Transferability of newly developed genomic lentil SSR markers to Cicer species

2019 ◽  
Author(s):  
Melike Bakır
Keyword(s):  
Microsatellite Markers ◽  
Information Content ◽  
Ssr Markers ◽  
Lens Culinaris ◽  
Polymorphic Information Content ◽  
Research Infrastructure ◽  
Great Effort ◽  
Average Value ◽  
Cicer Species ◽  
Ssr Primers

Development of microsatellite markers requires a great effort, expertise and research infrastructure. Therefore, cross genera or species transferability of already developed markers has constituted a significant alternative. In this study, transferability of newly developed 53 genomic lentil (Lens culinaris Medik.) SSR markers to 32 accessions of Cicer species including C. arietinum L., C. bijugum K.H. Rech., C. echinospermum P.H. Davis, C. reticulatum Ladiz., C. pinnatifidium Jaub. and Sp., C. anatolicum Alef. was investigated. Of these markers, 33.09% were found to be transferrable to C. arietinum, 37.7% to C. echinospermum, 35.8% to C.reticulatum, 39.6% to C. bijugum, 18.8% to C. pinnatifidium and finally 15.09% to C. anatolicum species. From these markers, 11.3% were found to be transferable to all Cicer species. Transferable 6 polymorphic SSR primers had 19 alleles in 32 accessions with a mean of 3.16 alleles per locus. Polymorphic information content (PIC) values varied between 0.375 (Lc_MCu21) and 0.587 (Lc_MCu53) with an average value of 0.528. Transferable SSR markers were thought to provide significant contributions to inter and intra-specific studies in Cicer 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)

scholarly journals Genetic diversity and population structure of date palms (Phoenix dactylifera L.) in Ethiopia using microsatellite markers

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Workia Ahmed ◽  
Tileye Feyissa ◽  
Kassahun Tesfaye ◽  
Sumaira Farrakh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Information Content ◽  
Date Palm ◽  
Polymorphic Information Content ◽  
Phoenix Dactylifera ◽  
Mean Value ◽  
Date Palms ◽  
Expected Heterozygosity

Abstract Background Date palm tree (Phoenix dactylifera L.) is a perennial monocotyledonous plant belonging to the Arecaceae family, a special plant with extraordinary nature that gives eminent contributions in agricultural sustainability and huge socio-economic value in many countries of the world including Ethiopia. Evaluation of genetic diversity across date palms at DNA level is very important for breeding and conservation. The result of this study could help to design for genetic improvement and develop germplasm introduction programmes of date palms mainly in Ethiopia. Results In this study, 124 date palm genotypes were collected, and 10 polymorphic microsatellite markers were used. Among 10 microsatellites, MPdCIR085 and MPdCIR093 loci showed the highest value of observed and expected heterozygosity, maximum number of alleles, and highest polymorphic information content values. A total of 112 number of alleles were found, and the mean number of major allele frequency was 0.26, with numbers ranging from 0.155 (MPdCIR085) to 0.374 (MPdCIR016); effective number of alleles with a mean value of 6.61, private alleles ranged from 0.0 to 0.65; observed heterozygosity ranged from 0.355 to 0.726; expected heterozygosity varied from 0.669 to 0.906, polymorphic information content with a mean value of 0.809; fixation index individuals relative to subpopulations ranged from 0.028 for locus MPdCIR032 to 0.548 for locus MPdCIR025, while subpopulations relative to total population value ranged from − 0.007 (MPdCIR070) to 0.891 (MPdCIR015). All nine accesstions, neighbour-joining clustering analysis, based on dissimilarity coefficient values were grouped into five major categories; in population STRUCTURE analysis at highest K value, three groups were formed, whereas DAPC separated date palm genotypes into eight clusters using the first two linear discriminants. Principal coordinate analysis was explained, with a 17.33% total of variation in all populations. Generally, the result of this study revealed the presence of allele variations and high heterozygosity (> 0.7) in date palm genotypes. Conclusions Microsatellites (SSR) are one of the most preferable molecular markers for the study of genetic diversity and population structure of plants. In this study, we found the presence of genetic variations of date palm genotypes in Ethiopia; therefore, these genetic variations of date palms is important for crop improvement and conservation programmes; also, it will be used as sources of information to national and international genbanks.

scholarly journals Genotyping oil flax varieties using the microsatellite DNA marker system

2020 ◽  
Vol 21 (5) ◽  
pp. 531-539
Author(s):  
S. Z. Guchetl ◽  
T. A. Tchelyustnikova
Keyword(s):  
Information Content ◽  
Genetic Relatedness ◽  
Polymorphic Information Content ◽  
Biotic And Abiotic Stresses ◽  
Crop Acreage ◽  
Marker System ◽  
Average Value ◽  
Ssr Loci ◽  
New Varieties ◽  
Microsatellite Dna Marker

