scholarly journals GENETIC DIVERSITY OF Brassica rapa GERMPLASM OF KHYBER PAKHTUNKHWA PAKISTAN REVEALED BY MOLECULAR MARKERS

2019 ◽  
Vol 18 (6) ◽  
pp. 57-65
Author(s):  
Naushad Ali ◽  
Sardar Ali ◽  
Naqib Ullah Khan ◽  
Sohail Ahmad Jan ◽  
Malik Ashiq Rabbani ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Ssr Markers ◽  
Brassica Rapa ◽  
Arithmetic Mean ◽  
Group Method ◽  
Khyber Pakhtunkhwa ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Ssr Primers ◽  
Simple Sequence

A total of 96 indigenous Brassica rapa accessions were collected from different locations of Khyber Pakhtunkhwa, Pakistan. Simple Sequence Repeats (SSR) markers were used to identify the most diverse genotypes among the collected lots. Twenty six (26) different SSR primers were used for (genetic) variability among collected genotypes. These primers were selected from literature based on their previous results. These primers produced 135 scorable bands of which 75 were polymorphic, with an average of 55.5% polymorphic loci, and reflected the broader genetic background of the collected genotypes. An average 2.88 polymorphic bands with an average PIC value of 0.49 was recorded. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) divided all genotypes into three main groups. Group one contained three clusters, while group two and three had four and two clusters each. Based on the UPGMA dendrogram, genotypes collected from Kohat, Bannu, Swat and Haripur showed considerable amount of variation. From the present study, it is concluded that SSR markers can be proved as the best tool for the genetic variability of other local and exotic B. rapa genotypes.

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

2007 ◽  
Vol 132 (3) ◽  
pp. 357-367 ◽  
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.

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.

scholarly journals Morphometric and Genetic Variation in Three Populations of Indian Salmon (Polydactylus plebeius)

2013 ◽  
Vol 5 (3) ◽  
pp. 275-281
Author(s):  
Ramakrishnan THIRUMARAISELVI ◽  
Muthusamy THANGARAJ ◽  
Vellaichamy RAMANADEVI
Keyword(s):  
Univariate Analysis ◽  
Arithmetic Mean ◽  
Group Method ◽  
Morphometric Character ◽  
Clear Pattern ◽  
Arbitrary Primers ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Morphometric Analyses ◽  
The Status

Morphometric character analyses and RAPD was used to discriminate and ratify the status of three populations of Indian salmon, Polydactylus plebeius along the coromandel coast of India. Morphometric analyses showed a clear pattern of differentiation between the stocks and revealed the discreteness of two groups, southern stock (Pazhayar) and northern stock (Cuddalore). The univariate analysis of variance showed significant differences between means of the samples for most morphometric descriptors. A total of 1077 scorable bands were produced using all ten arbitrary primers in three populations. An un-weighted pair-group method with arithmetic mean (UPGMA) dendrogram was constructed based on genetic values to show the genetic relationship among the three populations. The genetic diversity (H) of P. plebeius in Cuddalore was more (0.0733 ± 0.0648) than Pazhayar (0.0609 ± 0.0416) and Vellar (0.0613 ± 0.0344) populations. All the three populations had significantly (p

scholarly journals Isolation and Characterization of New Polymorphic Simple Sequence Repeat Loci in Chrysopogon aciculatus (Retz.) Trin.

HortScience ◽  
2016 ◽  
Vol 51 (3) ◽  
pp. 232-235 ◽  
Author(s):  
Xinyi Zhang ◽  
Li Liao ◽  
Yang Liu ◽  
Zhiyong Wang ◽  
Jianxiu Liu
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Magnetic Bead ◽  
Group Method ◽  
Amplification Efficiency ◽  
Sequence Repeat ◽  
Arithmetic Means ◽  
Pair Group ◽  
Isolation And Characterization ◽  
Simple Sequence

Chrysopogon aciculatus (Retz.) Trin. is a perennial turfgrass for its low management and resistance. To develop simple sequence repeat (SSR) markers for C. aciculatus, we used four Roche 454 pyrosequencing, combined with the magnetic bead enrichment method FIASCO (fast isolation by amplified fragment length polymorphism of sequences containing repeats) to isolate from the C. aciculatus. A total of 66,198 raw sequencing reads were obtained with 4289 sequences (6.48%) were fit for primer pair design. One hundred microsatellite loci were selected to test the primer amplification efficiency in 20 accessions, and out of these, 11 loci were polymorphic. The amount of observed alleles ranged from three to six, with an average of 3.64. Nei’s genetic diversity values ranged from 0.085 to 0.493, with an average of 0.293. Shannon’s information index values ranged from 0.141 to 0.686, with an average of 0.428. Twenty accessions were clustered into three groups by unweighted pair-group method with arithmetic means (UPGMA). These SSR markers will provide an ideal marker system to assist with gene targeting, cultivar variety or species identification, and marker-assisted selection in C. aciculatus species.

