scholarly journals Genetic Diversity Analysis between Different Varieties of Chickpea (Cicer arietinum L.) Using SSR Markers

2019 ◽  
Vol 7 (2) ◽  
pp. 236-242
Author(s):  
Summy Yadav ◽  
Vaidehi Shah ◽  
Bhavya Mod
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genomic Dna ◽  
Physiological Data ◽  
Diversity Analysis ◽  
Hierarchical Tree ◽  
Cicer Arietinum L ◽  
Equal Distance ◽  
Genomic Regions ◽  
Simple Sequence

The paper aims at evaluating genetic diversity among genomes of chickpea comprising of 5 different varieties with the help of simple sequence repeats (SSR) molecular markers. Genomic DNA isolated from all varieties was checked with 15 different SSR markers specific for ENDPOINT PCR using PCR based techniques. Amplification bands with different markers enabled identification of the genomic regions responsible for Drought Tolerance in chickpea. All 15 SSR markers chosen gave monomorphic bands.  A hierarchical tree was also constructed using UPGMA Dendogram for figuring out the exact genetic distance of cultivars using band amplification data. It depicted GUJ-1 and GUJ-2 are closest of all cultivars. GUJ-5 is at the center having GUJ-3 and UJJAVAL at an almost equal distance but GUJ-5 and GUJ-3 are more related. Physiological data also supported this genetic evidence. Int. J. Appl. Sci. Biotechnol. Vol 7(2): 236-242

Development of EST-SSR markers and genetic diversity analysis among three Artemia species from different geographic populations

Crustaceana ◽  
2019 ◽  
Vol 92 (7) ◽  
pp. 841-851
Author(s):  
Xuekai Han ◽  
Ruyi Xu ◽  
Yuyu Zheng ◽  
Meirong Gao ◽  
Liying Sui
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Polymorphic Information Content ◽  
Diversity Analysis ◽  
Food Items ◽  
Geographical Populations ◽  
Geographic Populations ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Artemia is one of the most important live food items used in larviculture. In order to study the genetic diversity of Artemia in China, 170 novel simple sequence repeats (SSR) markers were identified from expressed sequence tags (ESTs) of the transcriptome library of Artemia parthenogenetica. Of these, 8 microsatellite loci were developed to characterize three geographical populations of Artemia. The results showed the expected and observed heterozygosity varied from 0.43 to 0.50 and from 0.59 to 0.64, respectively. The PIC (polymorphic information content) ranged from 0.37 to 0.45. These observations indicated that the Yuncheng population has the highest genetic diversity, whereas the Shuanghu population has the lowest. The Fst value (genetic differentiation coefficient) indicated that the three populations are highly differentiated. Genetic identity analyses revealed that the Yuncheng and Shuanghu populations have the closest relationship. The SSR markers described here will serve as a valuable tool for further studies in population and conservation genetics on Artemia.

scholarly journals MOLECULAR CHARACTERIZATION OF FIVE SELECTED BRINJAL (Solanum melongena L) GENOTYPES USING SSR MARKERS

2008 ◽  
Vol 21 (1) ◽  
pp. 01-06 ◽  
Author(s):  
A. K. M. Khorsheduzzaman ◽  
M. Z. Alam ◽  
M. M. Rahman ◽  
M. A. K. Mian ◽  
M. I. H. Mian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Banding Pattern ◽  
Genomic Dna ◽  
Molecular Level ◽  
Narrow Range ◽  
Solanum Melongena ◽  
Pcr Amplification ◽  
Simple Sequence

Five brinjal (Solanum melongena L.) genotypes were selected for characterization using Simple Sequence Repeats (SSR) markers. All the genotypes showed considerable variation in respect of morphological, anatomical and biochemical aspects. For study of relatedness, plant genomic DNA was extracted by CTAB based method using 11 randomly selected primers produced from Calgene Inc. USA. The primers developed 22 bands through PCR amplification out of which 15 from 3 primers and were polymorphic. Genetic similarities of SSR profiles were estimated based on Jaccard’s coefficient value. The dendrogram generated two clusters and they were clearly distinct and separated from each other. Cluster-I consisted of genotypes TURBO and BL009; and cluster-II comprised of genotypes EG058, EG075 and ISD006. Genotype TURBO and BL009 were identified as the diverse genotype and showed a maximum of 17% dissimilarity from EG058, EG075 and ISD006. The similarity value ranged from 0.83 to 1.00 which indicated the presence of narrow range of genetic diversity at molecular level but have still a possibility of crossing among the genotypes of two clusters. The banding pattern of different genotypes could be utilized as reference for further comparisons.DOI: http://dx.doi.org/10.3329/bjpbg.v21i1.17041

scholarly journals Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

2020 ◽  
Author(s):  
Lei Zhu ◽  
Hua yu Zhu ◽  
Yan man Li ◽  
Xiang bin Wu ◽  
Jin tao Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Comparative Genomics ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Diversity Analysis ◽  
Motif Length ◽  
Genetic Diversity Analysis ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence

