scholarly journals Estimation of Genetic Diversity in Genus Mentha Collected From Azad Jammu And Kashmir, Pakistan

2019 ◽  
Author(s):  
Fozia Abasi ◽  
Israr Ahmad ◽  
Sami Ullah khan ◽  
Khawaja Shafique Ahmad ◽  
Aneela Ulfat ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Molecular Data ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Means ◽  
Jammu And Kashmir ◽  
Pair Group ◽  
High Level

ABSTRACTMints are perennial aromatic herbs used both for medicinal and aromatic purposes. Flora of Pakistan has reported six species of genus Mentha. Taxonomy of genus Mentha is more complex and confusing due to inter specific hybridization. The present research is the first documented report from Pakistan for the purpose to dissect Mentha specimens using molecular tools. A total of 17 SCoT and SSR markers used to dissect genetic diversity among 41 Mentha specimens. The results revealed substantial variation among Mentha specimens. The molecular data analyzed through NTSYS and Power marker software’s. Dendrogram constructed on the base of similarity coefficients generated using weighted pair group method of arithmetic means (UPGMA) recorded high level of polymorphism. Polymorphic Information Content (PIC) for molecular markers recorded in the range of 5-8. Mean genetic distance (GD) was estimated in the range from 0.35% to 100%. The minimum and maximum GD recorded in one combination each as P2-P4 and M41-P10. The present study was explored the efficiency of SCoT and SSR markers for evaluating the genetic diversity of medicinal plants. The present research was concluded that both morphological and molecular dendrogram determined considerable level of diversity among Mentha species. Furthermore, specific primers and DNA chloroplast technology could be needed for further molecular analysis to refine the data more up to varietal level.

Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity

Biologia ◽  
2008 ◽  
Vol 63 (2) ◽  
Author(s):  
Rajinder Singh ◽  
Noorhariza Zaki ◽  
Ngoot-Chin Ting ◽  
Rozana Rosli ◽  
Soon-Guan Tan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Oil Palm ◽  
Polymorphic Information Content ◽  
Strong Association ◽  
Geographic Location ◽  
Group Method ◽  
Pair Group ◽  
High Level ◽  
Nucleotide Repeats

AbstractA total of 5,521 expressed sequence tags (ESTs) from oil palm were used to search for type and frequency of simple sequence repeat (SSR) markers. Dimeric repeat motifs appeared to be the most abundant, followed by tri-nucleotide repeats. Redundancy was eliminated in the original EST set, resulting in 145 SSRs in 136 unique ESTs (114 singletons and 22 clusters). Primers were designed for 94 (69.1%) of the unique ESTs (consisting of 14 consensus and 80 singletons). Primers for 10 EST-SSRs were developed and used to evaluate the genetic diversity of 76 accessions of oil palm originating from seven countries in Africa, and the standard Deli dura population. The average number of observed and effective alleles was 2.56 and 1.84, respectively. The EST-SSR markers were found to be polymorphic with a mean polymorphic information content value of 0.53. Genetic differentiation (F ST) among the populations studied was 0.2492 indicating high level of genetic divergence. Moreover, the UPGMA (unweighted pair-group method with arithmetic mean) analysis revealed a strong association between genetic distance and geographic location of the populations studied. The germplasm materials exhibited higher diversity than Deli dura, indicating their potential usefulness in oil palm improvement programmes. The study also revealed that the populations from Nigeria, Congo and Cameroon showed the highest diversity among the germplasm evaluated in this study. The EST-SSRs further demonstrated their worth as a new source of polymorphic markers for phylogenetic analysis, since a high percentage of the markers showed transferability across species and palm taxa.

scholarly journals Molecular characterization of mulberry genotypes and species in Turkey

2020 ◽  
Vol 48 (2) ◽  
pp. 549-557 ◽  
Author(s):  
Emine ORHAN ◽  
Meleksen AKIN ◽  
Sadiye P. EYDURAN ◽  
Sezai ERCISLI
Keyword(s):  
Ssr Markers ◽  
Phenotypic Diversity ◽  
Polymorphic Information Content ◽  
Morus Alba ◽  
Group Method ◽  
Pair Group ◽  
Morus Nigra ◽  
Similarity Ratio ◽  
White Mulberry ◽  
High Level

