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Noppradit B, Klinnawee L, Leeratiwong C, Praparatana R, Puttarak P. Centella asiatica (L.) Urb. and Hydrocotyle umbellata L. identification and quality assessment: A methodology comparison. PHYTOCHEMICAL ANALYSIS : PCA 2024; 35:1383-1398. [PMID: 38747201 DOI: 10.1002/pca.3371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 08/03/2024]
Abstract
INTRODUCTION Centella is an important genus in the Apiaceae family. It includes Centella asiatica, which has significant edible and medicinal values. However, this species is easily confused due to its similar morphological traits to Hydrocotyle umbellata, hindering its utilization in the consumer and pharmacological industries. OBJECTIVE The study aims to differentiate these two closely related plant species using reliable methods of confirming the authenticity of natural herbal medicines. METHODS Our work mainly focuses on the basic morphological characteristics, chemical markers, genetic fingerprints, and their biological responses. RESULTS The plants can be clearly differentiated using their leaf shapes, stipules, petioles, inflorescences, and fruit structures. Although the phytochemical compositions of the C. asiatica extract were similar to that of H. umbellata which included flavonoids, tannins, and saponins important to the plant's ability to reduce inflammation and promote healing of wounds, the H. umbellata extract showed significantly higher toxicity than that of C. asiatica. High-performance liquid chromatography analysis was used to identify chemical fingerprints. The result revealed that C. asiatica had major triterpene glycoside constituents including asiaticoside, asiatic acid, madecassoside, and madecassic acid, which have a wide range of medicinal values. In contrast, triterpenoid saponins were not identified in H. umbellata. Furthermore, using SCoT1-6 primers was possible to effectively and sufficiently created a dendrogram which successfully identified the closeness of the plants and confirmed the differences between the two plant species. CONCLUSION Therefore, differentiation can be achieved through the combination of morphometrics, molecular bioactivity, and chemical analysis.
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Affiliation(s)
- Benjaporn Noppradit
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Lompong Klinnawee
- Department of Biology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Plant Cell and Physiology for Sustainable Agriculture Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Charan Leeratiwong
- Department of Biology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | | | - Panupong Puttarak
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Songkhla, Thailand
- Phytomedicine and Pharmaceutical Biotechnology Excellence Center, Prince of Songkla University, Songkhla, Thailand
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Abdelhameed AA, Ali M, Darwish DBE, AlShaqhaa MA, Selim DAFH, Nagah A, Zayed M. Induced genetic diversity through mutagenesis in wheat gene pool and significant use of SCoT markers to underpin key agronomic traits. BMC PLANT BIOLOGY 2024; 24:673. [PMID: 39004709 PMCID: PMC11247860 DOI: 10.1186/s12870-024-05345-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 06/26/2024] [Indexed: 07/16/2024]
Abstract
BACKGROUND This research explores the efficacy of mutagenesis, specifically using sodium azide (SA) and hydrazine hydrate (HZ) treatments, to introduce genetic diversity and enhance traits in three wheat (Triticum aestivum L.) genotypes. The experiment entails subjecting the seeds to different doses of SA and HZ and cultivating them in the field for two consecutive generations: M1 (first generation) and M2 (second generation). We then employed selective breeding techniques with Start Codon Targeted (SCoT) markers to select traits within the wheat gene pool. Also, the correlation between SCoT markers and specific agronomic traits provides insights into the genetic mechanisms underlying mutagenesis-induced changes in wheat. RESULTS In the study, eleven genotypes were derived from parent varieties Sids1, Sids12, and Giza 168, and eight mutant genotypes were selected from the M1 generation and further cultivated to establish the M2 generation. The results revealed that various morphological and agronomical characteristics, such as plant height, spikes per plant, spike length, spikelet per spike, grains per spikelet, and 100-grain weight, showed increases in different genotypes from M1 to M2. SCoT markers were employed to assess genetic diversity among the eleven genotypes. The bioinformatics analysis identified a correlation between SCoT markers and the transcription factors ABSCISIC ACID INSENSITIVE3 (ABI3) and VIVIPAROUS1 (VP1), crucial for plant development, growth, and stress adaptation. A comprehensive examination of genetic distance and the function identification of gene-associated SCoT markers may provide valuable insights into the mechanisms by which SA and HZ act as mutagens, enhancing wheat agronomic qualities. CONCLUSIONS This study demonstrates the effective use of SA and HZ treatments to induce gene diversity through mutagenesis in the wheat gene pool, resulting in the enhancement of agronomic traits, as revealed by SCoT markers. The significant improvements in morphological and agronomical characteristics highlight the potential of mutagenesis techniques for crop improvement. These findings offer valuable information for breeders to develop effective breeding programs to enhance wheat quality and resilience through increased genetic diversity.
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Affiliation(s)
- Ahmed Ali Abdelhameed
- Agricultural Botany Department (Genetics), Faculty of Agriculture, Al-Azhar University, Assuit Branch, Assuit, 71524, Egypt
| | - Mohammed Ali
- Maryout Research Station, Genetic Resources Department, Desert Research Center, 1 Mathaf El-Matarya St., El-Matareya, Cairo, 11753, Egypt
| | | | | | - Dalia Abdel-Fattah H Selim
- Department of Agricultural Botany, Faculty of Agricultural, Menoufia University, Shebin El-Kom, 32511, Egypt
| | - Aziza Nagah
- Botany and Microbiology Department, Faculty of Science, Benha University, Benha, 13518, Egypt
| | - Muhammad Zayed
- Department of Botany and Microbiology, Faculty of Science, Menoufia University, Shebin El-Kom, 32511, Egypt.
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Liang Q, Pan H, He X, Wang S, Hou Y, Xiao H, Xu G, Yi R, Lin D, Yang Z. Population structure and genetic diversity of mango ( Mangifera indica L.) germplasm resources as revealed by single-nucleotide polymorphism markers. FRONTIERS IN PLANT SCIENCE 2024; 15:1328126. [PMID: 39022611 PMCID: PMC11251951 DOI: 10.3389/fpls.2024.1328126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
Introduction Mango is a vital horticultural fruit crop, and breeding is an essential strategy to enhance ongoing sustainability. Knowledge regarding population structure and genetic diversity in mango germplasm is essential for crop improvement. Methods A set of 284 mango accessions from different regions of the world were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction to generate genomic single-nucleotide polymorphism (SNP). Results After filtering, raw data containing 539.61 M reads were obtained. A total of 505,300 SLAFs were detected, of which, 205,299 were polymorphic. Finally, 29,136 SNPs were employed to dissect the population structure, genetic relationships, and genetic diversity. The 284 mango accessions were divided into two major groups: one group consisted mainly of mango accessions from Australia, the United States, Cuba, India, Caribbean, Israel, Pakistan, Guinea, Burma, China, and Sri Lanka, which belonged to the Indian type (P1); the other group contained mango accessions from the Philippines, Thailand, Indonesia, Vietnam, Cambodia, Malaysia, and Singapore, which belonged to Southeast Asian type (P2). Genetic diversity, principal component analysis (PCA), and population structure analyses revealed distinct accession clusters. Current results indicated that the proposed hybridization occurred widely between P1 and P2. Discussion Most of the accessions (80.99%) were of mixed ancestry, perhaps including multiple hybridization events and regional selection, which merits further investigation.
