Potential of Start Codon Targeted (SCoT) Markers to Estimate Genetic Diversity and Relationships among Chinese  Elymus sibiricus Accessions

Zhang, Junchao; Xie, Wengang; Wang, Yanrong; Zhao, Xuhong

doi:10.3390/molecules20045987

Cited by 64 publications

(37 citation statements)

References 35 publications

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“…Evaluation of SCoT markers has Fig. 4 The dendrogram of the six examined soybean cultivars as constructed using protein patterns unweighted pair-group arithmetic (UPGMA) and similarity matrices computed according to Jaccardʼ coefficient already been established in Elymus sibiricus and Vigna unguiculata (Zhang et al, 2015;Igwe et al, 2017), respectively. In the present study, there is no linkage between GC content of primer and the clarification of the banding profile was reported which is in harmony with Marilla and Scoles (1996).…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic relationships of some Egyptian soybean cultivars (Glycine max L.) using SCoT marker and protein pattern

Rayan

Osman

2019

Bull Natl Res Cent

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Background: Electrophoretic SDS-PAGE and SCoT-PCR techniques were used to study the fingerprints and genetic diversity of six Egyptian soybean (Glycine max L.) genotypes (Giza111, Giza21, Giza82, Giza35, Giza22, and Giza83). Results: SDS-PAGE revealed a total of 23 bands with a polymorphism 30.43%. The maximum number of bands (22) was recorded in Giza111 and Giza82, while the minimum number of bands (18) was recorded in Giza35. The highest similarity index for SDS-PAGE (0.909) was observed between Giza111 and Giza82, while the lowest similarity index (0.714) was recorded between Giza35 and Giza83. SCoT technique was performed by using 11 primers to generate reproducible polymorphic products. The total number of bands was 106, from them 52 polymorphic and 54 monomorphic bands with a polymorphism 49.11%. The dendrogram of both SDS-PAGE and SCoT markers revealed two main clusters; the first cluster includes the cultivars Giza111and Giza21, while the second cluster includes the cultivars Giza82, Giza35, Giza22, and Giza83. The second group was further subdivided into two subgroups; the first subgroup includes cultivars (Giza82 and Giza35) while the second subgroup includes cultivars Giza22 and Giza83. Conclusion: The markers used in this study created a number of polymorphic bands among the different cultivars that can be utilized as molecular markers for their differentiation. The obtained data indicated that SCoT and SDS-PAGE techniques could be used efficiently for identification and differentiation of the selected genotypes.

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Section: Discussionmentioning

confidence: 99%

Phylogenetic relationships of some Egyptian soybean cultivars (Glycine max L.) using SCoT marker and protein pattern

Rayan

Osman

2019

Bull Natl Res Cent

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“…These results indicate that the EST-SSR markers developed in this study had a higher level of polymorphism compared with the genomic SSR markers reported by Lei et al 4 . Furthermore, a series of achievements on the genetic diversity of wild E. sibiricus germplasm and populations were reported 3 19 53 54 , and these showed a clear demarcation between accessions from different regions. However, the dendrogram of 15 E .…”

Section: Discussionmentioning

confidence: 99%

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing

Zhou

Luo

et al. 2016

Sci Rep

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Siberian wildrye (Elymus sibiricus L.) is a perennial, self-fertilizing grass that plays an important role in animal husbandry and environmental sustenance. However, the transcriptomic and genomic information on this species is very limited, which hinders genetic and breeding studies. In the present study, 76,686,804 clean reads were generated from 11 different tissue samples of E. sibiricus by Illumina paired-end sequencing, and the reads were deposited into the NCBI SRA database (SRX574376). A total of 8,769 EST-SSRs were identified from 94,458 unigene sequences, which were obtained by de novo assembly. Moreover, 1,078 primer pairs were successfully designed, and 500 pairs were randomly selected to assess polymorphisms in 15 E. sibiricus accessions. A total of 112 primer pairs were polymorphic, and the polymorphism information content (PIC) values ranged from 0.39 to 0.81, indicating a high level of informativeness. Furthermore, these 112 polymorphic primer pairs were used to evaluate the transferability to 13 other related species, and 55 EST-SSR markers were found to be polymorphic among these 13 Elymus species. This study collected the global sequence data for E. sibiricus, and the newly developed markers will prove valuable in facilitating genetic diversity in E. sibiricus and related Elymus species.

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“…In total, 273 polymorphic bands were detected with an average of 11.4 bands per primer. In the study ZHANG et al (2015) used SCoT markers to study the genetic diversity and relationships among 53 Elymus sibiricus accessions. KHAN et al (2016) studied genetic differences to evaluate the level and distribution of diversity among genotypes of Mentha using SCoT markers.…”

Section: Resultsmentioning

confidence: 99%

Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

et al. 2019

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In the present study, 111 castor genotypes were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. The selected primers amplified DNA fragments across the 111 genotypes studied with the number of amplified fragments varying from 3 (SCoT 14) to 10 (SCoT 30 and SCoT 44) and the amplicon size varied from 100 to 3000 bp. Of the 246 amplified bands, 186 were polymorphic with an average of 5.03 fragments per primer. The percentage of polymorphic bands ranged from 57.14 % (SCoT 34) to 100.00 % (SCoT 28 and SCoT 33) with an average of 77.50%. The polymorphic information content (PIC) values varied from 0.372 (SCoT 14) to 0.818 (SCoT 30) with an average of 0.677. A dendrogram was constructed from a genetic distance matrix based on profiles of the 37 SCoT primers using the unweighted pair-group method with the arithmetic average (UPGMA). According to analysis, the collection of 111 diverse accessions of castor was clustered into two main clusters (1 and 2). The first cluster were subdivided into two subclusters (1a and 1b). Subclaster 1a contained 11 genotypes of castor and subclaster 1b contained 6 genotypes of castor. Subclaster 2 were subdivided into two subclusters (2a and 2b). Subclaster 2a contained 44 castor genotypes and subclaster 2b contained 50 castor genotypes. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.

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Potential of Start Codon Targeted (SCoT) Markers to Estimate Genetic Diversity and Relationships among Chinese Elymus sibiricus Accessions

Cited by 64 publications

References 35 publications

Phylogenetic relationships of some Egyptian soybean cultivars (Glycine max L.) using SCoT marker and protein pattern

Phylogenetic relationships of some Egyptian soybean cultivars (Glycine max L.) using SCoT marker and protein pattern

Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing

Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes

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