Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP

Genome ◽  
2012 ◽  
Vol 55 (6) ◽  
pp. 459-470 ◽  
Author(s):  
Ximei Li ◽  
Daojun Yuan ◽  
Hantao Wang ◽  
Xuemei Chen ◽  
Bin Wang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Fiber Quality ◽  
Single Strand Conformation Polymorphism ◽  
Utilization Efficiency ◽  
Ssr Primers ◽  
Base Transition ◽  
Pcr Products ◽  
Cotton Fiber Quality ◽  
Simple Sequence ◽  
Conformation Polymorphism

Simple sequence repeat (SSR) markers are widely used in plant genetics and breeding. However, there are many SSR markers that do not reveal polymorphism in cotton. Traditional SSR genotyping methods only provide information on product sizes. This leaves many marker polymorphism undetected, thus, lowering the utility of SSRs. In the present study, monomorphic SSRs between two mapping parents, ‘Emian22’ and 3-79, were subjected to single-strand conformation polymorphism (SSCP) analysis to reveal polymorphism. Of the 4194 monomorphic SSR primer pairs, 158 pairs (3.77%) showed polymorphism and revealed 174 polymorphic loci. Sequence analysis showed that the differences in PCR products between the mapping parents were solely due to base transition or transversion, which was in agreement with SSCP principles. SSCP also revealed SSRs with motifs of AT/TA and GAA/CTT were more polymorphic in dinucleotides and trinucleotides, respectively. Genetic mapping integrated 160 loci into our interspecific BC1 linkage map, 5 of which associated with QTLs related to cotton fiber quality. The technique discussed in the present study enables us to detect polymorphism of monomorphic SSRs, and increase the utilization efficiency of the existing SSR primers.

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

HortScience ◽  
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.

scholarly journals Efficient Fingerprinting of the Tetraploid Salix psammophila Using SSR Markers

Forests ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 176
Author(s):  
Lei Hao ◽  
Yongguang Zhai ◽  
Guosheng Zhang ◽  
Dongye Lu ◽  
Haiguang Huang
Keyword(s):  
Ssr Markers ◽  
Intellectual Property Rights ◽  
Simple Sequence Repeat ◽  
Northwest China ◽  
Phenotypic Traits ◽  
Identification Rate ◽  
Desert Shrub ◽  
Marker Combination ◽  
Ssr Primers ◽  
Simple Sequence

Salix psammophila C. Wang et Ch. Y. Yang is an important desert shrub that is mainly distributed in northwest China, including the Mu Us sandland and Kubuqi desert. It plays a crucial role in vegetation rehabilitation and as a forestation plant. The traditional identification of its accessions based on phenotypic traits is usually unreliable. SSR (Simple Sequence Repeat) has the advantages of repeatability and codominant inheritance, and most species have had specific SSR primers developed for them already. Currently, there is no simple and rapid method used for identifying the tetraploid Salix psammophila with SSR markers. In this study, we construct fingerprints among 261 accessions of S. psammophila by screening of marker combinations. We identified a nine-marker combination which could completely distinguish each of the 261 accessions to their unique fingerprinting profiles. For this marker combination (G+I+J+N+O+Q+S+T+U), identification rate of combined markers (MC2) and total Polymorphism Information Content (PIC) were the highest, at 100% and 6.05, respectively. We used fingerprinting profiles with the nine-marker combination to produce two-dimensional barcodes, which could be screened rapidly and conveniently using a barcode scanned by a computer. The results of this study can provide an efficient genetic toolkit for identification, traceability management and protection of intellectual property rights of particular accessions of tetraploid S. psammophila.

Female Twins with Severe Christmas Disease (Hemophilia B)

1993 ◽  
Vol 70 (05) ◽  
pp. 774-776 ◽  
Author(s):  
Karin Wollina ◽  
D J Bowen ◽  
G Syrbe ◽  
F Zintl
Keyword(s):  
Single Strand Conformation Polymorphism ◽  
Factor Ix ◽  
Hemophilia B ◽  
Chain Reaction ◽  
Hybridization Probe ◽  
Pcr Products ◽  
Exon 1 ◽  
Polymerase Chain ◽  
Cg Dinucleotides ◽  
Conformation Polymorphism

SummaryHemophilia B is an X-linked bleeding disorder. We report on female twins, who were conspicious in prolonged bleeding after venipuncture as well as hematomas after intramuscular injections even in the first months of their life. Their father suffering from a severe hemophilia B deceased in 1992. Their mother, half-brother and grandmother from their father’s side had no signs of bleeding disorders. Clotting analysis performed in both twins revealed a markedly prolonged partial thromboplastin time (>100 s). The factor IX levels were below 2%. In order to detect mutations, a general screen using the polymerase chain reaction (PCR) followed by single strand conformation polymorphism (SSCP) analysis of the PCR products have been performed. PCR products have been cut into smaller fragments using restriction endonucleases (RE) for an in-depth SSCP screen. A general screen for gross abnormalities in the factor IX gene including deletions, insertions and rearrangements was performed by Southern blot analysis of RE-digests of genomic DNA using the factor IX cDNA as a hybridization probe. Furthermore, we screened for mutations in the CG dinucleotides comprising part of RE-recognition sequences (exon 1, 2, 3, 4, 5, and 8). By all methods applied herein, no mutations have been detected in these twins. On the basis of our results the hemophilia B of these twins might be explained by extreme non-random lyonization.

