scholarly journals Genetic variability in peas (Pisum sativum L.) from Turkey asssessed with molecular and morphological markers

2019 ◽  
Vol 31 (1) ◽  
pp. 101-116
Author(s):  
Fatih Hanci
Keyword(s):  
Genetic Variability ◽  
Pisum Sativum ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Morphological Markers ◽  
Pisum Sativum L ◽  
Euclidean Distances ◽  
Simple Sequence

AbstractThe aim of this study was to identify the molecular and morphological characteristics of Turkish pea accessions (Pisum sativum L.). The genetic diversity among 130 Turkish landraces and 2 commercial varieties in a total of 132 pea accessions was assessed with 14 simple sequence repeat (SSR) markers. Forty-eight (48) polymorphic alleles were identified using 14 SSR markers. The pairwise Dice coefficients of similarity between accessions ranged from 0.091 to 0.960. The polymorphism information content (PIC) value ranged from 0.585 to 0.861. Overall, 50 morphological traits were evaluated. Cluster analysis was carried out on a matrix of Euclidean distances. The accessions were divided into three main groups. Principal component analysis (PCA) was used to identify the weight of each morphological characteristic. According to the results, the highest eigenvalue was observed in PC-I (13.88) followed by PC-II (11.42), and PC-III (7.32). The first fifteen PCs with eigenvalues > 1 explained 74.08% of the variability. The results showed that the molecular markers were useful and polymorphic, sufficient to allocate all the evaluated accessions. This research has provided significant insights into the genetic variability of Turkish pea accessions.

scholarly journals Molecular characterization using SSR markers in 50 shrub pea genotypes (Pisum sativum L.) from the GRICAND Collection, Colombia

2019 ◽  
Vol 13 (2) ◽  
pp. 208-218
Author(s):  
Juan Diego Duque-Zapata ◽  
Jaime Eduardo Muñoz ◽  
Oscar Checa-Coral
Keyword(s):  
Pisum Sativum ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Morphological Characteristics ◽  
High Similarity ◽  
Expected Heterozygosity ◽  
Pisum Sativum L ◽  
Simple Sequence

The pea (Pisum sativum L.) is one of the more important legume crops produced globally. We studied the structure and genetic diversity in a collection of 50 pea accessions with 16 simple sequence repeat (SSR) markers, whose average polymorphic information content (PIC) was 0.62. The SSR markers amplified a total of 28 alleles with an average of 4 alleles per locus, with locus AB71 and D21 amplifying the largest number of alleles (6). The observed heterozygosity (Ho) was 0.09±0.08 and the expected heterozygosity (He) was 0.42, indicating an elevated level of inbreeding (Fis = 0.60). The genetic relationships were inferred with a similarity index (DICE) and a bayesian analysis (STRUCTURE), detecting 2 clusters for the genotypes, with a high similarity of the morphological characteristics of each genotype. The results of this study will be useful for the creation of future breeding programs.The pea (Pisum sativum L.) is one of the more important legume crops produced globally. We studied the structure and genetic diversity in a collection of 50 pea accessions with 16 simple sequence repeat (SSR) markers, whose average polymorphic information content (PIC) was 0.62. The SSR markers amplified a total of 28 alleles with an average of 4 alleles per locus, with locus AB71 and D21 amplifying the largest number of alleles (6). The observed heterozygosity (Ho) was 0.09±0.08 and the expected heterozygosity (He) was 0.42, indicating an elevated level of inbreeding (Fis = 0.60). The genetic relationships were inferred with a similarity index (DICE) and a bayesian analysis (STRUCTURE), detecting 2 clusters for the genotypes, with a high similarity of the morphological characteristics of each genotype. The results of this study will be useful for the creation of future breeding programs.

scholarly journals The application of high resolution melting in the analysis of simple sequence repeat and single nucleotide polymorphism markers in a pea (Pisum sativum L.) population

2014 ◽  
Vol 50 (No. 2) ◽  
pp. 151-156 ◽  
Author(s):  
M. Knopkiewicz ◽  
M. Gawłowska ◽  
W. Święcicki
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
High Resolution Melting ◽  
Melting Curve ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pisum Sativum L ◽  
Pcr Product ◽  
Simple Sequence