Abstract Background The Cucurbita genus contains important economic crops in the world, while limited molecular markers have been developed in the past years. Simple sequence repeats (SSR) markers are powerful tools for the study of genetic mapping construction, genetic diversity analysis and genome wide association. The availability of pumpkin genome information has made it possible to analyze SSRs in genome wide across three Cucurbita species. Results In this paper, based on the whole genome sequences, 34,375 SSR loci were found in C. moschata, 30,577 SSR loci were found in C. maxima and 38,104 SSR loci were found in C. pepo. C. pepo has the maximum density of SSRs with an average of 145 SSR/Mb. In general, the frequency in total SSR loci decreased with the increase of the motif length, dinucleotide motifs were the most common motifs in the three species, and for the same repeat types, the SSR frequency decreased sharply with the increase of the repeat number. Most of those SSR loci were suitable for marker development (84.75% in C. moscata, 94.53% in C. maxima and 95.09% in C. pepo). Based on those markers, we compared and analyzed the cross-species SSR markers between C. pepo and other Cucurbitaceae species by silico-PCR. Using these cross-species primers, the high collinear relationships between C. pepo and the other two species were detected, respectively. Furthermore, the application of SSR markers in genetic diversity analysis was tested in C. pepo, the results showed that they were good tools to be used in genetic diversity analysis. Conclusion In this study, the genome wide SSR markers were detected from three Cucurbita species, and some of their applications were proved by comparative genomics and genetic diversity analysis. The large number of genome-wide SSR markers and crossspecies markers would promote the basic and applied studies of Cucurbita species, such as gene mapping, QTLs mapping, comparative genomics and marker-assisted breeding.

scholarly journals KEANEKARAGAMAN GENETIK KAPULASAN [NEPHELIUM RAMBOUTAN-AKE (LABILL.) LEENH.] DI JAWA BERDASARKAN MARKA SSR DAN ISSR

Floribunda ◽  
2020 ◽  
Vol 6 (4) ◽  
Author(s):  
Nina Ratna Djuita ◽  
Alex Hartana ◽  
Tatik Chikmawati ◽  
Dorly
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genomic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Sequence Repeat ◽  
Polymorphic Bands ◽  
Simple Sequence

Nina Ratna Djuita, Alex Hartana, Tatik Chikmawati, Dorly. 2020. Genetic Diversity of Pulasan [Nephelium ramboutan-ake (Labill.) Leenh.] of Java Based on SSR and ISSR Markers. Floribunda 6(4): 117–126. —  Pulasan is one of the potential local fruits to be developed. This study aimed to analyze the genetic diversity of pulasan of Java using Simple Sequence Repeat (SSR) and Inter Simple Sequence Repeat (ISSR) markers and to obtain information whether primers of the markers could be used to distinguish male and her-maphrodite plants. The results showed that two primers in the SSR markers and seven primers in the ISSR markers produced polymorphic bands. The genomic DNA of the pulasan amplified with SSR markers produced bands 140–500 bp, while those from the ISSR markers were 150–1500 bp. The population of pulasan in Babakan Madang has the highest genetic diversity, while that of Patean is the lowest. Genetic variation of pulasan based on SSR and ISSR markers in the population and among populations have different compositions. Variation in the population is 72% while among the population is 28%. Primers of LML Y6 and LML Y12 from SSR markers and primers of ISSR 2, 3, 4, 5, 6, 8, 9 cannot be used to distinguish male and hermaphrodite pulasan plants. Nina Ratna Djuita, Alex Hartana, Tatik Chikmawati, Dorly. 2020. Keanekaragaman Genetik Kapulasan [Nephelium ramboutan-ake (Labill.) Leenh.] di Jawa Berdasarkan Marka SSR dan ISSR. Floribunda 6(4): 117–126. —  Kapulasan merupakan salah satu buah lokal yang potensial untuk dikembangkan. Penelitian ini bertujuan untuk menganalisis keanekaragaman genetik kapulasan di Jawa dengan menggunakan marka Simple Sequence Repeat (SSR) dan Inter Simple Sequence Repeat (ISSR) serta untuk mendapatkan informasi apakah primer dari marka tersebut dapat dipakai untuk membedakan tumbuhan jantan dan hermafrodit.  Hasil penelitian menunjukkan bahwa dua primer pada marka SSR dan tujuh primer pada marka ISSR menghasilkan pita polimorfik. DNA genom kapulasan yang diamplifikasi dengan  marka SSR menghasilkan pita-pita dengan ukuran 110–500 bp, sedangkan dari marka ISSR berukuran 150–1500 bp. Populasi kapulasan di Babakan Madang mempunyai keanekaragaman genetik paling tinggi, sedangkan populasi di Patean paling rendah. Variasi genetik kapulasan berdasarkan  marka SSR dan ISSR di dalam populasi dan di antara populasi mempunyai komposisi yang berbeda. Variasi di dalam populasi sebesar 72 % sedangkan di antara populasi sebesar 28%. Primer LML Y6 dan LML Y12 dari marka SSR dan primer ISSR 2, 3, 4, 5, 6, 8, 9  tidak dapat digunakan untuk membedakan tumbuhan kapulasan jantan dan hermafrodit.   