scholarly journals GENETIC DIVERSITY OF Brassica rapa GERMPLASM OF KHYBER PAKHTUNKHWA PAKISTAN REVEALED BY MOLECULAR MARKERS

2019 ◽  
Vol 18 (6) ◽  
pp. 57-65
Author(s):  
Naushad Ali ◽  
Sardar Ali ◽  
Naqib Ullah Khan ◽  
Sohail Ahmad Jan ◽  
Malik Ashiq Rabbani ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Ssr Markers ◽  
Brassica Rapa ◽  
Arithmetic Mean ◽  
Group Method ◽  
Khyber Pakhtunkhwa ◽  
Upgma Dendrogram ◽  
Pair Group ◽  
Ssr Primers ◽  
Simple Sequence

A total of 96 indigenous Brassica rapa accessions were collected from different locations of Khyber Pakhtunkhwa, Pakistan. Simple Sequence Repeats (SSR) markers were used to identify the most diverse genotypes among the collected lots. Twenty six (26) different SSR primers were used for (genetic) variability among collected genotypes. These primers were selected from literature based on their previous results. These primers produced 135 scorable bands of which 75 were polymorphic, with an average of 55.5% polymorphic loci, and reflected the broader genetic background of the collected genotypes. An average 2.88 polymorphic bands with an average PIC value of 0.49 was recorded. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) divided all genotypes into three main groups. Group one contained three clusters, while group two and three had four and two clusters each. Based on the UPGMA dendrogram, genotypes collected from Kohat, Bannu, Swat and Haripur showed considerable amount of variation. From the present study, it is concluded that SSR markers can be proved as the best tool for the genetic variability of other local and exotic B. rapa genotypes.

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.

Genetic diversity of Crotalaria germplasm assessed through phylogenetic analysis of EST-SSR markers

Genome ◽  
2006 ◽  
Vol 49 (6) ◽  
pp. 707-715 ◽  
Author(s):  
M L Wang ◽  
J A Mosjidis ◽  
J B Morris ◽  
R E Dean ◽  
T M Jenkins ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Germplasm Collection ◽  
High Similarity ◽  
Ssr Primers ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Crotalaria Spectabilis

The genetic diversity of the genus Crotalaria is unknown even though many species in this genus are economically valuable. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago and soybean were used to assess the genetic diversity of the Crotalaria germplasm collection. This collection consisted of 26 accessions representing 4 morphologically characterized species. Phylogenetic analysis partitioned accessions into 4 main groups generally along species lines and revealed that 2 accessions were incorrectly identified as Crotalaria juncea and Crotalaria spectabilis instead of Crotalaria retusa. Morphological re-examination confirmed that these 2 accessions were misclassified during curation or conservation and were indeed C. retusa. Some amplicons from Crotalaria were sequenced and their sequences showed a high similarity (89% sequence identity) to Medicago truncatula from which the EST-SSR primers were designed; however, the SSRs were completely deleted in Crotalaria. Highly distinguishing markers or more sequences are required to further classify accessions within C. juncea.Key words: Crotalaria germplasm, EST-SSR, genetic diversity, phylogeny.

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.

Screening differentially displayed PCR products by single-strand conformation polymorphism gels

1999 ◽  
pp. 341-354 ◽  
Author(s):  
Françoise Mathieu-Daudé ◽  
Nick Benson ◽  
Frank Kullmann ◽  
Rhonda Honeycutt ◽  
Michael McClelland ◽  
...  
Keyword(s):  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Pcr Products ◽  
Conformation Polymorphism

SSR markers for identification of purity of melon hybrids

2008 ◽  
Vol 5 (3) ◽  
pp. 223-229 ◽  
Author(s):  
Li Ju-Fen ◽  
Ma Guo-Bin ◽  
Xu Ling
Keyword(s):  
Ssr Markers ◽  
Cucumis Melo ◽  
Field Tests ◽  
Hybrid Purity ◽  
Ssr Primers ◽  
Hybrid Seeds ◽  
Polymerase Chain ◽  
Parental Lines ◽  
Hybrid Lines ◽  
Simple Sequence

AbstractThe hybrid purity of melon (Cucumis melo L.) was tested by polymerase chain reaction (PCR) assay based on simple sequence repeat (SSR) markers in two F1 melon hybrids (‘Dongfangmi 1’ and ‘Dongfangmi 2’) and their parental lines. Twelve pairs of SSR primers for ‘Dongfangmi 1’ and three pairs for ‘Dongfangmi 2’ were selected. Results showed that self-inbred seeds were effectively distinguished from F1 hybrid seeds using these SSR primers, a finding that was consistent with the results recorded from field tests. ‘Dongfangmi 1’ and ‘Dongfangmi 2’ were identified from their parental lines, and seven other uterine hybrid lines by multiplex primers MS48+MS60 and MS4+MS20, respectively. Contamination of F1 hybrid seeds caused by self-inbred and other unknown pollens can be effectively and more reliably detected by PCR assays with multiplex SSR primers.

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