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Affiliation(s)
- Qingzhi Liang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Hongbing Pan
- Fruits Research Institute, Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Xiaolong He
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Songbiao Wang
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Yuanhua Hou
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- College of Tropical Crops, Yunnan Agricultural University, Puer, China
| | - Hua Xiao
- College of Electronic and Information Engineering, Guangdong Ocean University, Zhanjiang, China
| | - Guangzhao Xu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Runhua Yi
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Dongbo Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Zhuanying Yang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
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Aly AA, Safwat G, Eliwa NE, Eltawil AHM, Abd El-Aziz MH. Changes in morphological traits, anatomical and molecular alterations caused by gamma-rays and zinc oxide nanoparticles in spinach (Spinacia oleracea L.) plant. Biometals 2023; 36:1059-1079. [PMID: 37173538 PMCID: PMC10545649 DOI: 10.1007/s10534-023-00505-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Spinach seeds were irradiated with gamma-rays after that soaked in zinc oxide nanoparticles (ZnO-NPs) at 0.0, 50, 100 and 200 ppm for twenty-four hours at room temperature. Vegetative plant growth, photosynthetic pigments, and proline contents were investigated. Also, anatomical studies and the polymorphism by the SCoT technique were conducted. The present results revealed that the germination percentage was at the maximum values for the treatment of 100 ppm ZnO-NPs (92%), followed by 100 ppm ZnO-NPs + 60 Gy (90%). The application of ZnO-NPs resulted in an enhancement in the plant length. The maximum of chlorophylls and carotenoids content was recorded in the treatment, 100 ppm ZnO-NPs + 60 Gy. Meanwhile, the irradiation dose level (60 Gy) with all ZnO-NPs treatments increased proline content and reached its maximum increase to 1.069 mg/g FW for the treatment 60 Gy combined with 200 ppm ZnO-NPs. Also, the anatomical studies declared that there were variations between the treatments; un-irradiated and irradiated combined with ZnO-NPs plants which reveal that the leave epidermal tissue increased with 200 ppm ZnO-NPs in both the upper and lower epidermis. While irradiated plants with 60 Gy combined with 100 ppm ZnO-NPs gave more thickness of upper epidermis. As well as SCoT molecular marker technique effectively induced molecular alterations between the treatments. Where, SCoT primers targeted many new and missing amplicons that are expected to be associated with the lowly and highly expressed genes with 18.2 and 81.8%, respectively. Also, showed that the soaking in ZnO-NPs was helped for reducing molecular alteration rate, both spontaneous and induced by gamma irradiation. This nominates ZnO-NPs as potential nano-protective agents that can reduce irradiation-induced genetic damage.
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Affiliation(s)
- Amina A Aly
- Natural Products Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt.
| | - Gehan Safwat
- Faculty of Biotechnology, October University for Modern Science and Arts (MSA), Giza, Egypt
| | - Noha E Eliwa
- Natural Products Department, National Center for Radiation Research and Technology, Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Ahmed H M Eltawil
- Faculty of Biotechnology, October University for Modern Science and Arts (MSA), Giza, Egypt
| | - M H Abd El-Aziz
- Genetic Department Faculty of Agriculture, Mansoura University, Mansoura, Egypt
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Palacıoğlu G, Alkan M, Derviş S, Bayraktar H, Özer G. Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism. Mol Biol Rep 2023; 50:8271-8279. [PMID: 37578578 DOI: 10.1007/s11033-023-08735-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi. MATERIALS AND METHODS This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers. RESULTS The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei's diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers. CONCLUSIONS SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.
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Affiliation(s)
- Gülsüm Palacıoğlu
- Department of Plant Protection, Faculty of Agriculture, Şırnak University, Şırnak, Turkey
| | - Mehtap Alkan
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Sibel Derviş
- Department of Plant and Animal Production, Vocational School of Kızıltepe, Mardin Artuklu University, Mardin, Turkey
| | - Harun Bayraktar
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey.
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
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Hromadová Z, Gálová Z, Mikolášová L, Balážová Ž, Vivodík M, Chňapek M. Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean. PLANTS (BASEL, SWITZERLAND) 2023; 12:2763. [PMID: 37570917 PMCID: PMC10420954 DOI: 10.3390/plants12152763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023]
Abstract
Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes.
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Affiliation(s)
| | | | | | | | | | - Milan Chňapek
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (Z.H.); (Z.G.); (L.M.); (Ž.B.); (M.V.)
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Infraspecific genetic diversity and seed fatty acid composition in Sesamum indicum L. populations (Pedaliaceae) in Iran. BIOCHEM SYST ECOL 2023. [DOI: 10.1016/j.bse.2023.104618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Rahimi M, Ranjbaran E. Investigating the geographical, phenotypic and genetic diversity of Sickleweed populations by bioclimatic parameters, morphological traits and SCoT molecular markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:421-433. [PMID: 37033768 PMCID: PMC10073401 DOI: 10.1007/s12298-023-01296-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/20/2023] [Accepted: 03/11/2023] [Indexed: 06/19/2023]
Abstract
Sickleweed (Falcaria vulgaris) is important due to its nutritional value and medicinal effects on the human body. The 15 different Sickleweed populations were collected based on an unbalanced nest design with 10 replications and nine morphological traits were measured on them. The diversity was investigated with 15 primers of SCoT marker. The genetic diversity was investigated by ANOVA, cluster analysis and Bayesian statistical model based on morphological traits, bioclimatic and SCoT. Grouping the study areas based on bioclimatic parameters by UPGMA method showed that these areas were divided into two groups and were similar in terms of climatic similarities and bioclimatic information. The results of analysis of variance showed that there was a significant difference between populations at the level of one percent for the studied traits. The cluster analysis based traits by the UPGMA method divided these populations into two groups. The phenotypic diversity of these populations was largely consistent with the geographical diversity. The primers used for SCoT marker produced 137 polymorphic bands on the populations, The UPGMA cluster analysis with molecular data placed the studied populations into three groups and four subgroups. Grouping based on the Bayesian method placed the populations into nine groups, although the populations were not differentiated and were a mixture of all nine groups. High genetic diversity for the studied Sickleweed populations have showed valuable insights into the evolution of this plant and provides basic data for designing appropriate management practices for breeding Sickleweed populations.
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Affiliation(s)
- Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Elaheh Ranjbaran
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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Rai MK. Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. PLANTA 2023; 257:34. [PMID: 36622439 DOI: 10.1007/s00425-023-04067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.
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Affiliation(s)
- Manoj K Rai
- Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, MP, 484887, India.
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Explore the genetic diversity of the genus Pleione based on ITS and SCoT marker. BIOCHEM SYST ECOL 2022. [DOI: 10.1016/j.bse.2022.104450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Al-Khayri JM, Mahdy EMB, Taha HSA, Eldomiaty AS, Abd-Elfattah MA, Abdel Latef AAH, Rezk AA, Shehata WF, Almaghasla MI, Shalaby TA, Sattar MN, Ghazzawy HS, Awad MF, Alali KM, Jain SM, Hassanin AA. Genetic and Morphological Diversity Assessment of Five Kalanchoe Genotypes by SCoT, ISSR and RAPD-PCR Markers. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11131722. [PMID: 35807674 PMCID: PMC9268761 DOI: 10.3390/plants11131722] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 05/14/2023]
Abstract
Determining the appropriate parents for breeding programs is the most important decision that plant breeders must make to maximize the genetic variability and produce excellent recombinant genotypes. Several methods are used to identify genotypes with desirable phenotypic features for breeding experiments. In this study, five kalanchoe genotypes were morphologically characterized by assessing plant height, number of inflorescences, number of flowers, flower length, flower diameter and number of petals. The analysis showed the distinction of yellow kalanchoe in the plant height trait, while the orange kalanchoe was distinguished in the number of inflorescences, the number of flowers and flower length traits, whereas the violet kalanchoe possessed the largest flower diameter and the highest number of petals. The molecular profiling was performed by random amplified polymorphism DNA (RAPD), inter-simple sequence repeats (ISSR) and start codon targeted (SCoT)-polymerase chain reaction (PCR) tools. Genomic DNA was extracted from young leaves and the PCR reactions were performed using ten primers for each SCoT, ISSR and RAPD marker. Only four out of ten primers showed amplicon profiles in all PCR markers. A total of 70 bands were generated by SCoT, ISSR and RAPD-PCR with 35 polymorphic bands and 35 monomorphic bands. The total number of bands of RAPD, ISSR and SCoT was 15, 17 and 38, respectively. The polymorphism percentages achieved by RAPD, ISSR and SCoT were 60.25%, 15% and 57%, respectively. The cluster analysis based on morphological data revealed two clusters. Cluster I consisted of violet and orange kalanchoe, and cluster II comprised red, yellow and purple kalanchoe. Whereas the cluster analysis based on molecular data revealed three clusters. Cluster I included only yellow kalanchoe, cluster II comprised orange and violet kalanchoe while cluster III comprised red, and purple kalanchoe. The study concluded that orange, violet and yellow kalanchoe are distinguished parents for breeding economically valued traits in kalanchoe. Also, the study concluded that SCoT and RAPD markers reproduced reliable banding patterns to assess the genetic polymorphism among kalanchoe genotypes that consider the basis stone for genetic improvements in ornamental plants.