Molecular Profiling of Chilli Germplasm By Using SSR Marker

2021 ◽  
Vol 19 (1) ◽  
pp. 1-13
Author(s):  
MI Haque ◽  
S Ishtiaque ◽  
MM Islam ◽  
TA Mujahidi ◽  
MA Rahim
Keyword(s):  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Group Method ◽  
Arithmetic Means ◽  
Average Value ◽  
Pair Group ◽  
Index Matrix ◽  
Ssr Primers ◽  
Ssr Loci

The molecular characterization of chilli germplasm was done based on estimation of genetic diversity among the germplasm by using SSR markers. Forty chilli germplasms were analyzed using eight SSR primers. The SSR primers produced 30 SSR loci with an average value of 3.75 alleles per SSR locus. The similarity index matrix ranged from zero to 2.74. Polymorphic information content (PIC) of the SSR primers ranged from 0.543 to 0.735 with an average value of 0.658. The highest number (five) of allele was observed in primer CAMS-647, whereas the primers CAMS-864, CAMS-880 and CAMS-885 showed lowest number (three) of allele. The smallest allele was found in case of primer CAMS- 236 (176 bp), while the longest allele was detected for the primer CAMS- 864 (288 bp). Based on similarity matrix using the un-weighed Pair Group Method of Arithmetic Means (UPGMA) dendrogram, chilli germplasms were grouped into four main clusters. SSR markers showed genetic variability in the studied chilli germplasm.  SAARC J. Agric., 19(1): 1-13 (2021)

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 Genetic Diversity and Relationships among Local Olive (Olea europeaea L.) Genotypes from Gaziantep Province and Notable Cultivars in Turkey, Based on SSR Markers

2016 ◽  
Vol 44 (2) ◽  
pp. 557-562
Author(s):  
Ebru SAKAR ◽  
Hulya UNVER ◽  
Mehmet ULAS ◽  
Biljana LAZOVIC ◽  
Sezai ERCISLI
Keyword(s):  
Ssr Markers ◽  
Genetic Relationships ◽  
Group Method ◽  
Similarity Coefficients ◽  
Olive Cultivar ◽  
Banding Patterns ◽  
Pair Group ◽  
Ssr Analysis ◽  
Ssr Primers ◽  
Similarity Ratio

Olive and olive oil have a prominent place in the cultures of the countries within the Mediterranean basin including Turkey. The genetic relationships among 30 olive (Olea europaea L.) genotypes sampled from Gaziantep province in Turkey were examined using 10 simple sequence repeat (SSR) markers (DCA9, DCA11, DCA15, DCA18UDO4, UDO9, UDO11, UDO12, UDO22, UDO24). Also, three well known Turkish and one foreign olive cultivar were also included within the SSR analysis. The number of alleles per locus of the SSR markers ranged from 5 (DCA15, UDO9) to 14 (DCA9) (average 7.9), for a total of 79 alleles. Similarity coefficients were calculated on the basis of 79 amplified bands. A dendrogram was created according to the 10 SSR markers by the unweighted pair-group method. The banding patterns obtained from the SSR primers allowed all of the genotypes/cultivars to be distinguished. According to the dendrogram, the 33 olive genotypes and cultivars were clustered into five main clusters. The most closely related genotypes were 'Oguzeli 3' and 'Yavuzeli 1' with 0.80 similarity ratio. The most genetically divergent cultivars were 'Yavuzeli 6' and 'Kilis Yaglik' (0.30), 'Yavuzeli 6' and 'Saurani' (0.20), 'Nizip 7' and 'Yavuzeli 4' (0.15), 'Islahiye 5' and 'Nizip Yaglik' (0.10). In conclusion, SSR analysis can be an efficient method for olive genotypes and cultivar identification and can offer valuable informative data to identify olive genotypes and cultivars grown in Turkey.

scholarly journals Genetic Diversity of Iraqi Date Palms Revealed By Microsatellite Polymorphism

2011 ◽  
Vol 136 (4) ◽  
pp. 282-287 ◽  
Author(s):  
Hussam S.M. Khierallah ◽  
Saleh M. Bader ◽  
Michael Baum ◽  
Alladin Hamwieh
Keyword(s):  
Genetic Diversity ◽  
Date Palm ◽  
Phoenix Dactylifera ◽  
Principal Coordinate Analysis ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Ssr Primers ◽  
High Level ◽  
Simple Sequence

Genetic diversity in 30 date palm (Phoenix dactylifera L.) cultivars in Iraq representing 24 female and six male cultivars was investigated using 22 microsatellite [simple sequence repeat (SSR)] primers. The tested SSR markers showed a high level of polymorphism. A total of 188 alleles were detected at the 22 loci ranging from three to 21 with an average of 8.54 alleles per locus. The average of heterozygosity for all cultivars was 0.503; genetic distance among cultivars varied from 0.171 to 0.938 indicating diverse relationships. The cultivar Ghanami Akhder was highly divergent from ‘Ghnami Ahmer’, whereas ‘Jamal Al-Dean’ was very closely related to ‘Qitaz’. Unweighted pair group method arithmetic average ordered date palm cultivars into two main clusters. Principal coordinate analysis exhibited the similar clusters of cultivars as in the dendrogram.

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.

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