The tendency to increase crop acreage of oil flax requires the development of new varieties with high indicators of ecological plasticity, productivity and resistance to biotic and abiotic stresses. The application of modern biotechnolog ical approaches based on the use of molecular markers can accelerate the assessment of genetic differences and the dete rmination of potential of the source material for breeding. The research was aimed at assessment of the genotyping parameters of some oil flax varieties of VNIIMK breeding using the system of microsatellite markers. Seventeen variety samples of flax were used as the material for the research. DNA was isolated using CTAB buffer. Eleven SSR loci were used for the identification of varieties. Ten polymorphic loci were identified during the research. The total number of counted alleles is 32. The size of alleles varied in the range of 111-210 bps. The number of alleles per locus ranged from 2 to 6 with an average value of 3.20. The value of the index of polymorphic information content (PIC) was from 0.29 to 0.75 with an average parameter value of 0.51. The effective number of alleles for different loci is determined in the range of 1.40-3.94 with an average value of 2.28. The level of information content of the marker system (PIC 0.51) corresponds to that for identifying sets of genotypes from collections with a limitation in geographical origin. There were established differences in the frequency of occurrence of alleles. The discriminatory potential of the used marker system allowed to identify 15 variety samples. Two genotypes with common origin were identical. The degree of genetic relatedness of the studied flax genotypes has been evaluated. The obtained results will serve as the basis for the subsequent construction of genetic passports of oil flax varieties of VNIIMK breeding.

scholarly journals Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

2018 ◽  
Author(s):  
Bruce F Murray ◽  
Michael A Reid ◽  
Shu-Biao Wu
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Extreme Variability ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

scholarly journals Microsatellite markers for identification of a group of italian olive accessions

2009 ◽  
Vol 66 (5) ◽  
pp. 685-690 ◽  
Author(s):  
Innocenzo Muzzalupo ◽  
Francesca Stefanizzi ◽  
Amelia Salimonti ◽  
Rosanna Falabella ◽  
Enzo Perri
Keyword(s):  
Microsatellite Markers ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Olea Europaea ◽  
Fruit Trees ◽  
Ssr Primers ◽  
Olive Cultivars ◽  
Olea Europaéa

Cultivar characterization for fruit trees certification requires fast, efficient and reliable techniques. Microsatellite markers (SSR) were used in the molecular characterization of 23 genotypes of Olea europaea subsp europaea. The DNA from the olive cultivars was analyzed using nine pre-selected SSR primers (GAPU59, GAPU71A, GAPU71B, GAPU103A, UDO99-01, UDO99-12, UDO99-28 and UDO99-39) and revealed 29 alleles, which allowed each genotype to be identified. In the dendrogram, the nine primers allowed the 23 olive genotypes to be grouped into subgroups corresponding to the same cultivar denominations. SSR markers proved to be efficient and reliable for the molecular characterization of Italian olive cultivars.

scholarly journals Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran

2017 ◽  
Vol 60 (3) ◽  
pp. 183-189 ◽  
Author(s):  
Mohammad Taghi Vajed Ebrahimi ◽  
Mohammadreza Mohammadabadi ◽  
Ali Esmailizadeh
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Information Content ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Extraction Procedure ◽  
Shannon Index ◽  
Group Method ◽  
Salting Out ◽  
Pair Group

Abstract. Investigation of genetic relationship among populations has been traditionally based on the analysis of allele frequencies at different loci. The prime objective of this research was to measure the genetic polymorphism of five microsatellite markers (McMA2, BM6444, McMA26, HSC, and OarHH35) and study genetic diversity of 14 sheep types in Iran. Genomic DNA was extracted from blood samples of 565 individuals using an optimized salting-out DNA extraction procedure. The polymerase chain reaction (PCR) was successfully performed with the specific primers. Some locus–population combinations were not at Hardy–Weinberg equilibrium (P < 0. 05). The microsatellite analysis revealed high allelic and gene diversity in all 14 breeds. Pakistani and Arabi breeds showed the highest mean number of alleles (11.8 and 11 respectively), while the highest value for polymorphic information content was observed for the Arabi breed (0.88). A UPGMA (unweighted pair group method with arithmetic mean) dendrogram based on the Nei's standard genetic distance among studied breeds showed a separate cluster for Arabi and Pakistani breeds and another cluster for other breeds. The Shannon index (H0) for McMA2, BM6444, McMA26, HSC, and OarHH35 was 2.31, 2.17, 2.27, 2.04 and 2.18, respectively, and polymorphic information content (PIC) values were 0.88, 0.92, 0.87, 0.84, and 0.86 for McMA2, BM6444, McMA26, HSC, and OarHH35, respectively. The high degree of variability demonstrated within the studied sheep types implies that these populations are rich reservoirs of genetic diversity that must be preserved.