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Affiliation(s)
- Jameel M. Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.); (K.M.A.)
- Correspondence: (J.M.A.-K.); (A.A.H.A.L.); (A.A.H.)
| | - Ehab M. B. Mahdy
- National Gene Bank (NGB), Agricultural Research Centre (ARC), Giza 12613, Egypt;
| | - Heba S. A. Taha
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt; (H.S.A.T.); (A.S.E.)
| | - Ahmed S. Eldomiaty
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt; (H.S.A.T.); (A.S.E.)
| | | | - Arafat Abdel Hamed Abdel Latef
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
- Correspondence: (J.M.A.-K.); (A.A.H.A.L.); (A.A.H.)
| | - Adel A. Rezk
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.); (K.M.A.)
| | - Wael F. Shehata
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.); (K.M.A.)
| | - Mustafa I. Almaghasla
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (M.I.A.); (T.A.S.)
- Plant Pests, and Diseases Unit, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia
| | - Tarek A. Shalaby
- Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia; (M.I.A.); (T.A.S.)
- Horticulture Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
| | - Muhammad N. Sattar
- Central Laboratories, King Faisal University, P.O. Box 420, Al-Ahsa 31982, Saudi Arabia;
| | - Hesham S. Ghazzawy
- Date Palm Research Center of Excellence, King Faisal University, Al-Ahsa 31982, Saudi Arabia;
| | - Mohamed F. Awad
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Khalid M. Alali
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.); (K.M.A.)
| | - Shri Mohan Jain
- Department of Agricultural Sciences, University of Helsinki, 00014 Helsinki, Finland;
| | - Abdallah A. Hassanin
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt; (H.S.A.T.); (A.S.E.)
- Correspondence: (J.M.A.-K.); (A.A.H.A.L.); (A.A.H.)
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Dissection of genetic diversity and population structure in oregano (Origanum acutidens L.) genotypes based on agro-morphological properties and start codon targeted (SCoT) markers. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-00989-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Alotaibi MO, Abd-Elgawad ME. ISSR and SCoT for Evaluation of Hereditary Differences of 29 Wild Plants in Al Jubail Saudi Arabian. Saudi J Biol Sci 2022; 29:3223-3231. [PMID: 35844376 PMCID: PMC9280174 DOI: 10.1016/j.sjbs.2022.01.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 11/26/2022] Open
Abstract
This survey is concerned with the hereditary differences of 29 wild plants collected from fifteen different regions in Al Jubail, Saudi Arabia using two molecular marker systems, viz. inter simple sequence repeat (ISSR) and start codon targeted (SCoT) molecular markers. Ten ISSR and ten SCoT primers amplified a total of 142 and 163 bands with a 87% and 84% polymorphism, respectively. The average number of polymorphic bands for each pair of ISSR and SCoT primers combinations was 12.4 and 13.7, respectively. The highest genetic similarity for ISSR (0.97) and SCoT (0.90) were recognized between Zygophyllum qatarense-22 and Juncus rigidus-23, and between Zygophyllum qatarense-28 and Zygophyllum qatarense-29, whereas the lowest was (0.59) differentiated between Zygophyllum qatarense-6 and Salsola imbricate-18 for ISSR and between Cyperus conglomeratus-7 and Halopeplis perfoliata-14 for SCoT. This considers confirmed the value of molecular techniques such as ISSR and SCoT to assess the hereditary differences among the selected 29 weeds for hereditary preservation and plant enhancement.
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Jena RC, Chand PK. Multiple DNA marker-assisted diversity analysis of Indian mango (Mangifera indica L.) populations. Sci Rep 2021; 11:10345. [PMID: 33990638 PMCID: PMC8121829 DOI: 10.1038/s41598-021-89470-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/16/2021] [Indexed: 11/09/2022] Open
Abstract
Arbitrary (65 RAPD, 25 ISSR, 23 DAMD), gene-targeted (22 SCoT, 33 CBDP) and co-dominant sequence specific (40 SSR) markers were used individually, or in combinations, to examine the genetic variability within and among 70 selected Indian mango genotypes based on geographic origin (East India, West India, North India, South India) and fruit status (Selection, Hybrid, Landrace). The highest genetic variability was demonstrated by the East Indian populations, followed by those from South India, West India, and North India, when measured in terms of Na, Ne, H, I, PB%, Ht and Hs. Interestingly, the local genotypes of Odisha, which forms a part of East Indian populations, showed the highest diversity compared to hybrid or selection groups, suggesting that the indigenous genotypes hold a greater potential for exploiting the unique and favourable alleles. The maximum genetic variability was detected in geographical/fruit status populations with SSRs (Na-1.76/1.88, Ne-1.48/1.51, H-0.28/0.30, I-0.41/0.45, PB%-76.1/86.9, Ht-0.31/0.32 and Hs-0.28/0.30), followed by CBDPs and SCoTs, reflecting their preeminence for examining the level of genetic polymorphism and diversity. Outcome of AMOVA based analyses as well as low-to-moderate coefficient of genetic differentiation (Gst) and high gene flow (Nm) indicated a greater amount of intra-population genetic variation compared to heterogeneity at inter-population level. Information generated through this investigation could facilitate conservation and further exploitation of mango germplasm including genetic improvement through breeding.
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Affiliation(s)
- Ram Chandra Jena
- Plant Biotechnology Laboratory, Post-Graduate Department of Botany, Utkal University, VaniVihar, Bhubaneswar, Odisha, 751004, India
| | - Pradeep Kumar Chand
- Plant Biotechnology Laboratory, Post-Graduate Department of Botany, Utkal University, VaniVihar, Bhubaneswar, Odisha, 751004, India.
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Genetic Diversity Analysis of Tomato (Solanum lycopersicum L.) with Morphological, Cytological, and Molecular Markers under Heat Stress. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7040065] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tomatoes are usually consumed daily in the human diet. High temperatures reduce the number of tomato yields per year. Heat stress has been considered one of the most prominent causes of alterations in morphological and molecular characteristics in crops that decrease normal growth, production, and yield in diverse plants, including tomatoes (Solanum lycopersicum L.). In this study, we evaluated six tomato lines, namely G1, G2, G3, G4, G5, and G6, at morphological, molecular, and cytological levels under heat stress. The average results of two seasons (2018 and 2019) clarified that the G6, G1, and G2 lines recorded the highest flowering values, as well as some fruit and vegetative growth traits. Furthermore, G6 and G2 had the maximum number of fruits/plant, whereas G2 and G1 produced the highest yield/plant under high temperatures. The number of chromosomes in all lines was 2n = 24, except for G5, in which the number was 2n = 26, whereas chromosome sizes were small, ranging from 323.08 to 464.48 µm. The G1 cultivar was a symmetrical cultivar (primitive), having the highest total form percentage (TF%) and symmetry index (Syi) values and the minimum karyotype asymmetry index (ASK) value, whereas G4 was asymmetrical (advanced). Molecular marker analysis demonstrated that intersimple sequence repeat (ISSR) primers 49A, HB-14, 49A, 49B, and 89B presented the highest values for polymorphism percentage P%, marker index (MI), effective multiplex ratio (EMR), and polymorphism information content (PIC), respectively. In contrast, OP-A3, OP-B3, SCoT 2, and SCoT 12 primers showed the highest PIC, EMR, MI, P%, and resolving power (Rp) values across the studied random amplified polymorphic DNA (RAPD) and start codon-targeted (SCoT) primers. Moreover, ISSR revealed the highest number of unique specific markers (6), followed by RAPD (4) and SCoT (3) markers. Cluster analysis of combined cytological data and data relating to molecular marker attributes separated the G1, G2, and G3 lines into one group, whereas the other lines were clustered in another group. On the whole, the application of combined analysis using morphological, cytological, and molecular genetics techniques could be considered to provide suitable parameters for studying the evolution of the genetic divergence between the studied tomato lines.
