9% and 87.9%, respectively. A high level of marker polymorphism was observed in apple [Malus ×domestica (66.7%)], whereas a low level was observed in pear [Pyrus sp. (51.5%)]. In addition, the PCR products from seven SSR primer pairs were selected for sequence analysis, and 89.2% of the fragments were found to contain SSRs. SSR motifs were conserved among loquat, apple, and pear. According to our sequencing results for real SSR loci, ≈12,490 SSR loci were present in these loquat unigenes. The cluster dendrogram showed a distinct separation into different groups for these three species, indicating that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the species of Maloideae in the Rosaceae. The results of our identified SSRs should be useful for genetic linkage map construction, quantitative trait locus mapping, and molecular marker-assisted breeding of loquat and related species.

scholarly journals Genetic diversity and fingerprinting of 33 standard flue-cured tobacco varieties for use in distinctness, uniformity, and stability testing

2020 ◽  
Author(s):  
Binbin He ◽  
Ruimei Geng ◽  
Lirui Cheng ◽  
Xianbin Yang ◽  
Hongmei Ge ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Relationships ◽  
Morphological Identification ◽  
Information Index ◽  
Nicotiana Tabacum L ◽  
Dus Testing ◽  
Identification Technique ◽  
Technical Basis ◽  
Simple Sequence

Abstract Background: At present, the distinctness, uniformity, and stability (DUS) testing of flue-cured tobacco ( Nicotiana tabacum L.) depends on field morphological identification, which is problematic in that it is intensive, time-consuming, and susceptible to environmental impacts. In order to improve the efficiency and accuracy of tobacco DUS testing, the development of a molecular marker-based method for genetic diversity identification is urgently needed. Results: In total, 91 simple sequence repeats (SSR) markers with clear and polymorphic amplification bands were obtained with polymorphism information content, Nei index, and Shannon information index values of 0.3603, 0.4040, and 0.7228, respectively. Clustering analysis showed that the 33 study varieties, which are standard varieties for flue-cured tobacco DUS testing, could all be distinguished from one another. Further analysis showed that a minimum of 25 markers were required to identify the genetic diversity of these varieties. Following the principle of two markers per linkage group, 48 pairs of SSR markers were selected. Correlation analysis showed that the genetic relationships revealed by the 48 SSR markers were consistent with those found using the 91 SSR markers. Conclusions: The genetic fingerprints of the 33 standard varieties of flue-cured tobacco were constructed using 48 SSR markers, and an SSR marker-based identification technique for new tobacco varieties was developed. This study provides a reliable technological approach for determining the novelty of new tobacco varieties and offers a solid technical basis for the accreditation and protection of new tobacco varieties.

Genetic relationships of sesame germplasm collection as revealed by inter-simple sequence repeats

2002 ◽  
Vol 121 (3) ◽  
pp. 259-262 ◽  
Author(s):  
D. H. KIM ◽  
G. ZUR ◽  
Y. DANIN-POLEG ◽  
S. W. LEE ◽  
K. B. SHIM ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Inter Simple Sequence Repeats ◽  
Simple Sequence

Characterisation and inheritance of polymorphic plastid microsatellites in Abies

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 857-864 ◽  
Author(s):  
G. G. Vendramin ◽  
B. Ziegenhagen
Keyword(s):  
Population Genetics ◽  
Simple Sequence Repeats ◽  
Natural Populations ◽  
Abies Alba ◽  
Chloroplast Microsatellites ◽  
Length Variation ◽  
Pcr Products ◽  
Considerable Length ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Two polymorphic microsatellite loci were identified and sequenced in the genus Abies, using primer pairs derived from chloroplast simple sequence repeats (SSRs) of Pinus thunbergii. PCR products exhibited considerable length variation among six different Abies species and within Abies alba. F1 progeny of both an interspecific and an intraspecific reciprocal cross confirmed that the two SSRs were predominantly paternally inherited. The maternal size variant predominantly occurred in the megagametophytes analysed. First analysis of the two chloroplast microsatellites in seven natural populations of A. alba revealed 36 different haplotypes. The use of these highly polymorphic SSRs as potential markers in population genetics is discussed.Key words: Abies, chloroplast simple sequence repeats, sequences, inheritance, intraspecific variation, population genetics.

Simple sequence repeat primers used in polymerase chain reaction amplifications to study genetic diversity in barley

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 112-117 ◽  
Author(s):  
M. P. Sánchez de la Hoz ◽  
J. A. Dávila ◽  
Y. Loarce ◽  
E. Ferrer
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
Simple Sequence Repeats ◽  
Genetic Relationships ◽  
Arbitrary Sequence ◽  
Chain Reaction ◽  
Barley Cultivars ◽  
Dinucleotide Motif ◽  
Polymerase Chain ◽  
Simple Sequence

In combination with oligonucleotides of arbitrary sequence, 5′ anchored oligonucleotides based on simple sequence repeats were used in polymerase chain reaction amplifications to produce barley DNA fingerprints. The aim of this work was (i) to develop a simple nonradioactive experimental procedure to reveal polymorphism in regions containing SSRs, (ii) to determine the genetic nature of polymorphisms, and (iii) to investigate the efficacy of polymorphisms contained in such fingerprints in disclosing genetic relationships between 14 European barley cultivars with known pedigrees. Different 10-mer oligonucleotides containing a dinucleotide motif were used as single primers and also in pairs with 10-mer oligonucleotides of arbitrary sequence. Further, the arbitrary oligonucleotides were used as single primers to produce RAPDs. Thirteen combinations of primers containing either GT(CA)4 or GC(CA)4 were selected on the basis of number and intensity of scorable bands in silver-stained 7% polyacrylamide gels. Of the fragments scored, 58.4% were polymorphic. Inheritance of these random amplified microsatellite polymorphic fragments (RAMP) was studied in doubled-haploid lines from the F1 of 'Steptoe' × 'Morex'. Fifty percent of the primers generated codominant markers. Genetic similarities between cultivars were estimated from RAMP and RAPD data. Principal coordinate analysis performed on RAMP data revealed a clear separation of winter six-rowed, winter two-rowed, and spring two-rowed barley. The dendograms generated faithfully reflected the genealogies of the barley cultivars. RAPD failed to show clearly the germplasm sources of the experimental cultivars. Key words : simple sequence repeats, microsatellites, amplification, genetic diversity, barley.

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