Genetic divergence studies through microsatellite markers in pigeonpea [Cajanus cajan (L) Millsp.]

2018 ◽  
Author(s):  
Pankaj Sharma ◽  
Inderjit Singh ◽  
Asmita Sirari ◽  
Sarvjeet Singh ◽  
Gaurav Khosla
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Cajanus Cajan ◽  
Polymorphic Information Content ◽  
Germplasm Characterization ◽  
Male Sterile ◽  
Dissimilarity Coefficient ◽  
Improvement Programs ◽  
Characterization Studies ◽  
Simple Sequence

The Genetic diversity was assessed among 96 pigeonpea accessions including 15 male sterile, 13 maintainer and 68 germplasm lines using 44 Simple Sequence Repeats (SSR) markers distributed over all the 11 chromosomes. Out of 44 SSR markers, 33 were polymorphic which showed 75% polymorphism among the used markers. For an individual primer, the alleles amplified varied from 2 to 4 with an average of 2.54. The Polymorphic Information Content (PIC) values ranged from 0.26 (CCM 0183) to 0.78 (CCM 0402 and CCM 0721). Based on 112 alleles amplified by SSR markers, the 96 genotypes were alienated into eight clusters. Cluster I and cluster VII were the largest with 22 genotypes each, cluster III and cluster IV were the smallest with two genotypes each, while cluster II, cluster V, cluster VI and cluster VIII consisted of 10, 15, 14 and 9 genotypes, respectively. Genotypes Pusa 991 and ULA 11 were found to be the most distant genotypes with highest dissimilarity coefficient (32%) where as AL 112A and AL 113A were the least distant genotypes with lowest dissimilarity coefficient (2%). Thus, highly distant genotypes can be used in pigeonpea improvement programs for getting desirable segregants. The selected panel of polymorphic SSR markers performed well in detection of genetic diversity patterns and can be used for future germplasm characterization studies in pigeonpea.

scholarly journals Analysis of genetic diversity and population structure in Asparagus species using SSR markers

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Manish Kapoor ◽  
Pooja Mawal ◽  
Vikas Sharma ◽  
Raghbir Chand Gupta
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Mean Value ◽  
Discrete Groups ◽  
Base Pairs ◽  
High Genetic Diversity ◽  
Pharmaceutical Industries ◽  
Improvement Programs ◽  
Northwest India ◽  
Simple Sequence

Abstract Background Various Asparagus species constitute the significant vegetable and medicinal genetic resource throughout the world. Asparagus species serve as important commodity of food and pharmaceutical industries in India. A diverse collection of Asparagus species from different localities of Northwest India was investigated for its genetic diversity using simple sequence repeat (SSR) markers. Results Polymorphic SSR markers revealed high genetic diversity. Primer SSR-15 amplified maximum of 8 fragments while 3 primers, namely, SSR-43, SSR-63, and AGA1 amplified minimum of 3 fragments. Collectively, 122 alleles were amplified in a range between 3 and 8 with an average of 5 alleles per marker. The size of the amplified alleles ranged between 90 and 680 base pairs. Polymorphism information content (PIC) value varied from a highest value of 0.499 in primer AGA1 to a lowest value of 0.231 in primer SSR-63 with a mean value of 0.376 showing considerable SSR polymorphism. Dendrogram developed on the basis of Jaccard’s similarity coefficient and neighbor-joining tree segregated all the studied Asparagus species into two discrete groups. Structure analysis based on Bayesian clustering allocated different accessions to two independent clusters and exhibited low level of individual admixture. Conclusions The genetic diversity analysis showed a conservative genetic background for maximum species of asparagus. Only Accessions of Asparagus adscendens were split into two diverse clusters suggesting a wide genetic base of this species as compared to other species. Overall genetic diversity was high, and this germplasm of Asparagus can be used in future improvement programs. The findings of current research on Asparagus germplasm can make a momentous contribution to initiatives of interbreeding, conservation, and improvement of Asparagus in future.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽  
2015 ◽  
Vol 50 (8) ◽  
pp. 1143-1147 ◽  
Author(s):  
Benard Yada ◽  
Gina Brown-Guedira ◽  
Agnes Alajo ◽  
Gorrettie N. Ssemakula ◽  
Robert O.M. Mwanga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Population Improvement ◽  
High Level ◽  
Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

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.