scholarly journals Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

2018 ◽  
Author(s):  
Bruce F Murray ◽  
Michael A Reid ◽  
Shu-Biao Wu
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Extreme Variability ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

scholarly journals Application of wheat SSR markers for detection of genetic diversity in triticale (x Triticosecale witt. )

Genetika ◽  
2015 ◽  
Vol 47 (3) ◽  
pp. 983-992
Author(s):  
Zelmíra Balázová ◽  
Andrej Trebichalský ◽  
Zdenka Gálová ◽  
Radomíra Hornyák-Gregáňová
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Ssr Marker ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Average Frequency ◽  
Polymorphic Markers ◽  
Average Value ◽  
Ssrs Markers

Present study aims to testify usefulness of particular wheat SSR markers for the detection of genetic diversity degree in the set of 59 triticale cultivars and new lines coming from different European countries and USA. For this purpose, a set of fifteen SSR markers were used. One SSR marker (Xwmc429) gave a uniform spectrum. The set of fourteen polymorphic markers provided 94 alleles with an average frequency of 6.71 alleles per locus. The number of alleles ranged between 2 (Xbarc 195) and 10 (Xbarc 137). Resulting from the number and frequency of alleles, diversity index (DI), polymorphic information content (PIC) and probabilities of identity (PI) were calculated. An average value of PIC for 14 markers was 0.640, the highest value was calculated for wheat SSR marker Xgwm 46 (0.809). Based on UPGMA algorithm, a dendrogram was constructed. It was able to separate 57 of 59 cultivars (96,6 %) from each other. American new-line NE-422T significantly separated from all cultivars and new lines. Only two french cultivars Bienvenu and Wilfried had not been separated from each other. A tested set of SSR markers allowed to better understand genetic relationships among European cultivars and American new lines. In general, a dendrogram along with results of calculated genetic indicators such as PIC, PI and DI point out at SSRs markers as high informative and usefull tool in genetic diversity research between close-related species.

scholarly journals Development of SSR Markers and Genetic Diversity Evaluation of Mycocentrospora Acerina Causing Round Spot of Panax Notoginseng in Yunan Province, China

2022 ◽  
Author(s):  
Huiling Wang ◽  
Kuan Yang ◽  
Liwei Guo ◽  
Lifen Luo ◽  
Chi He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Yunnan Province ◽  
Polymorphic Information Content ◽  
Polyacrylamide Gel Electrophoresis ◽  
Panax Notoginseng ◽  
Expected Heterozygosity ◽  
Ssr Primers ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Abstract Sanqi round spot, which is caused by Mycocentrospora acerina, is a destructive disease limits the production of Panax notoginseng in Yunnan province of China. However, the disease has not been studied comprehensively. In the current study, we identify M. acerina polymorphic microsatellite markers using CERVUS 3.0 and compare the genetic diversity of its isolates from P. notoginseng round spot using Simple Sequence Repeat (SSR) markers and polyacrylamide gel electrophoresis. Thirty-two SSR markers with good polymorphism were developed using MISA and CERVUS 3.0. The genetic diversity of 187 M. acerina isolates were evaluated using 14 representative SSR primers, and the polymorphic information content values of 14 sites ranged from 0.813 to 0.946, with a total of 264 alleles detected at 14 microsatellite loci. The average expected heterozygosity was 0.8967. The genetic diversity of M. acerina in Yunnan province does not reflect geographic specificity.

scholarly journals Microsatellites in the analysis of wheat genetic diversity

Genetika ◽  
2014 ◽  
Vol 46 (3) ◽  
pp. 1047-1063
Author(s):  
Ankica Kondic-Spika ◽  
Milica Nicic ◽  
Ljiljana Brbaklic ◽  
Dragana Trkulja ◽  
Dragana Miladinovic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Information Content ◽  
Ssr Markers ◽  
Microsatellite Loci ◽  
Polymorphism Information Content ◽  
Null Alleles ◽  
Wheat Genotypes ◽  
Rare Alleles ◽  
High Level

Microsatellite markers (SSR) were used to study wheat genetic diversity. A set of 87 wheat genotypes was analysed with four SSR markers. Primers used for the amplification of adequate microsatellite loci (Xgwm) are according to R?DER et al. (2002). Results were obtained using Applied Biosystems 3130 genetic analyser. Total of 28 alleles were determined, i.e. average of 7 alleles per marker. Number of alleles for individual markers ranged from six (Xgwm3) to eight (Xgwm18). The presence of two null alleles for Xgwm18 and Xgwm155 was found. There were five rare alleles (frequency <2%). Polymorphism information content (PIC) values ranged from 0.52 for Xgwm408 to 0.80 for Xgwm18. Mean PIC value was 0.69 for all markers, which signifies a high level of the detected polymorphism. According to the data collected through the analysis of four markers, most genotypes can be grouped in clusters. The results show usefulness of microsatellite markers in detecting polymorphism, identifying genotypes and assessing genetic diversity.

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