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Zhong M, Yang X, Hu Y, Huang L, Peng Y, Li Z, Liu Q, Wang X, Zhang X, Nie G. Identification of candidate reference genes for quantitative RT-PCR in Miscanthus sinensis subjected to various abiotic stresses. Mol Biol Rep 2020; 47:2913-2927. [PMID: 32222917 DOI: 10.1007/s11033-020-05392-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 03/24/2020] [Indexed: 12/22/2022]
Abstract
Quantitative real-time PCR (qRT-PCR) has been widely used for studying gene expression at the transcript level. Its accuracy usually relies on the reference genes that are utilized for data normalization. Miscanthus sinensis, a perennial C4 grass with high biomass and strong resistance to adversities, is often utilized as a high value energy crop. However, no reliable reference genes have been investigated for normalizing gene expression for this species. In this study, 12 candidate reference genes were selected to identify their stability under five different abiotic stress treatments (drought, salt, cadmium, chromium and arsenic) by using geNorm, NormFinder, BestKeeper and RefFinder softwares. The results showed that 18S rRNA and Unigene33312 were the best reference genes under drought treatments. Unigene33312 and Unigene33024 were found to be the most stably expressed genes under salt stress and Cd stress. Moreover, Unigene33024 and PP2A were the most suitable reference genes under Cr stress and Unigene33024 and Sb09g019750 were deemed more suitable reference genes under As stress. In total, considering all the samples, Unigene33024 and PP2A were the most stable genes while ACTIN and Unigene26576 were the least stable reference genes for internal control. The expression patterns of two target genes (Cu/Zn SOD and CAT) were used to further verify those selected reference genes under different conditions. The results showed that the most and the least stable reference genes had clearly different expression patterns. This work comprehensively estimated the stability of reference genes in M. sinensis which may give insight to the reference genes selection in other tissues as well as other related varieties. These suggested reference genes would assist in further putative gene expression validation in M. sinensis.
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Affiliation(s)
- Minyi Zhong
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xinying Yang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yiyue Hu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yan Peng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhou Li
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiuxu Liu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xia Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Gang Nie
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Tyagi R, Sharma V, Sureja AK, Das Munshi A, Arya L, Saha D, Verma M. Genetic diversity and population structure detection in sponge gourd ( Luffa cylindrica) using ISSR, SCoT and morphological markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:119-131. [PMID: 32158125 PMCID: PMC7036400 DOI: 10.1007/s12298-019-00723-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 09/05/2019] [Accepted: 10/16/2019] [Indexed: 06/01/2023]
Abstract
Investigation of genetic diversity is essential for the selection of parents for crop breeding and conservation of genetic resources. To estimate the genetic variability and population structure in the midst of 45 accessions of sponge gourd brought together from different geographical areas of India, morphological traits and two molecular markers, ISSR and SCoT markers were compared. Principal components analysis of 20 morphological traits showed 72.70% variability and significant positive correlations between fruit traits. All three marker techniques clustered all accessions into two groups with few outgroups. High level of polymorphism was observed among ISSR (74.6%) and SCoT (71.5%) primers. The Bayesian model revealed the hidden grouping and showed admixture type of population. The diversity pattern is influenced by genetic marker used, as different molecular markers have different polymorphism evaluation efficiency. This study can be helpful in amplifying the genetic base and selection of specific traits for breeding. Thus, ISSR and SCoT markers are potential marker for identification in sponge gourd and provide valuable data on its genetic correlation and structure.
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Affiliation(s)
- Ruchi Tyagi
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali, Rajasthan 304022 India
| | - Vinay Sharma
- Department of Bioscience and Biotechnology, Banasthali University, Banasthali, Rajasthan 304022 India
| | - Amish Kumar Sureja
- Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Anilabh Das Munshi
- Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Lalit Arya
- Division of Genomic Resources, ICAR-NBPGR, New Delhi, 110012 India
| | - Dipnarayan Saha
- Present Address: ICAR-Central Research Institute for Jute and Allied Fibres (ICAR), Barrackpore, India
| | - Manjusha Verma
- Division of Genomic Resources, ICAR-NBPGR, New Delhi, 110012 India
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Gupta V, Jatav PK, Haq SU, Verma KS, Kaul VK, Kothari SL, Kachhwaha S. 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. J Genet 2019. [DOI: 10.1007/s12041-019-1095-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Nasrollahi S, Badakhshan H, Sadeghi A. Analyzing Sunn pest resistance in bread wheat genotypes using phenotypic characteristics and molecular markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:765-778. [PMID: 31168238 PMCID: PMC6522623 DOI: 10.1007/s12298-019-00662-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 03/12/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Sunn pest is one of the most destructive insects in the western and central parts of Asia causing severe reductions of wheat yield and flour quality. Therefore, an effort was undertaken to find effective resistance by analyzing genetic variation among 25 wheat genotypes artificially infested in field-cages as well as using start codon targeted (SCoT) polymorphism and inter- retrotransposon amplified polymorphism (IRAP) markers. High variation was revealed amongst genotypes with Sunn pest resistance characteristics including Bayat, Bezostaya, Sayson, Line93, Line120, Rashagol, Golsepi and AarasGolsoor, which were classified as resistant to moderately resistant. SCoTs and IRAPs were determined as efficient markers for studying genetic diversity. The non-parametric Kruskal-Wallis test was conducted to evaluate the effect of specific SCoT and IRAP amplicons on Sunn pest resistance characteristics for wheat genotypes. The stepwise regression analysis exhibited seven informative SCoTs and IRAPs explaining the highest resistance characteristics variation ranging from 25.7-50.1 to 17.6-40.1, respectively. The relationship between resistance of genotypes and informative SCoT and IRAP amplicons was found based on canonical discriminant analysis showing the capacity of informative markers for functional marker selection method and screening the wheat germplasms for Sunn pest resistance characteristics.
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Affiliation(s)
- Shilan Nasrollahi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Hedieh Badakhshan
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Amin Sadeghi
- Department of Plant Protection, College of Agriculture, University of Kurdistan, Sanandaj, Iran
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Xu YX, Shen SY, Chen W, Chen L. Analysis of Genetic Diversity and Development of a SCAR Marker for Green Tea (Camellia sinensis) Cultivars in Zhejiang Province: The Most Famous Green Tea-Producing Area in China. Biochem Genet 2019; 57:555-570. [PMID: 30734883 DOI: 10.1007/s10528-019-09909-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/28/2019] [Indexed: 11/24/2022]
Abstract
Camellia sinensis (L.) O. Kuntze is one of the most important non-alcoholic beverage crops in Asian and African countries. In recent years, many green tea cultivars have been released and played an important role in improving the production and quality of tea trees. The objectives of this study were to assess the genetic diversity of the eighteen main green tea cultivars in Zhejiang Province-the most famous green tea-producing area of China-using start codon-targeted (SCoT) markers and to develop a specific sequence-characterized amplified region (SCAR) marker for application in cultivar diagnosis. Thirty-one SCoT primers produced 264 loci, 226 of which were polymorphic. The genetic similarity coefficients among these green tea cultivars ranged from 0.587 to 0.814, indicating that a high level of genetic diversity was present. Both a UPGMA dendrogram and a PCoA plot grouped the tea cultivars into three groups. The partitioning of groups in the UPGMA and PCoA was similar, and much of the clustering was highly consistent with the classification of tea cultivars according to their genetic backgrounds. A unique SCoT band, SCoT4-1649, specific to the tea cultivar 'Yingshuang,' was transformed into a SCAR marker. This SCAR marker is highly useful for the identification and germplasm conservation of green tea cultivars.
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Affiliation(s)
- Yan-Xia Xu
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Si-Yan Shen
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Wei Chen
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China
| | - Liang Chen
- National Center for Tea Improvement, Tea Research Institute of the Chinese Academy of Agricultural Sciences/ Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, 310008, China.
