scholarly journals Identification of Local Citrus Breeds Using the Start-Codon Targeted Polymorphism Technique Combined with Clonal Sequencing

2021 ◽  
Vol 25 (01) ◽  
pp. 68-74
Author(s):  
Yanjun Guo
Keyword(s):  
Genetic Diversity ◽  
Start Codon ◽  
Sequencing Analysis ◽  
Similarity Coefficients ◽  
High Genetic Diversity ◽  
Protein Coding ◽  
Scot Marker ◽  
Citrus Germplasm ◽  
Mutational Hotspots ◽  
Citrus Varieties

This study explored the genetic diversity of 35 citrus accessions using start-codon targeted (SCoT) markers. Total 15 primers were used to amplify products ranging in length from 100 to 2000 bp. A total of 133 fragments were amplified and found that 126 (95%) were polymorphic. The genetic similarity coefficients among the 35 accessions ranged from 0.67 to 1.00, indicating that the SCoT markers could reveal high genetic diversity in the citrus germplasm. A cluster analysis showed that local citrus breeds of Sihui city fell into one cluster, possibly reflecting the geographical distribution of the tested samples. The sizesof the fragments of eight local citrus cultivars amplified by one of the primers ranged from 951 to 1001 bp, and the similitude was 95.17%high. Both single-base mutations, insertions and deletions were identified among the fragments and comparison with asequence database suggested that the amplified region was part of a ribosomal protein-coding sequence. Using Scot marks combined with clonal sequencing, each of the test samples had one or more mutation sites that could be used as markers to differentiate from the other seven test samples. Thus, the resolution of the genetic diversity among the local citrus breeds revealed by the SCoT technique was enhanced by the subsequent sequencing analysis of specific fragments. The experimental results also provide evidence that the relationship between CitrusnobilisL our. ‘gonggan’ and C. hanianaHort. ex Tseng ‘Sihuihanggan’ is that between parent and offspring hybrids and not between bud-mutation strains. The SCoT marker is a targeted gene molecular marker, based on the characteristic bands of primers, it can be used as a marker to isolate genes of local citrus varieties and also for investigating mutational hotspots of the segene.© 2021Friends Science Publishers

scholarly journals Start codon targeted (SCoT) polymorphism reveals genetic diversity of Manilkara in Thailand

2020 ◽  
Vol 21 (2) ◽  
Author(s):  
Ongkarn Vanijajiva
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Genetic Improvement ◽  
Morphological Characters ◽  
Start Codon ◽  
Similarity Coefficients ◽  
Scot Marker ◽  
Marker Analysis ◽  
Dna Profiles ◽  
Relationship Of

Abstract. Vanijajiva O. 2020. Start codon targeted (SCoT) polymorphism reveals genetic diversity of Manilkara in Thailand. Biodiversitas 21: 666-673. Manilkara consists of four species, namely, Manilkara hexandra, M. kauki, M. littoralis, and M. zapota in Thailand. Particularly, M. zapota (sapodilla), commonly known as Lamut in Thailand, is one of commercially notable edible fruits continues to be a highly valued tree and the fruits are a source of food and income. The objective of this research was to determine the diversity and relationship of Manilkara accessions derived from districts in Thailand based on DNA profiles. Genetic diversity and relationship of all accessions were investigated using Start Codon Targeted (SCoT) marker analysis. Of 30 SCoT primers screened, 27 SCoT primers were identified to be polymorphism. A total of 176 DNA bands with size varied from 120 bp to 1200 bp were amplified, and 101 (57.38%) of them were polymorphic. Based on similarity coefficients, total of 36 accessions were clustered into two groups. The cluster of polymorphism generated by SCoT was associated with their locality and morphological characters. Therefore, the present data provide high-valued information for the management of germplasm, genetic improvement, and conservation of the genetic resources of Manilkara accessions.

scholarly journals SCoT Markers Analysis of Genetic Diversity of Polygonatum, A Medicinal and Edible Plant

2021 ◽  
Author(s):  
Shi dong Cao ◽  
Senmiao Chen ◽  
Shuyu Cao ◽  
Nipi Chen ◽  
Bo Jin
Keyword(s):  
Genetic Diversity ◽  
Start Codon ◽  
Group Method ◽  
Germplasm Resources ◽  
Edible Plant ◽  
High Genetic Diversity ◽  
Pair Group ◽  
Scot Marker ◽  
Anti Cancer ◽  
Valuable Marker

