Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity

Gupta, Vibha; Jatav, Pradeep Kumar; Haq, Shamshad Ul; Verma, Kumar Sambhav; Kaul, Varsha Khurana; Kothari, S. L.; Kachhwaha, Sumita

doi:10.1007/s12041-019-1095-0

Cited by 27 publications

(18 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This may be due to SCoT detects polymorphisms in coding sequences, because the primers were designed to amplify from the short conserved region surrounding the ATG translation start codon (Collard and Mackill 2009;Gorji et al 2011). Therefore, amplification products generated from the SCoT marker technique may be associated with functional genes and their corresponding traits (Xiong et al 2009;Gajera et al 2014;Agarwal et al 2019;Gupta et al 2019). Future studies on this plant should include reciprocal transplants of Thai individuals, as well as common gardens of plants grown from seed.…”

Section: Resultsmentioning

confidence: 99%

“…It has several advantages over RAPD, ISSR, and AFLP, as it is more consistent, produce more reproducible and reliable bands and can be used effectively for population studies, genetic mapping in different plants and in the marker-assisted selection programs (Gorji et al 2011;Xiong et al 2011;Alikhani et al 2014;Gajera et al 2014;Yue et al 2019). Similar to RAPD and ISSR markers, SCoT are important markers that could be used for different genetic application such as, to assess genetic diversity and structure, in bulk segregation analyses, quantitative trait loci (QTL) mapping and DNA fingerprinting (Luo et al 2012;Gao et al 2014;Emami et al 2018;Gupta et al 2019). These markers are directly involved in relation to gene function and can be utilized in genotyping and to explore polymorphism.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Vanijajiva

2020

Biodiversitas

View full text Add to dashboard Cite

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.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Vanijajiva

2020

Biodiversitas

View full text Add to dashboard Cite

show abstract

“…We used SCoT primers in our study for hybrid conformity tests as they are correlated with functional genes and corresponding traits (Mulpuri, Muddanuru, & Francis, 2013). Moreover, SCoT markers are highly reproducible due to the use of longer primers and are potent source for reproducible results (Gupta et al, 2019). F 1 progeny was confirmed for hybridity through phenotyping and genotyping.…”

Section: Discussionmentioning

confidence: 99%

Overcoming interspecific barriers in Sorghum and molecular characterization of the derivatives

Kurella

2020

Plant Breeding

View full text Add to dashboard Cite

Crop improvement in sorghum has progressed extensively availing the variation available in the primary gene pool of S. bicolor. Crossing further, the yield plateau can be accomplished by bringing in the genes from tertiary gene pool into the cultivated gene pool. Earlier efforts for wide hybridization in sorghum with tertiary gene pool were not successful due to inhibition of wild pollen germination on the stigma of cultivated species. In the current study, elite lines of cultivated Sorghum species were pollinated with wild species using different floral treatments. The results showed that spray with the synthetic auxin, 2,4‐dichlorophenoxyacetic acid, has promoted the seed set. Overall, 76% crosses showed seed set, but many seeds were underdeveloped and deformed. F1 progeny showed traits of both cultivated and wild parents. Hybrids were confirmed through PCR analysis. Many (80%) F1 plants were sterile, and 20% of F1s were advanced to F2 generation. Wide variation was observed in F2 progeny, and the phenotype selections were made and are being evaluated in the field.

show abstract

“…Marker as SCoT has many advantages over the other commonly used molecular markers for instance AFLP, RAPD and ISSR, as it has been shown to have more reproducibility, stability, as well as producing dependable bands. In addition, it's easy to design, highly polymorphic, and provides ample genetic information of the plant (Satya et al, 2015;Gupta et al, 2019). Such advantages are validated in the latest researches made for the mango genetic diversity, (Zhou et al, 2020), Manilkara (Vanijajiva, 2020), Vitis vinifera (Yue et al, 2019), kiwifruit (Chen et al, 2018).…”

Section: Introduction Introduction Introduction Introductionmentioning

confidence: 94%

Physiological variation of irradiated red radish plants and their phylogenic relationship using SCoT and CDDP markers

Aly

Eliwa

Borik

et al. 2021

Not Bot Horti Agrobo

View full text Add to dashboard Cite

Greenhouse experiment is carried out to explore the outcome of γ-radiation on physiological and genetic variation in red radish (Raphanus sativus) for two generations. Gamma rays from 60Co were used to penetrate red radish seeds with different dose levels (0.0, 10, 20, 40 and 80 Gy). Plants generated from irradiated seeds and from self-pollination of these plants, called M1 and M2 generations, respectively. Some morphological and physiological traits were then determined, and the genetic diversity of both generations was studied using Start Codon Targeted (SCoT) and Conserved DNA-Derived Polymorphism (CDDP) molecular markers. All studied morphological traits (number of leaves/plants, leave height, root diameter, and root weight) were steadily improved by raising irradiation dose rate, reaching a cumulative raise at the irradiation doe level 40 Gy and decreased at dose level 80 Gy. Photosynthetic pigments of red radish plants released a notable increase by increasing gamma rays dose level for chlorophyll (a), chlorophyll (b) and carotenoids for 40 Gy dose rate. Proline content was elevated proportionally to the irradiation dose level, with the greatest increase seen at dose level of 80 Gy. Moreover, phytochemical screening was detected for the both two generations. Fourteen SCoT primers generated a total number of banding patterns of 194 with average 13.86 and the primer SCoT-33 released the highest number banding patterns (21). The percentage mean of polymorphism for all the SCoT primers was 74.66% and was 66.49 and 63.74% for M1 and M2 respectively. Furthermore, fifteen CDDP primers generated a total number of banding patterns of 186 and the primer CDDP-5 relieved the highest number of banding patterns (20). The percentage mean of polymorphism for all the CDDP primers was 73.41% and was 64.38 and 65.91% for M1 and M2 respectively. It could be concluded that gamma irradiation exhibited an appropriate variation in red radish M1 and M2 which was detected by SCoT and CDDP molecular markers.

show abstract

Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity

Cited by 27 publications

References 60 publications

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

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

Overcoming interspecific barriers in Sorghum and molecular characterization of the derivatives

Physiological variation of irradiated red radish plants and their phylogenic relationship using SCoT and CDDP markers

Contact Info

Product

Resources

About