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Ahmad R, Anjum MA, Malik W. RETRACTED ARTICLE: Characterization and Evaluation of Mango Germplasm Through Morphological, Biochemical, and Molecular Markers Focusing on Fruit Production: An Overview. Mol Biotechnol 2018; 61:631. [PMID: 30315501 DOI: 10.1007/s12033-018-0129-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Riaz Ahmad
- Department of Horticulture, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Muhammad Akbar Anjum
- Department of Horticulture, Bahauddin Zakariya University, Multan, 60800, Pakistan.
| | - Waqas Malik
- Genomics Lab, Department of Plant Breeding & Genetics, Bahauddin Zakariya University, Multan, 60800, Pakistan
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Amer A, Taha H, Ammar N, Salama M, El-Alfy T. Applicability of Different Molecular Markers Techniques for Genetic Distinguish Between Two Genera <I>Cressa</I> Linn. and <I>Cuscuta</I> Yunck. Family Convolvulaceae. Pak J Biol Sci 2018; 21:179-186. [PMID: 30311474 DOI: 10.3923/pjbs.2018.179.186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE The DNA fingerprinting is used to determine the relationship between species in the same genus or between genera related to the same family. The aim of this study was to determine the relationships between two samples related to the same family Convolvulaceae, representing two genera, Cressa Linn. and Cuscuta Yunck. by RAPD, ISSR and SCoT molecular techniques (PCR based DNA fingerprint). MATERIALS AND METHODS The RAPD, ISSR and SCoT based DNA fingerprinting techniques were implemented to identify the fingerprint diversity between two genera, Cressa Linn. and Cuscuta Yunck-belonging to the family Convolvulaceae. RESULTS Applying of RAPD technique revealed that using OP-A02, OP-A09, OP-A10, OP-C04 and OP-M01 primers recorded 60, 83.33, 100, 50 and 70.66% polymorphism, respectively. On the other hand, ISSR technique recorded 40, 50, 100, 66.67, 33.33 and 37.5% polymorphism with 44B, HB-08, HB-09, HB-10, HB-11 and HB-12 primers, respectively. However, amplification of SCoT technique, SCoT 1, SCoT 2, SCoT 3, SCoT 4, SCoT 6, SCoT 8, SCoT 10 and SCoT 12 primers recorded 33.33, 28.57, 14.28, 66.66, 25, 40, 42.85 and 50%, respectively . The total polymorphism recorded 73.33, 54.58 and 37.7% for RAPD, ISSR and SCoT techniques, respectively. CONCLUSION The result of this study indicated that SCoT technique was more efficient and sustainable for distinguish between two genera under investigation.
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Rafizadeh A, Koohi-Dehkordi M, Sorkheh K. Molecular insights of genetic variation in milk thistle (Silybum marianum [L.] Gaertn.) populations collected from southwest Iran. Mol Biol Rep 2018; 45:601-609. [PMID: 29882084 DOI: 10.1007/s11033-018-4198-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/24/2018] [Indexed: 10/14/2022]
Abstract
Milk thistle (Silybum marianum) is among the world's popular medicinal plants. Start Codon Targeted (SCoT) marker system was utilized to investigate the genetic variability of 80 S. marianum genotypes from eight populations in Iran. SCoT marker produced 255 amplicons and 84.03% polymorphism was generated. The SCoT marker system's polymorphism information content value was 0.43. The primers' resolving power values were between 4.18 and 7.84. The percentage of polymorphic bands was between 33.3 and 100%. The Nei's gene diversity (h) was 0.19-1.30 with an average 0.72. The Shannon's index (I) ranged from 0.29 to 1.38 with an average value of 0.83. The average gene flow (0.37) demonstrated a high genetic variation among the studied populations. The variation of 42% was displayed by the molecular variance analysis among the populations while a recorded variation of 58% was made within the populations. Current investigation suggested that SCoT marker system could effectively evaluate milk thistle genotypes genetic diversity.
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Affiliation(s)
- Azam Rafizadeh
- Department of Agricultural Science, Payame-Noor University, P. O. Box 19395-3697, Tehran, Iran
| | - Mehrana Koohi-Dehkordi
- Department of Agricultural Science, Payame-Noor University, P. O. Box 19395-3697, Tehran, Iran.
| | - Karim Sorkheh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P. O. Box 61355/144, Ahvaz, Iran
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Balážová Ž, Gálová Z, Vivodík M, Chňapek M, Hornyák Gregáňová R. Molecular analysis of buckwheat using gene specific markers. POTRAVINARSTVO 2018. [DOI: 10.5219/954] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Buckwheat (Fagopyrium esculentum) is a pseudo-cereal which has spread troughout the world and nowadays it represents cultural, economic and nutritionally important pseudocereal. It´s enviromentally friendly, characterized by high fiber, routine, protein and B vitamins, and is general-purpose. The goal of the present study was to analyze 17 genotypes of buckwheat by using 7 SCoT markers. In total, 52 fragments were detected, of which 38 were polymorphic. The average number of polymorphic fragments was 5.43. The most polymorphic fragments were detected in SCoT 26 and SCoT 29 markers, and the average percentage of polymorphism was 73.36 %. SCoT 29 reached the highest percentage of polymorphism (87.5 %) and SCoT 36 was lowest (60 %). The DI values ”‹”‹ranged from 0.625 (SCoT 36) to 0.887 (SCoT 26) and the average DI value was 0.749. The average PIC value was 0.729 with PIC values ranging from 0.386 (SCoT 36) to 0.831 (SCoT 26). To determine the genetic diversity of 17 genotypes of the buckwheat, a dendrogram was created using the hierarchical cluster analysis. The genotypes were divided into two major clusters (I and II). Cluster I was divided into three other subgroups. Sixteen genotypes were included in cluster I and the genotype of Madawaska (USA) was genetically the farthest in cluster II. Genetically the closest were the varieties of Ballada (Russia) and Bamby (Austria). Used SCoT markers were sufficiently polymorphic, were able identify and differentiate chosen set of buckwheat genotypes.
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Feng S, Zhu Y, Yu C, Jiao K, Jiang M, Lu J, Shen C, Ying Q, Wang H. Development of Species-Specific SCAR Markers, Based on a SCoT Analysis, to Authenticate Physalis (Solanaceae) Species. Front Genet 2018; 9:192. [PMID: 29910824 PMCID: PMC5992434 DOI: 10.3389/fgene.2018.00192] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 05/11/2018] [Indexed: 11/13/2022] Open
Abstract
Physalis is an important genus in the Solanaceae family. It includes many species of significant medicinal value, edible value, and ornamental value. However, many Physalis species are easily confused because of their similar morphological traits, which hinder the utilization and protection of Physalis resources. Therefore, it is necessary to create fast, sensitive, and reliable methods for the Physalis species authentication. Intended for that, in this study, species-specific sequence-characterized amplified region (SCAR) markers were developed for accurate identification of the closely related Physalis species P. angulata, P. minima, P. pubescens, and P. alkekengi var. franchetii, based on a simple and novel marker system, start codon targeted (SCoT) marker. A total of 34 selected SCoT primers yielded 289 reliable SCoT loci, of which 265 were polymorphic. Four species-specific SCoT fragments (SCoT3-1404, SCoT3-1589, SCoT5-550, and SCoT36-520) from Physalis species were successfully identified, cloned, and sequenced. Based on these selected specific DNA fragments, four SCAR primers pairs were developed and named ST3KZ, ST3MSJ, ST5SJ, and ST36XSJ. PCR analysis of each of these primer pairs clearly demonstrated a specific amplified band in all samples of the target Physalis species, but no amplification was observed in other Physalis species. Therefore, the species-specific SCAR primer pairs developed in this study could be used as powerful tools that can rapidly, effectively, and reliably identify and differentiate Physalis species.