Mulberries are one of the most important traditional fruit in Turkey and either consumed fresh or processed into several traditional products. Mulberry trees (genotypes) belong to Morus alba L., Morus nigra L., and Morus rubra L. shows high phenotypic diversity. In this study, 26 genotypes of Morus nigra, 21 genotypes of Morus rubra and 26 genotypes and landraces of Morus alba sampled from different parts of eastern Anatolia region in Turkey were fingerprinted using 16 simple sequence repeat (SSR) markers. Among SSR markers, the number of alleles per locus ranged from 2 (SS01, SS05) to 11 (MulSTR3) with an average of 5.19. A total of 83 alleles were obtained for the 16 SSR markers. The polymorphic information content ranged from 0.43 to 0.84 with an average of 0.61 per locus. In this study, MulSTR3, MulSTR5, MulSTR6, SS04 and SS20 were found to be the most useful SSR markers to detect genetic differences between mulberry species, genotypes and landraces. Genetic similarity ratio ranged from 0.24 to 0.94 with a mean similarity value of 0.41 indicating a high level of polymorphism among the mulberry species, genotypes and landraces. Clustering based on Jaccard's similarity coefficient and an unweighted pair group method with arithmetic mean (UPGMA) revealed 3 main clusters that corresponded with species. The results of the present study indicate that white mulberry landraces and genotypes were more diverse than the red and black mulberry genotypes. Therefore, white mulberry genotypes can be a good source for the mulberry-breeding programme due to its better genetic diversity as well as its high economical and yield properties.

scholarly journals Genetic Diversity and Population Structure of Alnus cremastogyne as Revealed by Microsatellite Markers

Forests ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 278 ◽  
Author(s):  
Hong-Ying Guo ◽  
Ze-Liang Wang ◽  
Zhen Huang ◽  
Zhi Chen ◽  
Han-Bo Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographical Distribution ◽  
Mantel Test ◽  
Group Method ◽  
Arithmetic Means ◽  
Mountain Area ◽  
Pair Group ◽  
Hill Area ◽  
Population Genetic Variation ◽  
High Level

Alnus cremastogyne Burk. is a nonleguminous, nitrogen-fixing tree species. It is also the most important endemic species of Alnus Mill. in China, possessing important ecological functions. This study investigated population genetic variation in A. cremastogyne using 175 trees sampled from 14 populations native to Sichuan Province with 25 simple sequence repeat (SSR) markers. Our analysis showed that A. cremastogyne has an average of 5.83 alleles, 3.37 effective alleles, an expected heterozygosity of 0.63, and an observed heterozygosity of 0.739, indicating a relatively high level of genetic diversity. The A. cremastogyne populations in Liangshan Prefecture (Meigu, Mianning) showed the highest level of genetic diversity, whereas the Yanting population had the lowest. Our analysis also showed that the average genetic differentiation of 14 A. cremastogyne populations was 0.021. Analysis of molecular variance (AMOVA) revealed that 97% of the variation existed within populations; only 3% was among populations. Unweighted pair-group method with arithmetic means (UPGMA) clustering and genetic structure analysis showed that the 14 A. cremastogyne populations could be clearly divided into three clusters: Liangshan Prefecture population, Ganzi Prefecture population, the other population in the mountain area around the Sichuan Basin and central Sichuan hill area, indicating some geographical distribution. Further analysis using the Mantel test showed that this geographical distribution was significantly correlated with elevation.

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.

Analysis of genetic diversity of African yam bean using SSR markers derived from cowpea

2015 ◽  
Vol 14 (1) ◽  
pp. 50-56 ◽  
Author(s):  
Ndenum S. Shitta ◽  
Michael T. Abberton ◽  
Adenubi I. Adesoye ◽  
Daniel B. Adewale ◽  
Olaniyi Oyatomi
Keyword(s):  
Genetic Diversity ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Arithmetic Average ◽  
African Yam Bean ◽  
Pair Group ◽  
Ssr Primers ◽  
Nutritional Qualities ◽  
High Level ◽  
Average Cluster

African yam bean, AYB (Sphenostylis stenocarpa Hochst. ex. A. Rich Harms), is a tuberous legume of tropical Africa. AYB has the potential to significantly boost food security due to its considerable nutritional qualities. However, the crop is underutilized. To efficiently utilize AYB genetic resources for its improvement, it is necessary to understand the crop's diversity. This study investigated the amplification ability of 36 cowpea simple sequence repeat (SSR) primers across AYB genomic DNA, extracted from 67 accessions. Thirteen (36%) of the cowpea SSRs showed transferability in AYB. Eight of these SSRs amplified above 60% of AYB accessions and generated 55 polymorphic fragments with an average of 6.9 per primer. Polymorphic information content ranged from 0.6691 to 0.8857 with an average of 0.7791. This study also assessed the genetic diversity within 67 AYB accessions using eight cowpea (Vigna unguiculata L. Walp)-derived SSR primers. The result revealed a high level of genetic diversity with simple matching coefficient ranging from 0.458 to 1.000. A dendrogram depicting three main clusters was generated based on unweighted pair group method with arithmetic average. Cluster 1 was the most diverse with a dissimilarity range of 0.517–1.000. The level of genetic diversity revealed in this study indicates that the studied AYB germplasm can be exploited for genetic improvement. Additionally, the transferable markers will aid AYB genome research and also make possible the comparative mapping between AYB and cowpea.