The aim of this study was to verify the high resolution melting (HRM) method in the analysis of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers in pea (Pisum sativum L.). A recombinant inbred line population, Carneval × MP1401, was tested for three SNP and 103 SSR markers. HRM analysis was conducted on a LightScanner 96 instrument with LC Green dye. The melting curve shape permitted two polymorphic genotypes to be distinguished. The results were confirmed by gel electrophoresis. Three SSR markers were sequenced and analysed by the melting prediction software. The results confirmed the presence of one polymerase chain reaction (PCR) product with two melting domains. Sequence tagged site (STS) markers produced specific products: Psat_EST_00189_01_1 (300 bp), Pis_GEN_18_2_1 (400 bp), Pis_GEN_7_1-2_1 (600 bp). Amplicons contained one, four and seven single nucleotide polymorphisms, respectively. Melting curve differences enabled the population genotyping except for Psat_EST_00189_01_1 where resolution was too low. Primers for Psat_EST_00189_01_1 were redesigned to obtain a shorter (100 bp) PCR product which increased the resolution. The number of SNPs and amplicon length are crucial for HRM resolution. The HRM method is fast and has a high throughput. The melting analysis of 96 samples takes less than 10 min. Agarose gel analysis confirmed the reliability of HRM, which eliminates laborious post-PCR analysis.

scholarly journals Genetic Diversity and Population Structure of Traditional Greek and Cypriot Melon Cultigens (Cucumis melo L.) Based on Simple Sequence Repeat Variability

HortScience ◽  
2009 ◽  
Vol 44 (7) ◽  
pp. 1820-1824 ◽  
Author(s):  
Emmanouil N. Tzitzikas ◽  
Antonio J. Monforte ◽  
Abdelhak Fatihi ◽  
Zacharias Kypriotakis ◽  
Tefkros A. Iacovides ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Ssr Markers ◽  
Structure Analysis ◽  
Simple Sequence Repeat ◽  
Cucumis Melo ◽  
Sequence Repeat ◽  
Population Structure Analysis ◽  
Simple Sequence

Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure among traditional Greek and Cypriot melon cultigens (Cucumis melo L.). All SSR markers were polymorphic with a total number of 81 alleles, whereas all cultigens could be distinguished with at least one SSR, except cultigens 43 and 41. Reference accessions showed larger genetic variability with an average of four alleles per locus and 0.65 gene of diversity compared with an average of 2.47 alleles per locus and 0.30 of gene diversity for the Greek/Cypriot cultigens. Observed heterozygosity was very low, indicating a lack of outcrossing, at least in recent times. Unrooted neighbor-joining tree analysis and population structure analysis clustered the cultigens and the reference genotypes into five groups. All cultigens could be distinguished; the Cypriot cultigens were more closely related to the inodorus ‘Piel de Sapo’, whereas the Greek cultigens were located in an intermediate position between the inodorus ‘Piel de Sapo’ and the cantalupensis ‘Védrantais’. The cultigen ‘Kokkini’ was the most divergent among the Greek and Cypriot cultigens. This association between geographic origin and genetic similarity among Greek and Cypriot cultigens indicates geographic isolation. Most of the cultivars from the same cultivar group (i.e., inodorus, cantalupensis) clustered together, but some exceptions were found, suggesting that former inodorus landraces would have been transformed to cantalupensis as a result of intercrossing and further selection by farmers. Results of population structure analysis support mixing between cantalupensis and inodorus. ‘Agiou Basileiou’, an inodorus cultigen, was assigned to the subpopulation IV/II of which II is a pure cantalupensis subpopulation. Greek and Cypriot melon cultigens were developed from a broader germplasm base than western Mediterranean cultivars and exhibited useful for melon breeding programs genetic variability.

scholarly journals Genetic variability of Brazilian rice landraces determined by SSR markers

2009 ◽  
Vol 44 (7) ◽  
pp. 706-712 ◽  
Author(s):  
Tereza Cristina de Oliveira Borba ◽  
Clistiane dos Anjos Mendes ◽  
Élcio Perpétuo Guimarães ◽  
Tuliana Oliveira Brunes ◽  
Jaime Roberto Fonseca ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Molecular Data ◽  
Factorial Correspondence Analysis ◽  
Rice Cultivars ◽  
Market Demand ◽  
Breeding Programs ◽  
Rice Landraces ◽  
Simple Sequence