Assessing heat stress tolerance and genetic diversity among exotic and Indian wheat genotypes using simple sequence repeats and agro-physiological traits

2015 ◽  
Vol 15 (3) ◽  
pp. 208-220 ◽  
Author(s):  
K. T. Ramya ◽  
Neelu Jain ◽  
Nikita Gandhi ◽  
Ajay Arora ◽  
P. K. Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Heat Stress ◽  
Stress Tolerance ◽  
Ssr Markers ◽  
Agronomic Traits ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Phenotypic Traits ◽  
Heat Stress Tolerance ◽  
Simple Sequence

Genetic diversity and relationship of 92 bread wheat (Triticum aestivum L.) genotypes from India and exotic collections were examined using simple sequence repeat (SSR) markers and phenotypic traits to identify new sources of diversity that could accelerate the development of improved wheat varieties better suited to meet the challenges posed by heat stress in India. Genetic diversity assessed by using 82 SSR markers was compared with diversity evaluated using five physiological and six agronomic traits under the heat stress condition. A total of 248 alleles were detected, with a range of two to eight alleles per locus. The average polymorphic information content value was 0.37, with a range of 0.04 (cfd9) to 0.68 (wmc339). The heat susceptibility index was determined for grain yield per spike, and the genotypes were grouped into four categories. Two dendrograms that were constructed based on phenotypic and molecular analysis using UPGMA (unweighted pair group method with arithmetic mean) were found to be topologically different. Genotypes characterized as highly heat tolerant were distributed among all the SSR-based cluster groups. This implies that the genetic basis of heat stress tolerance in these genotypes is different, thereby enabling wheat breeders to combine these diverse sources of genetic variability to improve heat tolerance in their breeding programmes.

scholarly journals Development of Novel Genomic Simple Sequence Repeat (g-SSR) Markers and Their Validation for Genetic Diversity Analyses in Kalmegh [Andrographis paniculata (Burm. F.) Nees]

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1734
Author(s):  
Ramesh Kumar ◽  
Chavlesh Kumar ◽  
Ritu Paliwal ◽  
Debjani Roy Choudhury ◽  
Isha Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Andrographis Paniculata ◽  
The Novel ◽  
Neighbor Joining ◽  
Genomic Libraries ◽  
Genomic Resources ◽  
Population Structure Analysis ◽  
Simple Sequence

Kalmegh (Andrographis paniculata (Burm. F.) Nees) is one of the most important medicinal plants and has been widely explored as traditional medicine. To exploit its natural genetic diversity and initiations of molecular breeding to develop novel cultivars or varieties, developments of genomic resources are essential. Four microsatellite-enriched genomic libraries—(CT)14, (GT)12, (AG)15 and (AAC)8—were constructed using the genomic DNA of A. paniculata. Initially, 183 recombinant colonies were screened for the presence of CT, GT, AG, and AAC microsatellite repeats, out of which 47 clones found positive for the desired simple sequence repeats (SSRs). It was found that few colonies had more than one desirable SSR. Thus, a sum of 67 SSRs were designed and synthesized for their validation among 42 A. paniculata accessions. Out of the 67 SSRs used for genotyping, only 41 were found to be polymorphic. The developed set of g-SSR markers showed substantial genetic variability among the selected A. paniculata accessions, with an average polymorphic information content (PIC) value of 0.32. Neighbor-joining tree analysis, population structure analysis, analysis of molecular variance (AMOVA), and principal coordinate analysis (PCoA) illustrated the considerable genetic diversity among them. The novel g-SSR markers developed in the present study could be important genomic resources for future applications in A. paniculata.

Genetic diversity of mungbean (Vigna radiata L.) germplasm in Indonesia

2014 ◽  
Vol 12 (S1) ◽  
pp. S91-S94 ◽  
Author(s):  
Puji Lestari ◽  
Sue Kyung Kim ◽  
Reflinur ◽  
Yang Jae Kang ◽  
Nurwita Dewi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Vigna Radiata ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Conservation Strategy ◽  
Low Genetic Diversity ◽  
Breeding Programmes ◽  
The Mean ◽  
Simple Sequence