Abstract Background: As a traditional Chinese medicine, Polygonatum has been demonstrated to have immunomodulatory, antibacterial, anti-inflammatory, anti-aging, anti-cancer, hypoglycemic and other pharmacological effects. However, the germplasm resources of Polygonatum have been destroyed in recent years and the research on its genetic diversity is extremely scarce. In this study, the genetic diversity of 28 Polygonatum germplasms from 11 different provinces in China was evaluated by Start codon targeted (SCoT) marker. Results: A total of 365 bands were generated by 15 SCoT primers, of which 355 were polymorphic, with a high polymorphism of 97.3%. And the genetic similarity coefficient is between 0.59 and 0.75, indicating a high genetic diversity. UPGMA (Unweighted Pair Group Method with Arithmetic Mean) dendrogram, PCoA (Principal Coordinate Analysis) and Structure analysis have similar results in grouping Polygonatum germplasm and they are all divided into two populations. We found that there was a certain correlation between the genetic distance and geographical distance of Polygonatum germplasm. By analyzing other valid genetic diversity parameters (Na, Ne, H, I), it is clarified that Polygonatum has abundant alleles and abundant genetic diversity among populations. Conclusions: This study suggests that Polygonatum germplasm resources from different provenances have rich genetic diversity. The SCoT molecular marker is a valuable marker system and can be used for genetic analysis of Polygonatum resources. This will be helpful to further study the preservation and genetic improvement of Polygonatum germplasm.

Genetic diversity analysis of Iranian Nigella sativa L. landraces using SCoT markers and evaluation of adjusted polymorphism information content

2015 ◽  
Vol 15 (1) ◽  
pp. 64-71 ◽  
Author(s):  
Khaled Mirzaei ◽  
Ghader Mirzaghaderi
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphism Information Content ◽  
Nigella Sativa ◽  
Genetic Relationships ◽  
Start Codon ◽  
Discrimination Power ◽  
Black Cumin ◽  
Scot Marker ◽  
Mediterranean Regions

The genetic diversity of 39 Iranian black cumin (Nigella sativa L.) landraces was analysed using 14 polymorphic Start Codon Targeted (SCoT) markers. A total of 106 bands ranging from 3 (for SCoT70) to 13 (for SCoT23) were observed. Of them, 33 (31%) bands were polymorphic with a mean of 1.65 bands per primer. Polymorphism information content (PIC) per primer ranged from 0.035 (for SCoT12) to 0.133 (for SCoT70), with an average of 0.078. Besides PIC, Simpson's diversity (D) index was also calculated for each SCoT marker as an indication of discrimination power across population. The D index was used to adjust the PIC of the SCoT markers. As the adjusted PIC (PICD= PIC × D) was calculated based on both the PIC and the rate of band dispersion, this reflected the informativeness of a dominant marker more precisely than PIC. Genetic relationships were estimated using Jaccard's similarity coefficient-generated values between different pairs of genotypes that varied from 80 to 97% with an average of 88%. These coefficients were applied to construct a dendrogram using the UPGMA algorithm. A high genetic similarity was observed that might be due to the fact that N. sativa is a self-pollinated plant not originated from Iran and might have been imported from the Mediterranean regions.

scholarly journals Genetic diversity in NaN3-induced common bean mutants and commercial varieties detected by AFLP

2011 ◽  
Vol 11 (4) ◽  
pp. 365-369 ◽  
Author(s):  
CL Chen ◽  
HH Wang ◽  
TL Jeng ◽  
SJ Chuang ◽  
ML Wei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Similarity Coefficients ◽  
Phaseolus Vulgaris L ◽  
Jaccard Similarity ◽  
Aflp Data ◽  
High Genetic Diversity ◽  
Induced Mutants ◽  
Sources Of Variation ◽  
Induced Mutagenesis

