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

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.

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

Australian Journal of Crop Science ◽

10.21475/ajcs.19.13.07.p1638 ◽

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.

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Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

HortScience ◽

10.21273/hortsci12506-17 ◽

2018 ◽

Vol 53 (3) ◽

pp. 283-287

Author(s):

Xiu Cai Fan ◽

Hai Sheng Sun ◽

Ying Zhang ◽

Jian Fu Jiang ◽

Min Li ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Genetic Similarity ◽

Similarity Coefficient ◽

Srap Markers ◽

Average Percentage ◽

Allele Number ◽

Ssr Primers ◽

Vitis Davidii ◽

Simple Sequence

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

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

HortScience ◽

10.21273/hortsci.50.8.1143 ◽

2015 ◽

Vol 50 (8) ◽

pp. 1143-1147 ◽

Cited By ~ 8

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.

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

Crustaceana ◽

10.1163/15685403-00003916 ◽

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.

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

Plant Genetic Resources ◽

10.1017/s1479262115000532 ◽

2015 ◽

Vol 15 (3) ◽

pp. 208-220 ◽

Cited By ~ 1

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.

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Molecular characterization of almond accessions from the island of La Palma (Canary Islands, Spain) using SSR markers

Plant Genetic Resources ◽

10.1017/s1479262114000112 ◽

2014 ◽

Vol 12 (3) ◽

pp. 323-329 ◽

Cited By ~ 1

Author(s):

Guillermo Padilla ◽

Rafel Socias i Company ◽

Amando Ordás

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Average Value ◽

La Palma ◽

Expected Heterozygosity ◽

Commercial Cultivars ◽

Soft Shell ◽

Genetic Profiles ◽

Simple Sequence

In this study, 15 simple sequence repeat (SSR) markers were used for genetic diversity analysis of 45 almond accessions, which included 25 local cultivars from La Palma Island and three other commercial cultivars. A total of 110 amplification fragments were produced, with an average value of 7.9 alleles per locus. Twelve of the SSR markers can be considered as highly informative, with values of expected heterozygosity and power of discrimination above 0.5 and 0.8, respectively. Due to cases of synonymy and homonymy, 37 different genetic profiles were obtained, with the homonymy of the soft-shell varieties known as ‘Mollar’ being the most significant. Cluster analysis identified four groups within the accessions. One of these groups exclusively consisted of the two commercial cultivars ‘Guara’ and ‘Ferraduel’. The other commercial cultivar used in the study, ‘Desmayo Largueta’, was in a cluster with three cultivars from the same locality. The analysis of molecular variance revealed that the within-localities component accounts for most of the total variation, suggesting that La Palma almond cultivars did not originate independently in different parts of the island. The results of the study reveal the genetic singularity of La Palma almond cultivars and the genetic diversity among them.

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Genetic diversity of walnut (Juglans regia L.) seedlings through SSR markers in north-western Himalayan region of Jammu

Bangladesh Journal of Botany ◽

10.3329/bjb.v49i4.52517 ◽

2020 ◽

Vol 49 (4) ◽

pp. 1003-1012

Author(s):

Rafiq Ahmad Shah ◽

Parshant Baksi ◽

Amit Jasrotia ◽

Deep JI Bhat ◽

Rucku Gupta ◽

...

Keyword(s):

Genetic Diversity ◽

Decision Making ◽

Ssr Markers ◽

Juglans Regia ◽

Germplasm Management ◽

Expected Heterozygosity ◽

Western Himalayan Region ◽

Ssr Primers ◽

Genetic Dissimilarity ◽

North Western

screening of 25 SSR markers, revealed 23 clear and consistent amplification profiles in the entire walnut germplasm set. A total of 54 alleles were amplified by SSR primers and the number of alleles range from 2 to 3. The PIC value ranged from 0.36 to 0.68. The dendrogram classified all genotypes into two main clusters with various degrees of subclustering. Estimated genetic dissimilarity coefficient ranged from 0.36 to 0.85. Through model-based cluster analysis all genotypes were grouped into 5 genetically distinct subpopulations. The expected heterozygosity at a given locus was found to range from 0.520 to 0.5477. Similarly, population differentiation measurements (Fst) ranged from 0.2286 to 0.2909. These findings would be helpful for decision making in future walnut breeding studies, germplasm management activities to maximize genetic diversity in walnut germplasm and may also prove useful in future for conducting association mapping in walnut for different traits.

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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 ◽

10.3390/plants9121734 ◽

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.

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

Plant Genetic Resources ◽

10.1017/s1479262114000343 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S91-S94 ◽

Cited By ~ 7

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.

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Characterization of Genetic Diversity of Stone Fruit Rootstocks Used in Chile by Means of Microsatellite Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.137.5.302 ◽

2012 ◽

Vol 137 (5) ◽

pp. 302-310 ◽

Cited By ~ 3

Author(s):

María José Arismendi ◽

Patricio Hinrichsen ◽

Ruben Almada ◽

Paula Pimentel ◽

Manuel Pinto ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Ssr Markers ◽

Stone Fruit ◽

Identification System ◽

Expected Heterozygosity ◽

Commercially Important ◽

Taxonomic Groups ◽

Simple Sequence

Stone fruit (Prunus L.) production in Chile covers ≈43,000 ha and includes a wide variety of soils and climates requiring a large diversity of rootstocks. The most commercially important rootstock cultivars are 26 genotypes from three different taxonomic groups belonging to the subgenera Amygdalus (L.) Benth. Hook. (peach group), Prunus Focke [= Prunophora (Neck.)] Focke (plum group), and Cerasus (Adans.) Focke (cherry group) with eight, seven, and 10 individuals, respectively. To determine their genetic diversity, characterization by microsatellite markers [simple sequence repeat (SSR)] was conducted. Of a total of 20 SSR markers evaluated, 12 generated amplified products that were consistent in the three taxonomic groups. The number of alleles per marker ranged from 18 for PSM-3 to four in CPPCT-002. Clustering analysis, by both traditional hierarchical and model-based approaches, indicate that all genotypes are clustered in their respective taxonomic groups, including the interspecific hybrids. Genetic diversity, measured as the average distances (expected heterozygosity) between individuals in the same cluster, was higher in Cerasus (0.78) followed by Prunus (0.72) and Amygdalus (0.64). Total number of alleles observed was 133, of which 14, 33, and 35 from six, 10, and 10 loci were unique for the peach, plum, and cherry rootstock groups, respectively. Alleles shared among peach/plum, plum/cherry, and peach/cherry rootstock genotypes were 13, 14, and 18 from nine, seven, and seven loci, respectively. Only six alleles from five loci were common to the three taxonomic groups. In addition, to develop a rootstock identification system based on SSR markers, a minimum set of three markers (PMS-3, BPPCT-037, and BPPCT-036) able to differentiate the 26 genotypes was identified. This study is the first step toward establishing a stone fruit rootstock breeding program in Chile.

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