The objective of this study was to evaluate the genetic variability of rice (Oryza sativa) landraces collected in Brazilian small farms. Twelve simple sequence repeat (SSR) markers characterized 417 landraces collected in 1986, 1987 and 2003, in the state of Goiás, Brazil. The number of landraces with long and thin grain type increased in the evaluated period, probably due to market demand. Based on the molecular data, the genetic variability increased during this period and, as per to the factorial correspondence analysis, most of the accessions were grouped according to the year of collection. The incorporation of modern rice cultivars in landrace cultivation areas and the selection carried out by small farmers are the most probable factors responsible for increasing landrace genetic variability, during the evaluated period. Genotype exchange between farmers, selection practice and local environmental adaptation are able to generate novel adapted allele combinations, which can be used by breeding programs, to reinitiate the process.

scholarly journals Simple Sequence Repeat Markers Reveal Hungarian Plum (Prunus domestica L.) Germplasm as a Valuable Gene Resource

HortScience ◽  
2017 ◽  
Vol 52 (12) ◽  
pp. 1655-1660 ◽  
Author(s):  
Noémi Makovics-Zsohár ◽  
Magdolna Tóth ◽  
Dezső Surányi ◽  
Szilvia Kovács ◽  
Attila Hegedűs ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Allelic Variation ◽  
Genetic Relationships ◽  
Principal Component ◽  
Bootstrap Support ◽  
Limited Information ◽  
Sequence Repeat ◽  
Prunus Domestica ◽  
Simple Sequence

The hexaploid European plum (Prunus domestica L.) is an economically important fruit species with limited information on its genetic structure. Our objective was to fingerprint 55 cultivars using seven simple sequence repeat (SSR) markers to estimate the polymorphism level and determine allelic variation and genetic relationships among local and international cultivars. The primer pairs amplified a total of 135 alleles ranging from six to 27 alleles per locus, displaying high polymorphism. All genotypes were clearly distinguished with the seven SSRs used in this study. In a neighbor-joining cluster analysis, cultivars belonging to the same species did not group together. Foreign modern cultivars clustered together, and Hungarian landraces positioned distantly from those. STRUCTURE analysis indicated three genetically distinct groups of the studied genotypes. Each cluster of Hungarian landrace cultivars received strong bootstrap support (89% to 100%). Most genotypes kept under identical name showed different DNA fingerprints. A principal component analysis (PCA) confirmed the information provided by the dendrogram and clarified the origin of ʻFehérszilva’. Our results confirmed the potential of the application of SSR markers in plum breeding.

Genetic diversity studies in pea (Pisum sativum L.) using simple sequence repeat markers

2013 ◽  
Vol 12 (3) ◽  
pp. 3540-3550 ◽  
Author(s):  
P. Kumari ◽  
N. Basal ◽  
A.K. Singh ◽  
V.P. Rai ◽  
C.P. Srivastava ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Pisum Sativum ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Pisum Sativum L ◽  
Diversity Studies ◽  
Simple Sequence

Efficiency of different marker systems for molecular characterization of subtropical carrot germplasm

2010 ◽  
Vol 148 (2) ◽  
pp. 171-181 ◽  
Author(s):  
T. JHANG ◽  
M. KAUR ◽  
P. KALIA ◽  
T. R. SHARMA
Keyword(s):  
Genetic Variability ◽  
Ssr Markers ◽  
Dna Markers ◽  
Principal Component ◽  
Group Method ◽  
Data Set ◽  
Breeding Lines ◽  
Pair Group ◽  
Ssr Loci ◽  
Simple Sequence