The analysis of Amplified Fragment Length Polymorphism (AFLP) was used to estimate genetic diversity in common bean (Phaseolus vulgaris L.) variety Hwachia and in 34 NaN3-induced mutants and 11 commercial varieties introduced from China. Eight primer combinations generated 516 DNA fragments of the tested mutants and introduced varieties, of which 448 fragments were polymorphic. The calculated Jaccard similarity coefficients based on AFLP data ranged from 0.47 to 0.84. The molecular profiles obtained from eight AFLP primer pairs indicated a high genetic diversity among Hwachia, NaN3-induced mutants and introduced varieties. The extent of genetic variation was slightly higher between Hwachia and NaN3-induced mutants than between Hwachia and introduced commercial varieties. These results, supported by cluster analysis, suggest that NaN3-induced mutagenesis effectively broadens the genetic diversity of common bean varieties. Some of the produced mutants could be useful as sources of variation to develop new improved common bean varieties.

scholarly journals Gene-Targeted markers to assess genetic diversity and population structure within Tunisian Phoenix dactylifera L. cultivars

2020 ◽  
Vol 69 (1) ◽  
pp. 29-35
Author(s):  
Rhouma-Chatti Soumaya ◽  
Choulak Sarra ◽  
Moussa Maha ◽  
Chatti Khaled ◽  
Chatti Noureddine
Keyword(s):  
Genetic Diversity ◽  
Date Palm ◽  
Gene Diversity ◽  
Phoenix Dactylifera ◽  
Start Codon ◽  
Marker System ◽  
Average Value ◽  
Information Index ◽  
Scot Marker ◽  
Phoenix Dactylifera L

AbstractGenetic variability in date palm genotypes collected from different regions of southern Tunisia was analyzed using a Start Codon Targeted (SCoT) marker system. Thirty-one accessions collected from three locations were investigated. One hundred and nine amplicons were produced among which 84 % were polymorphic. The PIC value and the Rp values testified of the efficiency of used primers. The percentage of polymorphic loci (Pp) varied from 44.57 to 83.70 %, Nei‘s gene diversity (H) from 0.175 to 0.273 with a mean of 0.228, and Shannon‘s information index (I) values ranging from 0.257 to 0.409 with an average value of 0.338 were illustrated. The Tunisian date palm populations exhibited high genetic differentiation (GST = 0.319) and gene flow (Nm = 1.063). The AMOVA analysis presented 70 % of the variation within the population and 30 % of the variation between them. Phylogenetic analysis and the Bayesian clustering approach also revealed high genetic variation among genetic variants with a net divergence of the wild insular population of Kerkennah from other cultivars. The present investigation suggests the effectiveness of the SCoT marker system to estimate the genetic diversity of Phoenix dactylifera genotypes.

Analysis of genetic diversity in Elytrigia repens germplasm using intersimple sequence repeat (ISSR) markers

Botany ◽  
2012 ◽  
Vol 90 (3) ◽  
pp. 167-174
Author(s):  
Lin Meng ◽  
Xiaoyan Zhang ◽  
Peichun Mao ◽  
Xiaoxia Tian
Keyword(s):  
Genetic Diversity ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Similarity Coefficients ◽  
High Genetic Diversity ◽  
Pair Group ◽  
Elytrigia Repens ◽  
Polymorphic Bands ◽  
Mantel’S Test

The genetic diversity among 30 accessions of Elytrigia repens (L.) Nevski was analyzed using 100 intersimple sequence repeat (ISSR) primers, 12 of which generated distinct amplification products. Out of the 132 repeatable bands detected, 100 bands were polymorphic. The percentage of polymorphic bands was 70.66%, with a mean of 8.33 percentage of polymorphic bands per primer. The ISSR-based genetic similarity coefficients among the 30 accessions ranged from 0.509 to 0.873, revealing high genetic diversity. The 30 E. repens accessions were divided into eight groups based on an unweighted pair-group method with arithmetic mean cluster analysis and a principal components analysis. We found that genetic distance is correlated with geographical distance among the 30 E. repens accessions studied (r = 0.812, p < 0.05) using Mantel’s test. Our results confirm the potential value of genetic diversity preservation for future breeding programs.