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Affiliation(s)
- Shangguo Feng
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Yujia Zhu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Chenliang Yu
- The Institute of Vegetable, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Kaili Jiao
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mengying Jiang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jiangjie Lu
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Chenjia Shen
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qicai Ying
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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Vivodík M, Saadaoui E, Balážová Ž, Gálová Z, Petrovičová L. Genetic diversity and population structure in tunisian castor genotypes (Ricinus communis L.) Detected using scot markers. POTRAVINARSTVO 2018. [DOI: 10.5219/873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Due to the chemical and physical properties of castor oil (Ricinus communis L.) that make it a valuable raw material for numerous industrial applications, including the production of biofuel, interest to develop more and better varieties has been increased. In the present study, the representatives of the genus castor collected from 12 different parts of Tunisia were differentiated by the DNA fingerprinting patterns using 37 SCoT primers. PCR amplification of DNA using 37 primers for SCoT analysis produced 268 DNA fragments that could be scored in all 56 genotypes of Tunisian castor. The number of amplified fragments varied from 4 (SCoT 45, SCoT 31 and ScoT 17) to 10 (SCoT 3, SCoT 11, SCoT 14, SCoT 18 and SCoT 12). Of the 268 amplified bands 230 were polymorphic, with an average of 6.22 polymorphic bands per primer. To determine the level of polymorphism in the analysed group of Tunisian castor genotypes polymorphic information content (PIC) was calculated. The lowest values of polymorphic information content were recorded for SCoT 17 (0.411) and the the highest PIC values were detected for SCoT 14 (0.868) with an average of 0.751. 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 56 Tunisian castor genotypes were clustered into two main clusters (1 and 2). Of the 56 genotypes of Tunisian castor, 2 unique genotypes were separated (BA-5 and K-4). Genetically the closest were two genotypes from Tunisian region Souassi (S-2 and S-5) in subclaster 2bc. Results showed the utility of SCoT markers for estimation of genetic diversity of castor genotypes leading to genotype identification.
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Hao J, Jiao K, Yu C, Guo H, Zhu Y, Yang X, Zhang S, Zhang L, Feng S, Song Y, Dong M, Wang H, Shen C. Development of SCoT-Based SCAR Marker for Rapid Authentication of Taxus Media. Biochem Genet 2018; 56:255-266. [DOI: 10.1007/s10528-018-9842-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/19/2018] [Indexed: 10/18/2022]
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Al-Qurainy F, Khan S, Nadeem M, Tarroum M, Gaafar ARZ. Antioxidant System Response and cDNA-SCoT Marker Profiling in Phoenix dactylifera L. Plant under Salinity Stress. Int J Genomics 2017; 2017:1537538. [PMID: 28702461 PMCID: PMC5494121 DOI: 10.1155/2017/1537538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/23/2017] [Accepted: 05/02/2017] [Indexed: 01/24/2023] Open
Abstract
Many Phoenix dactylifera (date palm) cultivars are grown in the arid and semiarid regions of the world, including Saudi Arabia. P. dactylifera is highly tolerant to salinity stress. To investigate the response of Khalas cultivar of P. dactylifera, two-month-old plants were treated with sodium chloride (50, 100, and 150 mM NaCl) for three months. Our result showed that proline content was higher in all treated plants compared to control plants. Thiobarbituric acid reactive substances (TBARS) were increased at 100 and 150 mM NaCl treatments; however, the result was found nonsignificant between control and plants treated at 50 mM NaCl. Similarly, enzyme activities of catalase (CAT) and superoxide dismutase (SOD) were 0.805 and 0.722 U/mg protein/min, respectively, and were greater at 100 and 150 mM NaCl treatments compared to the control plants. Total chlorophyll content and fresh weight of shoots and roots decreased substantially with the increase of salinity. A cDNA start codon-targeted (cDNA-SCoT) marker showed a variation in different gene expressions profiling between treated and untreated plants under various NaCl concentrations.
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Affiliation(s)
- Fahad Al-Qurainy
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Salim Khan
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Nadeem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed Tarroum
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdel-Rhman Z. Gaafar
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Balážová Ž, Gálová Z, Vivodík M, Petrovičová L, Gregáňová RH. Molecular variability of oat based on gene specific markers. POTRAVINARSTVO 2017. [DOI: 10.5219/774] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oat (Avena sativa L.) is a grass planted as a cereal crop. Cultivation of oat is increasing in the recent years because of its good nutrition value. The aim of our study was to analyze genetic variability of oat accessions based on SCoT markers. Eighteen primers were used to study polymorfism of 8 oat genotypes. All 18 primers produced polymorphic and reproducible data. Altogether 153 different fragments were amplified of which 67 were polymorphic with an average number of 3.72 polymorphic fragments per genotype. The number of polymorphic fragments ranged from one (SCoT9, SCoT62) to nine (SCoT40). The percentage of polymorphic bands ranged from 14.29% (SCoT9) to 60% (SCoT59) with an average of 41.62%. Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The diversity index of the tested SCoT markers ranged from 0 (SCoT9, SCoT62) to 0.878 (SCoT40) with an average of 0.574. The polymorphic information content ranged from 0 (SCoT9, SCoT62) to 0.876 (SCoT40) with an average of 0.524. Dendrogram based on hierarchical cluster analysis using UPGMA algorithm grouped genotypes into two main clusters. Two genotypes, Taiko and Vok were genetically the closest. Results showed the utility of SCoT markers for estimation of genetic diversity of oat genotypes leading to genotype identification.
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Petrovičová L, Balážová Ž, Vivodík M, Gálová Z. Detection genetic variability of secale cereale L. by scot markers. POTRAVINARSTVO 2017. [DOI: 10.5219/726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rye (Secale cereale L.) is our traditional cereal used for baking. The genetic variability of grown rye has been reduced by modern agronomic practices, which subsequently prompted the importance of search for species that could be useful as a gene pool for the improving of flour quality for human consumption or for other industrial uses. Therefore, the aim of this study was to detect genetic variability among the set of 45 rye genotypes using 8 SCoT markers. Amplification of genomic DNA of 45 genotypes, using SCoT analysis, yielded 114 fragments, with an average of 14.25 polymorphic fragments per primer. The most polymorphic primer was SCoT 36, where 21 polymorphic amplification products were detected. In contract the lowest polymorphic primer was SCoT 45 with 5 polymorphic products. Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The hierarchical cluster analysis showed that the rye genotypes were divided into 2 main clusters. One rye genotype Motto, origin from Poland formed a separate subcluster (1b). Subscluster 2a included only genotype Valtické (CSK). In this experiment, SCoT proved to be a rapid, reliable and practicable method for revealing of polymorphism in the rye cultivars.
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Chai X, Dong R, Liu W, Wang Y, Liu Z. Optimizing Sample Size to Assess the Genetic Diversity in Common Vetch (Vicia sativa L.) Populations Using Start Codon Targeted (SCoT) Markers. Molecules 2017; 22:molecules22040567. [PMID: 28362323 PMCID: PMC6154542 DOI: 10.3390/molecules22040567] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/16/2022] Open
Abstract
Common vetch (Vicia sativa subsp. sativa L.) is a self-pollinating annual forage legume with worldwide importance. Here, we investigate the optimal number of individuals that may represent the genetic diversity of a single population, using Start Codon Targeted (SCoT) markers. Two cultivated varieties and two wild accessions were evaluated using five SCoT primers, also testing different sampling sizes: 1, 2, 3, 5, 8, 10, 20, 30, 40, 50, and 60 individuals. The results showed that the number of alleles and the Polymorphism Information Content (PIC) were different among the four accessions. Cluster analysis by Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and STRUCTURE placed the 240 individuals into four distinct clusters. The Expected Heterozygosity (HE) and PIC increased along with an increase in sampling size from 1 to 10 plants but did not change significantly when the sample sizes exceeded 10 individuals. At least 90% of the genetic variation in the four germplasms was represented when the sample size was 10. Finally, we concluded that 10 individuals could effectively represent the genetic diversity of one vetch population based on the SCoT markers. This study provides theoretical support for genetic diversity, cultivar identification, evolution, and marker-assisted selection breeding in common vetch.