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.

scholarly journals VALIDATION AND TRANSFERABILITY OF SIMPLE SEQUENCE REPEATS (SSR’S) FROM SOME SPECIES OF ACACIA GENUS TO ACACIA NILOTICA L.

2016 ◽  
Vol 8 (11) ◽  
pp. 95
Author(s):  
Amita Yadav ◽  
Manila Yadav ◽  
Sandeep Kumar ◽  
Dushyant Sharma ◽  
Jaya Parkash Yadav
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Climatic Conditions ◽  
Acacia Nilotica ◽  
Group Method ◽  
Acacia Species ◽  
Pair Group ◽  
High Level ◽  
Simple Sequence

Objective: In present study genetic transferability of SSR’s from related Acacia species to Acacia nilotica was evaluated along with its genetic diversity analysis from north Indian region. Methods: A total of 30 primers selected from 5 different Acacia species were screened for amplification and polymorphism. Dendrogram and 2 D Plot were constructed using NTSys PC version 2.02e. Different diversity parameters like Polymorphism information content (PIC), alleles per primer, number (no.) of amplicons were also calculated for each primer pair.Results: SSRs from Acacia tortilis, A. senegal and A. koa were highly transferable in A. nilotica. Out of 30, only twenty-two primers showed amplification with an average of 1.36 alleles per locus. Polymorphic information content (PIC) values ranged from 0.5 to 0.96 with an average of 0.81. Jaccard similarity coefficient (J) values ranged from 0.04 to 0.67 showing a high level of diversity. Un-weighted pair group method with arithmetic mean (UPGMA), based cluster analysis, divided all accessions into three main clusters.Conclusion: Geographical and climatic conditions showed a great impact on genetic diversity. The results indicated high transferability of genomic resources from related species and will facilitate more studies to characterize the relatively less studied Acacia niloticagenome. 

scholarly journals Climate Change and Fading Genetic Resources of Parkia biglobosa (Jacq.) in Nigeria Based on SSR Markers

2019 ◽  
Author(s):  
Jacob Popoola ◽  
James Agbolade ◽  
Abiodun Ajiboye ◽  
Omotolani Akinola ◽  
Francis Lewu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Principal Component ◽  
Sub Saharan Africa ◽  
Group Method ◽  
Parkia Biglobosa ◽  
Arithmetic Average ◽  
Ecological Zones ◽  
Pair Group

African locust bean (Parkia biglobosa (Jacq.) is a multi-purpose economic tree with genetic potentials in sub-Saharan Africa. Its cultivation and production is declining with increased aging and genetically threatened throughout its natural ranges. Research efforts are needed to change the present scenario to sustainable cultivation and utilization, hence this present study. This study was aimed at evaluating genetic diversity and geographical spread relationships of twenty landraces collected from different ecological zones of Nigeria using simple sequence repeat (SSR) markers. Ten SSR markers were screened and five primers (PbL02, PbL03, PbL04, PbL05 and PbL09) were selected based on clear amplification products and reproducible scorable bands. The SSR primers detected a total of 55 alleles ranged from 10 to 14 alleles with a mean of 11. The percentage polymorphisms were high and ranged from 68.75 % in PbL04 to 84.21 % in PbL05 with a mean of 74.16 %. The polymorphic information content (PIC) was in the range of 0.31 in PbL02 to 0.37 in PbL09. The genetic diversity and heterozygosity values ranged from 0.39 to 0.50 and 0.00 to 0.68 while the average genetic distance for all pair wise comparisons was 0.31.The first five Principal Component (PC) accounted for 70.20 % of the total variation out of which PC1 (31.50%) and PC2 (19.20%) extracted 49.70% molecular similarity. The dendrogram resulted in separation of the 19 landraces into three major clusters based on unweighted pair group method with arithmetic average. Cluster I comprised of five landraces: ABNo130 and BENo023; OYNo11, KANo125 and NiNo262 while cluster II had only one (BANo116). Cluster III was diverse comprising 13 landraces: ZANo188, KNNo162, KENo220, GMNo076 and EbNo260, ADNo64, EdNo164, KANo137, KENo217, KwNo270, NiNo241, OsNo206 and PLNo120. The homogeneity of alleles among the studied landraces suggested suspicion of loss of genetic intra-specific variation among the landraces of P. biglobosa which calls for concerted efforts toward better cultivation, conservation, management, utilization and genetic improvement of the species in Nigeria.

Sign in / Sign up

Export Citation Format

Share Document