Analysis of Diversity And Identification of SSR, SCoT, And ITAP Informative Amplicons For Grain Fe And Zn Content In Wheat Genotypes

2021 ◽  
Author(s):  
Hedieh Badakhshan ◽  
Rozhin Nosratifar
Keyword(s):  
Genetic Diversity ◽  
Start Codon ◽  
High Genetic Diversity ◽  
Wheat Genotypes ◽  
Zn Content ◽  
Content Identification ◽  
High Heritability ◽  
Genotype Interaction ◽  
Simple Sequence ◽  
Selection Of

Abstract Biofortification provides a promising method of solving microelement malnutrition in developing countries. For this purpose, a study was conducted to understand the grain Fe and Zn content variation in seventy prevalent Iranian wheat genotypes across three consecutive years, to assess genetic diversity, and to identify informative amplicons for high grain Fe and Zn content using three simple sequence repeat (SSR), start codon targeted (SCoT) polymorphism, and intron targeted amplified polymorphism (ITAP) markers. Grain Fe and Zn content was highly variable each year with high heritability. Despite the highly significant effect of year-genotype interaction, some stable genotypes were ranked highly all the three years for grain Fe and Zn content. The grain Fe and Zn contents were positively correlated in the second and third years. High genetic diversity was detected among the wheat genotypes using three different marker systems. A number of informative SSR, SCoT, and ITAP amplicons for high grain Fe and Zn were identified overall or in individual years. A few informative amplicons were common and stable for grain Fe and Zn content in the different years. The SSR alleles located on 3A, 4A, 4B, and 6B chromosomes were positively correlated with high Fe and Zn content, indicating that co-location of genes affected Fe and Zn content. Identification of informative alleles and amplicons for high grain Fe and Zn content could contribute to the development of sequence-based markers and improve the selection of genotypes with high micronutrient content.

Analysis of genetic diversity and relationships among genus Lycoris based on start codon targeted (SCoT) marker

2014 ◽  
Vol 57 ◽  
pp. 221-226 ◽  
Author(s):  
Yan-hui Gao ◽  
Yu-Qiu Zhu ◽  
Zai-kang Tong ◽  
Zhen-yuan Xu ◽  
Xiao-feng Jiang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Start Codon ◽  
Scot Marker

scholarly journals Phylogenetic Diversity of Marine Cyanophage Isolates and Natural Virus Communities as Revealed by Sequences of Viral Capsid Assembly Protein Gene g20

2002 ◽  
Vol 68 (4) ◽  
pp. 1576-1584 ◽  
Author(s):  
Yan Zhong ◽  
Feng Chen ◽  
Steven W. Wilhelm ◽  
Leo Poorvin ◽  
Robert E. Hodson
Keyword(s):  
Genetic Diversity ◽  
Geographic Distance ◽  
Open Ocean ◽  
Viral Capsid ◽  
Capsid Assembly ◽  
Sequencing Analysis ◽  
Phylogenetic Groups ◽  
High Genetic Diversity ◽  
Natural Virus ◽  
Capsid Assembly Protein

ABSTRACT In order to characterize the genetic diversity and phylogenetic affiliations of marine cyanophage isolates and natural cyanophage assemblages, oligonucleotide primers CPS1 and CPS8 were designed to specifically amplify ca. 592-bp fragments of the gene for viral capsid assembly protein g20. Phylogenetic analysis of isolated cyanophages revealed that the marine cyanophages were highly diverse yet more closely related to each other than to enteric coliphage T4. Genetically related marine cyanophage isolates were widely distributed without significant geographic segregation (i.e., no correlation between genetic variation and geographic distance). Cloning and sequencing analysis of six natural virus concentrates from estuarine and oligotrophic offshore environments revealed nine phylogenetic groups in a total of 114 different g20 homologs, with up to six clusters and 29 genotypes encountered in a single sample. The composition and structure of natural cyanophage communities in the estuary and open-ocean samples were different from each other, with unique phylogenetic clusters found for each environment. Changes in clonal diversity were also observed from the surface waters to the deep chlorophyll maximum layer in the open ocean. Only three clusters contained known cyanophage isolates, while the identities of the other six clusters remain unknown. Whether or not these unidentified groups are composed of bacteriophages that infect different Synechococcus groups or other closely related cyanobacteria remains to be determined. The high genetic diversity of marine cyanophage assemblages revealed by the g20 sequences suggests that marine viruses can potentially play important roles in regulating microbial genetic diversity.

Sign in / Sign up

Export Citation Format

Share Document