Despite widespread mungbean [Vigna radiata (L.) Wilczek] consumption in Indonesia, few molecular studies have been carried out on accessions and available data are minimal. In this study, we used 30 newly developed simple sequence repeat (SSR) markers designed from the mapped sequence scaffolds of the Korean Sunhwanokdu and Gyeonggijaerae 5 mungbean genomes. These markers were used to examine loci in 83 mungbean accessions collected from diverse geographical areas in Indonesia. A total of 107 alleles were detected among the accessions with 29 polymorphic markers. However, the mean of polymorphic information content (0.33) value and diversity index (0.38) value was indicative of low genetic diversity in this germplasm. The mungbean population structure was not clearly differentiated and the number of subpopulations was unclear. Neighbour-joining tree analysis revealed that the genetic cluster did not reflect the geographical origin of the accessions. Interestingly, the most agriculturally improved varieties were genetically similar to some landraces from one of the main mungbean-producing regions. These newly developed SSR markers could be useful for detecting genetic variability as a basis for establishing a conservation strategy for mungbean germplasm with the aim of enhancing Indonesian breeding programmes.

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 Genetic diversity analysis of soybean (Glycine max (L.) Merr.) genotypes making use of SSR markers

2019 ◽  
pp. 1113-1119
Author(s):  
Keitumetse Kujane ◽  
Moosa M Sedibe ◽  
Alina Mofokeng
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Molecular Data ◽  
Dna Ladder ◽  
Ssr Primers ◽  
Soybean Genotypes ◽  
Glycine Max L ◽  
Simple Sequence ◽  
Selection Of

In this study, we aimed to investigate the genetic diversity and polymorphism among 30 soybean genotypes maintained by the ARC using simple sequence repeat (SSR) markers. Soybean genotypes were characterized using 20 SSR primers. DNA was extracted using the standard cetyl trimethylammonium bromide method and amplified using PCR. Allele size was determined via comparison with a 100 base pair (bp) DNA ladder. Molecular data were analyzed, and a dendrogram and matrix were generated using GGT 2.0 software. A total of 216 alleles with an average of 10.8 alleles per locus were detected. The allele sizes ranged between 2 and 33 bp with an average of 18.7 bp. The polymorphic information content among genotypes varied from 0.85 (Satt001) to 0.75 (Satt43) with an average of 0.716, and heterozygosity ranged from 0.87 to 0.78 with an average of 0.7485. The most diverse genotypes were B 66 S 31, 69S 7, and R5-4-2 M, which indicated the efficiency of the SSR markers for the detection of genetic diversity. The results of the current study revealed the diversity among the soybean genotypes tested, which might aid breeders in the future in the selection of parents for breeding.

scholarly journals Genetic Diversity Assessment in Pea (Pisum sativum L.) using Microsatellite Markers

2021 ◽  
Vol 12 (5) ◽  
pp. 402-408
Author(s):  
Hanuman Ram ◽  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Molecular Diversity ◽  
Polymorphic Information Content ◽  
Association Studies ◽  
Pisum Sativum L ◽  
Diversity Assessment ◽  
Potential Use ◽  
Simple Sequence

The present study was conducted on genetic diversity analyses among 24 pea genotypes during 2017–2018 to assess the molecular diversity of pea genotypes using SSR markers. Out of 62, eleven markers were found to be polymorphic and the polymorphic information content (PIC) of the simple sequence repeat (SSR) markers ranged from 0.19 to as high as 0.64. Molecular profiling of these genotypes using 11 SSRs distributed throughout the genome generated 32 alleles with a mean of 2.91 alleles per locus. The genetic dissimilarity based on simple matching coefficient for 24 genotypes ranged from 0.00 to 0.91 with an average of 0.52. Cluster analyses grouped 24 genotypes into two major clusters with one outlier and supported by principal coordinate analysis (PCoA) in which genotypes were distributed across four quadrangles. Analysis of molecular variance (AMOVA) showed significant estimated value at degree of 1000 permutations. Percentage of variability was higher among individual (67%) than among populations (11%). Percentage of variability within individual was also higher (22%) than among populations (11%). Pop1 (I=0.707, He=0.446, and uHe=0.466) shows higher diversity than pop2 (I=0.630, He=0.381 and uHe=0.398). The percentage of polymorphic loci per population (PPL) ranged from 81.82% (pop2) to 90.91% (pop1) with an average of 86.36%. The present study demonstrates the utility of microsatellite markers for estimating molecular diversity as well as genotype identification in pea. This study also suggests a potential use of these markers in further association studies.

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