scholarly journals Development of Expressed Sequence Tag-Drived Simple Sequence Repeat Markers and Diversity Analysis of Phytophthora capsici in China

2013 ◽  
Vol 2 (3) ◽  
pp. 137-146
Author(s):  
Liu Pei-Qing ◽  
Wu Min-Liang ◽  
Li Ben-Jin ◽  
Lan Cheng-Zhong ◽  
Weng Qi-Yong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Phytophthora Capsici ◽  
Management Strategies ◽  
Diversity Analysis ◽  
Evolutionary Potential ◽  
Genetic Clusters ◽  
Expressed Sequence ◽  
Simple Sequence

Phytophthora capsici is a highly dynamic and destructive pathogen of vegetable and great interests on the genetic structure of P. capsici have grown in the world. However, there is little genetic information about P. capsici based on the EST-SSR markers. In this study, 193 SSR markers were developed and 33 selected markers were successfully detected and they were polymorphic with the number of alleles per locus ranging from 2 to 7. 4 SSR markers were further selected for genetic diversity analysis and Nei’s genetic diversity values of 15 populations ranged from 0.38 to 0.66, with an average of 0.53. The higher polymorphism and greater transport ability of these markers among P. capsici species were proved by the expected heterozygosity (He =0.64) and Shannon’s index of diversity (I =1.14), indicating that they maintained a substantial level of genetic diversity. Additionally, the genetic differentiation among the 4 markers (Fst =0.15) was moderate and the gene flow among groups was consequent (Nm =1.69). Clustering analyses revealed that 15 populations are made of two differentiated genetic clusters and are similar regarding genetic diversity composition. Our results suggest that there are considerable evolutionary potential of P. capsici in China and useful management strategies should be adapt to it.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

scholarly journals The new use of Sorghum bicolor-derived SSR markers to evaluate genetic diversity in 17 Australian Sorghum species

2005 ◽  
Vol 3 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Sally L. Dillon ◽  
Peter K. Lawrence ◽  
Robert J. Henry
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Ssr Markers ◽  
Diversity Indices ◽  
Basic Knowledge ◽  
Apparent Lack ◽  
Breeding Programmes ◽  
Diversity Studies ◽  
Potential Use ◽  
Simple Sequence

The Sorghum genus is extremely diverse both morphologically and geographically, however, relatively few of the 25 recognized species have been evaluated genetically. The apparent lack of basic knowledge pertaining to the levels of genetic diversity both within and between the 17 Australian wild species is a major obstacle to both their effective conservation and potential use in breeding programmes. Twelve Sorghum bicolor-derived simple sequence repeat (SSR) markers were evaluated for cross-species amplification in all 25 Sorghum species. The SSR markers were highly polymorphic, with diversity indices ranging from 0.59 to 0.99 with mean of 0.91. Five markers combined were able to differentiate 24 of the 25 Sorghum species, with intra-species polymorphism apparent. Sorghum bicolor-derived SSRs have proven to be an efficient source of markers for genetic diversity studies of the relatively poorly characterized Australian indigenous Sorghum species.

scholarly journals Population structure and genetic diversity analysis in Sali (Oryza sativa) rice germplasm of Assam using microsatellite markers

2021 ◽  
Vol 58 (2) ◽  
pp. 279-286
Author(s):  
Sandhani Saikia ◽  
Pratap Jyoti Handique ◽  
Mahendra K Modi
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Crop Improvement ◽  
Mean Value ◽  
Diversity Analysis ◽  
Rice Cultivars ◽  
Improvement Program ◽  
Information Index ◽  
Improvement Programs

Genetic diversity is the source of novel allelic combinations that can be efficiently utilized in any crop improvement program. To facilitate future crop improvement programs in rice, a study was designed to identify the underlying genetic variations in the Sali rice germplasms of Assam using SSR markers. The 129 SSR markers that were used in the study amplified a total of 765 fragments with an average of 5.93 alleles per locus. The Shannon's Information Index was found to be in the range from 0.533 to 1.786. The Polymorphism Information Content (PIC) fell into the range from 0.304 to 0.691 with a mean value of 0.55. The overall FST value was found to be 0.519 that indicated the presence of genetic differentiation amongst the genotypes used in the study. The Sali population was divided into two clusters. The information obtained from the present study will facilitate the genetic improvement of Sali rice cultivars.

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