Assessment of genetic diversity in 29 rose germplasms using SCoT marker

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.

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

Silvae Genetica ◽

10.2478/sg-2020-0005 ◽

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.

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

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210232 ◽

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.

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Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species

Gene ◽

10.1016/j.gene.2013.07.096 ◽

2013 ◽

Vol 529 (1) ◽

pp. 21-26 ◽

Cited By ~ 57

Author(s):

Paromik Bhattacharyya ◽

Suman Kumaria ◽

Shrawan Kumar ◽

Pramod Tandon

Keyword(s):

Genetic Diversity ◽

Start Codon ◽

Orchid Species ◽

Dendrobium Nobile ◽

Scot Marker ◽

Dendrobium Nobile Lindl ◽

Medicinal Orchid

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Assessment of genetic diversity in different geographically isolated Alhagi graecorum Boiss. populations using SCoT marker

Taeckholmia ◽

10.21608/taec.2019.19481.1008 ◽

2019 ◽

Vol 39 (1) ◽

pp. 44-66

Author(s):

ghada Abd El- hak ◽

shafik darwish ◽

Atef halim ◽

Hosam eldin zaki ◽

walaa rayan

Keyword(s):

Genetic Diversity ◽

Scot Marker ◽

Alhagi Graecorum ◽

Geographically Isolated

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Genetic diversity in Indian poppy (P. somniferum L.) germplasm using multivariate and SCoT marker analyses

Industrial Crops and Products ◽

10.1016/j.indcrop.2019.112050 ◽

2020 ◽

Vol 144 ◽

pp. 112050 ◽

Cited By ~ 1

Author(s):

Abhilasha Srivastava ◽

Soni Gupta ◽

Karuna Shanker ◽

Namita Gupta ◽

Anil Kumar Gupta ◽

...

Keyword(s):

Genetic Diversity ◽

Scot Marker

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

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2014.08.002 ◽

2014 ◽

Vol 57 ◽

pp. 221-226 ◽

Cited By ~ 16

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

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

10.21203/rs.3.rs-652340/v1 ◽

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.

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

International Journal of Agriculture and Biology ◽

10.17957/ijab/15.1639 ◽

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

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Genetic Analysis of Diversity within a Chinese Local Sugarcane Germplasm Based on Start Codon Targeted Polymorphism

BioMed Research International ◽

10.1155/2014/468375 ◽

2014 ◽

Vol 2014 ◽

pp. 1-10 ◽

Cited By ~ 17

Author(s):

Youxiong Que ◽

Yongbao Pan ◽

Yunhai Lu ◽

Cui Yang ◽

Yuting Yang ◽

...

Keyword(s):

Genetic Diversity ◽

Polymorphic Information Content ◽

Germplasm Collection ◽

Principal Component ◽

Breeding Value ◽

Start Codon ◽

Group Method ◽

Depth Information ◽

Scot Marker ◽

Sugarcane Germplasm

In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information content (PIC) values ranged from 0.783 to 0.907 with a mean of 0.861. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the 107 sugarcane accessions into six clusters at 0.674 genetic similarity coefficient level. Relatively abundant genetic diversity was observed among ROC22, ROC16, and ROC10, which occupied about 80% of the total sugarcane acreage in China, indicating their potential breeding value on Mainland China. Principal component analysis (PCA) partitioned the 107 sugarcane accessions into two major groups, the Domestic Group and the Foreign Introduction Group. Each group was further divided based on institutions, where the sugarcane accessions were originally developed. The knowledge of genetic diversity among the local sugarcane germplasm provided foundation data for managing sugarcane germplasm, including construction of a core collection and regional variety distribution and subrogation.

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