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Affiliation(s)
- Xutian Chai
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Rui Dong
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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Molecular evolution and phylogenetic analysis of biocontrol genes acquired from SCoT polymorphism of mycoparasitic Trichoderma koningii inhibiting phytopathogen Rhizoctonia solani Kuhn. INFECTION GENETICS AND EVOLUTION 2016; 45:383-392. [DOI: 10.1016/j.meegid.2016.09.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 09/12/2016] [Accepted: 09/30/2016] [Indexed: 11/19/2022]
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Wild Panax vietnamensis and Panax stipuleanatus markedly increase the genetic diversity of Panax notoginseng (Araliaceae) revealed by start codon targeted (SCoT) markers and ITS DNA barcode. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Genetic diversity of orchardgrass (Dactylis glomerata L.) cultivars revealed by simple sequence repeats (SSR) markers. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Zhang Y, Yan H, Jiang X, Wang X, Huang L, Xu B, Zhang X, Zhang L. Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers. Hereditas 2016; 153:4. [PMID: 28096766 PMCID: PMC5226102 DOI: 10.1186/s41065-016-0007-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/29/2016] [Indexed: 11/29/2022] Open
Abstract
Background To evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass (Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs. Results In this study, a high level of genetic variation was observed in the switchgrass samples and they had an average Nei’s gene diversity index (H) of 0.311. A total of 793 bands were obtained, of which 708 (89.28 %) were polymorphic. Using a parameter marker index (MI), the efficiency of the three types of markers (ISSR, SCoT, and EST-SSR) in the study were compared and we found that SCoT had a higher marker efficiency than the other two markers. The 134 switchgrass samples could be divided into two sub-populations based on STRUCTURE, UPGMA clustering, and principal coordinate analyses (PCA), and upland and lowland ecotypes could be separated by UPGMA clustering and PCA analyses. Linkage disequilibrium analysis revealed an average r2 of 0.035 across all 51 markers, indicating a trend of higher LD in sub-population 2 than that in sub-population 1 (P < 0.01). Conclusions The population structure revealed in this study will guide the design of future association studies using these switchgrass samples.
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Affiliation(s)
- Yu Zhang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China.,IRTA. Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB), Campus UAB - Edifici CRAG, Bellaterra - Cerdanyola del Vallès, Barcelona, 08193 Spain
| | - Haidong Yan
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaomei Jiang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaoli Wang
- Guizhou Institute of Prataculture, Guiyang, 550006 PR China
| | - Linkai Huang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xinquan Zhang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
| | - Lexin Zhang
- Grassland Science Department, Sichuan Agricultural University, Chengdu, 611130 China
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Sorkheh K, Amirbakhtiar N, Ercisli S. Potential Start Codon Targeted (SCoT) and Inter-retrotransposon Amplified Polymorphism (IRAP) Markers for Evaluation of Genetic Diversity and Conservation of Wild Pistacia Species Population. Biochem Genet 2016; 54:368-387. [PMID: 27056191 DOI: 10.1007/s10528-016-9725-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Wild pistachio species is important species in forests regions Iran and provide protection wind and soil erosion. Even though cultivation and utilization of Pistacia are fully exploited, the evolutionary history of the Pistacia genus and the relationships among the species and accessions is still not well understood. Two molecular marker strategies, SCoT and IRAP markers were analyzed for assessment of 50 accessions of this species accumulated from diverse geographical areas of Iran. A thorough of 115 bands were amplified using eight IRAP primers, of which 104 (90.4 %) have been polymorphic, and 246 polymorphic bands (68.7 %) had been located in 358 bands amplified by way of forty-four SCoT primers. Average PIC for IRAP and SCoT markers became 0.32 and 0.48, respectively. This is exposed that SCoT markers have been extra informative than IRAP for the assessment of variety among pistachio accessions. Primarily based on the two extraordinary molecular markers, cluster evaluation revealed that the 50 accessions taken for the evaluation may be divided into three distinct clusters. Those results recommend that the performance of SCoT and IRAP markers was highly the equal in fingerprinting of accessions. The results affirmed a low genetic differentiation among populations, indicating the opportunity of gene drift most of the studied populations. These findings might render striking information in breeding management strategies for genetic conservation and cultivar improvement.
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Affiliation(s)
- Karim Sorkheh
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O.Box 61355/144, Ahvaz, Iran.
| | - Nazanin Amirbakhtiar
- Department of seed and Plant improvement, Agricultural & Natural Resources Research and Education Center, P.O.Box 61333-3341, Ahvaz, Iran
| | - Sezai Ercisli
- Department of Horticulture, Agricultural Faculty, Ataturk University, 25240, Erzurum, Turkey
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Rajesh MK, Sabana AA, Rachana KE, Rahman S, Jerard BA, Karun A. Genetic relationship and diversity among coconut (Cocos nucifera L.) accessions revealed through SCoT analysis. 3 Biotech 2015; 5:999-1006. [PMID: 28324407 PMCID: PMC4624129 DOI: 10.1007/s13205-015-0304-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/24/2015] [Indexed: 11/22/2022] Open
Abstract
Coconut (Cocos nucifera L.) is one of the important palms grown both as a homestead and plantation crop in countries and most island territories of tropical regions. Different DNA-based marker systems have been utilized to assess the extent of genetic diversity in coconut. Advances in genomics research have resulted in the development of novel gene-targeted markers. In the present study, we have used a simple and novel marker system, start codon targeted polymorphism (SCoT), for its evaluation as a potential marker system in coconut. SCoT markers were utilized for assessment of genetic diversity in 23 coconut accessions (10 talls and 13 dwarfs), representing different geographical regions. Out of 25 SCoT primers screened, 15 primers were selected for this study based on their consistent amplification patterns. A total of 102 scorable bands were produced by the 15 primers, 88 % of which were polymorphic. The scored data were used to construct a similarity matrix. The similarity coefficient values ranged between 0.37 and 0.91. These coefficients were utilized to construct a dendrogram using the unweighted pair group of arithmetic means (UPGMA). The extent of genetic diversity observed based on SCoT analysis of coconut accessions was comparable to earlier findings using other marker systems. Tall and dwarf coconut accessions were clearly demarcated, and in general, coconut accessions from the same geographical region clustered together. The results indicate the potential of SCoT markers to be utilized as molecular markers to detect DNA polymorphism in coconut accessions.
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Liu YX, Xia T, Zheng YH, Zhi YQ, Zhou J. Genetic diversity and the population structure at two ploidy levels of Lycoris radiata as revealed by SCoT analysis. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Feng S, He R, Yang S, Chen Z, Jiang M, Lu J, Wang H. Start codon targeted (SCoT) and target region amplification polymorphism (TRAP) for evaluating the genetic relationship of Dendrobium species. Gene 2015; 567:182-8. [DOI: 10.1016/j.gene.2015.04.076] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 04/15/2015] [Accepted: 04/28/2015] [Indexed: 11/29/2022]
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Zhang J, Xie W, Wang Y, Zhao X. Potential of Start Codon Targeted (SCoT) markers to estimate genetic diversity and relationships among Chinese Elymus sibiricus accessions. Molecules 2015; 20:5987-6001. [PMID: 25853316 PMCID: PMC6272172 DOI: 10.3390/molecules20045987] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/28/2015] [Accepted: 04/01/2015] [Indexed: 11/16/2022] Open
Abstract
Elymus sibiricus as an important forage grass and gene pool for improving cereal crops, that is widely distributed in West and North China. Information on its genetic diversity and relationships is limited but necessary for germplasm collection, conservation and future breeding. Start Codon Targeted (SCoT) markers were used for studying the genetic diversity and relationships among 53 E. sibiricus accessions from its primary distribution area in China. A total of 173 bands were generated from 16 SCoT primers, 159 bands of which were polymorphic with the percentage of polymorphic bands (PPB) of 91.91%. Based upon population structure analysis five groups were formed. The cluster analysis separated the accessions into two major clusters and three sub-clusters, similar to results of principal coordinate analysis (PCoA). The molecular variance analysis (AMOVA) showed that genetic variation was greater within geographical regions (50.99%) than between them (49.01%). Furthermore, the study also suggested that collecting and evaluating E. sibiricus germplasm for major geographic regions and special environments broadens the available genetic base and illustrates the range of variation. The results of the present study showed that SCoT markers were efficient in assessing the genetic diversity among E. sibiricus accessions.