SUMMARYGenetic variability in carrots is a consequence of allogamy, which leads to a high level of inbreeding depression, affecting the development of new varieties. To understand the extent of genetic variability in 40 elite indigenous breeding lines of subtropical carrots, 48 DNA markers consisting of 16 inter simple sequence repeats (ISSRs), 10 universal rice primers (URPs), 16 random amplification of polymorphic DNA (RAPD) and six simple sequence repeat (SSR) markers were used. These 48 markers amplified a total of 591 bands, of which 569 were polymorphic (0·96). Amplicon size ranged from 200 to 3500 base pairs (bp) in ISSR, RAPD and URPs markers and from 100 to 300 bp in SSR markers. The ISSR marker system was found to be most efficient with (GT)n motifs as the most abundant SSR loci in the carrot genome. The unweighted pair group method with arithmetic mean (UPGMA) analysis of the combined data set of all the DNA markers obtained by four marker systems classified 40 genotypes in two groups with 0·45 genetic similarity with high Mantel matrix correlation (r=0·92). The principal component analysis (PCA) of marker data also explained 0·55 of the variation by first three components. Molecular diversity was very high and non-structured in these open-pollinated genotypes. The study demonstrated for the first time that URPs can be used successfully in genetic diversity analysis of tropical carrots. In addition, an entirely a new set of microsatellite markers, derived from the expressed sequence tags (ESTs) sequences of carrots, has been developed and utilized successfully.

scholarly journals Genetic variability of rice recurrent selection populations as affected by male sterility or manual recombination

2012 ◽  
Vol 47 (6) ◽  
pp. 808-814 ◽  
Author(s):  
Letícia da Silveira Pinheiro ◽  
Paulo Hideo Nakano Rangel ◽  
Rosana Pereira Vianello ◽  
Claudio Brondani
Keyword(s):  
Genetic Variability ◽  
Male Sterility ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Recurrent Selection ◽  
Sequence Repeat ◽  
The One ◽  
Simple Sequence

The objective of this work was to determine the effect of male sterility or manual recombination on genetic variability of rice recurrent selection populations. The populations CNA-IRAT 4, with a gene for male sterility, and CNA 12, which was manually recombined, were evaluated. Genetic variability among selection cycles was estimated using14 simple sequence repeat (SSR) markers. A total of 926 plants were analyzed, including ten genitors and 180 individuals from each of the evaluated cycles (1, 2 and 5) of the population CNA-IRAT 4, and 16 genitors and 180 individuals from each of the cycles (1 and 2) of CNA 12. The analysis allowed the identification of alleles not present among the genitors for both populations, in all cycles, especially for the CNA-IRAT 4 population. These alleles resulted from unwanted fertilization with genotypes that were not originally part of the populations. The parameters of Wright's F-statistic (F IS and F IT) indicated that the manual recombination expands the genetic variability of the CNA 12 population, whereas male sterility reduces the one of CNA-IRAT 4.

Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on molecular markers, and morphological and physiological characters

Genome ◽  
2005 ◽  
Vol 48 (2) ◽  
pp. 257-272 ◽  
Author(s):  
B Tar'an ◽  
C Zhang ◽  
T Warkentin ◽  
A Tullu ◽  
A Vandenberg
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Molecular Markers ◽  
Pisum Sativum ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Agronomic Characters ◽  
Breeding Programs ◽  
Pisum Sativum L ◽  
Simple Sequence

Random amplified polymorphic DNA, simple sequence repeat, and inter-simple sequence repeat markers were used to estimate the genetic relations among 65 pea varieties (Pisum sativum L.) and 21 accessions from wild Pisum subspecies (subsp.) abyssinicum, asiaticum, elatius, transcaucasicum, and var. arvense. Fifty-one of these varieties are currently available for growers in western Canada. Nei and Li's genetic similarity (GS) estimates calculated using the marker data showed that pair-wise comparison values among the 65 varieties ranged from 0.34 to 1.00. GS analysis on varieties grouped according to their originating breeding programs demonstrated that different levels of diversity were maintained at different breeding programs. Unweighted pair-group method arithmetic average cluster analysis and principal coordinate analysis on the marker-based GS grouped the cultivated varieties separately from the wild accessions. The majority of the food and feed varieties were grouped separately from the silage and specialty varieties, regardless of the originating breeding programs. The analysis also revealed some genetically distinct varieties such as Croma, CDC Handel, 1096M-8, and CDC Acer. The relations among the cultivated varieties, as revealed by molecular-marker-based GS, were not significantly correlated with those based on the agronomic characters, suggesting that the 2 systems give different estimates of genetic relations among the varieties. However, on a smaller scale, a consistent subcluster of genotypes was identified on the basis of agronomic characters and their marker-based GS. Furthermore, a number of variety-specific markers were identified in the current study, which could be useful for variety identification. Breeding strategies to maintain or enhance the genetic diversity of future varieties are proposed.Key words: Pisum sativum, molecular markers, genetic relationships, cluster analysis.

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