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Affiliation(s)
- Junchao Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Wengang Xie
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Xuhong Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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Satya P, Karan M, Jana S, Mitra S, Sharma A, Karmakar P, Ray D. Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species. Meta Gene 2015; 3:62-70. [PMID: 25750860 PMCID: PMC4349193 DOI: 10.1016/j.mgene.2015.01.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 01/06/2015] [Accepted: 01/09/2015] [Indexed: 11/18/2022] Open
Abstract
Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie (Boehmeria nivea L. Gaudich.). A total of 155 genotypes from five populations were investigated for SCoT polymorphism, which produced 136 amplicons with 87.5% polymorphism. Polymorphism information content and resolving power of the SCoT markers were 0.69 and 3.22, respectively. The Indian ramie populations exhibited high SCoT polymorphism (> 50%), high genetic differentiation (GST = 0.27) and moderate gene flow (Nm = 1.34). Analysis of molecular variance identified significant differences for genetic polymorphism among the populations explaining 13.1% of the total variation. The domesticated population exhibited higher genetic polymorphism and heterozygosity compared to natural populations. Cluster analysis supported population genetic analysis and suggested close association between introduced and domesticated genotypes. The present study shows effectiveness of employing SCoT markers in a cross pollinated heterozygous species like Boehmeria, and would be useful for further studies in population genetics, conservation genetics and cultivar improvement. Genetic diversity and population structure of ramie (Boehmeria nivea) were assessed by SCoT markers. SCoT markers revealed high polymorphism and resolving ability in Boehmeria nivea. The wild ramie showed moderate heterozygosity and gene flow with high genetic variation, suggesting unidirectional gene flow. The domesticated population exhibited highest heterozygosity and close association with introduced population.
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Affiliation(s)
- Pratik Satya
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
- Corresponding author.
| | - Maya Karan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
| | - Sourav Jana
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
| | - Sabyasachi Mitra
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
| | - Amit Sharma
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
| | - P.G. Karmakar
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, India
| | - D.P. Ray
- ICAR-National Institute of Research on Jute and Allied Fibre Technology, Kolkata 700040, India
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Gao YH, Zhu YQ, Tong ZK, Xu ZY, Jiang XF, Huang CH. Analysis of genetic diversity and relationships among genus Lycoris based on start codon targeted (SCoT) marker. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Huang X, Zhang X, Huang L, Ma Y, Yin G, Lee S, Zeng J, Liu H. Genetic diversity of Hemarthria altissima and its related species by EST-SSR and SCoT markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.09.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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44
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Luo C, He XH, Hu Y, Yu HX, Ou SJ, Fang ZB. Oligo-dT anchored cDNA-SCoT: a novel differential display method for analyzing differential gene expression in response to several stress treatments in mango (Mangifera indica L.). Gene 2014; 548:182-9. [PMID: 25017057 DOI: 10.1016/j.gene.2014.07.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 10/25/2022]
Abstract
Differential display is a powerful technique for analyzing differences in gene expression. Oligo-dT cDNAstart codon targeted marker (cDNA-SCoT) technique is a novel, simple, cheap, rapid, and efficient method for differential gene expression research. In the present study, the oligo-dT anchored cDNA-SCoT technique was exploited to identify differentially expressed genes during several stress treatments in mango. A total of 37 primers combined with oligo-dT anchor primers 3side amplified approximately 150 fragments of 150 bp to 1500 bp in length. Up to 100 fragments were differentially expressed among the stress treatments and control samples, among which 92 were obtained and sequenced. Out of the 92 transcript derived fragments (TDFs), 70% were highly homologous to known genes, and 30% encoded unclassified proteins with unknown functions. The expression pattern of nine genes with known functions involved in several abiotic stresses in other species was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) under cold (4 °C), salinity (NaCl), polyethylene glycol (PEG, MW 6000), and heavy metal treatments in leaves and stems at different time points (0, 24, 48, and 72 h). The expression patterns of the genes (TDF4, TDF7, TDF23, TDF45, TDF49, TDF50, TDF57, TDF91 and TDF92) that had direct or indirect relationships with cold, salinity, drought and heavy metal stress response were analyzed through qRT-PCR. The possible roles of these genes are discussed. This study suggests that the oligo-dT anchored cDNA-SCoT differential display method is a useful tool to serve as an initial step for characterizing transcriptional changes induced by abiotic stresses and provide gene information for further study and application in genetic improvement and breeding in mango.
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Affiliation(s)
- Cong Luo
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Xin-Hua He
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China; Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning, Guangxi 530007, China.
| | - Ying Hu
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Hai-xia Yu
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Shi-Jin Ou
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Zhong-Bin Fang
- College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
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Genetic diversity of orchardgrass (Dactylis glomerata L.) germplasms with resistance to rust diseases revealed by Start Codon Targeted (SCoT) markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2013.12.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Potential of Start Codon Targeted (SCoT) markers for DNA fingerprinting of newly synthesized tritordeums and their respective parents. J Appl Genet 2014; 55:307-12. [PMID: 24733248 DOI: 10.1007/s13353-014-0211-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 01/31/2023]
Abstract
Hexaploid tritordeum (H(ch)H(ch)AABB; 2n = 42) results from the cross between Hordeum chilense (H(ch)H(ch); 2n = 14) and cultivated durum wheat (Triticum turgidum ssp. durum (AABB; 2n = 28). Morphologically, tritordeum resembles the wheat parent, showing promise for agriculture and wheat breeding. Start Codon Targeted (SCoT) polymorphism is a recently developed technique that generates gene-targeted markers. Thus, we considered it interesting to evaluate its potential for the DNA fingerprinting of newly synthesized hexaploid tritordeums and their respective parents. In this study, 60 SCoT primers were tested, and 18 and 19 of them revealed SCoT polymorphisms in the newly synthesized tritordeum lines HT27 and HT22, respectively, and their parents. An analysis of the presence/absence of bands among tritordeums and their parents revealed three types of polymorphic markers: (i) shared by tritordeums and one of their parents, (ii) exclusively amplified in tritordeums, and (iii) exclusively amplified in the parents. No polymorphism was detected among individuals of each parental species. Three SCoT markers were exclusively amplified in tritordeums of lines HT22 and HT27, being considered as polyploidization-induced rearrangements. About 70% of the SCoT markers of H. chilense origin were not transmitted to the allopolyploids of both lines, and most of the SCoTs scored in the newly synthesized allopolyploids originated from wheat, reinforcing the potential use of tritordeum as an alternative crop.
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Hidayat T, Arif SM, Samad AA. Molecular biodiversity of selected mango cultivars based on DNA sequences of internal transcribed spacer region. Pak J Biol Sci 2014; 16:1072-5. [PMID: 24502175 DOI: 10.3923/pjbs.2013.1072.1075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The mango (Mangifer indica L.) is an important species of the family Anacardiaceae and is one of the most important crops cultivated commercially in many parts of the world. Hence, a better understanding of the phylogeny in this species is crucial as it is the basis knowledge of improving its genetic resources which is beneficial for breeding programs. Phylogenetic relationships among 13 mango cultivars from Indonesia, Malaysia and Taiwan were carried out by comparing DNA sequence data sets derived from the Internal Transcribed Spacer (ITS) region pfnuclear ribosomal DNA (nrDNA). Analysis using parsimony method showed that the cultivars were classified into three major groups. The first group composed almost Malaysian cultivars although with low bootstrap value, the second group consisted of mainly Taiwan cultivars and the last group included mostly Indonesia one. The results indicated that some cultivars have a close relationships with each other even it is originated from different countries. With regards to the relationship among these cultivars, this gives better insight for generating new cultivar.
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Affiliation(s)
- Topik Hidayat
- Department of Biology Education, Universitas Pendidikan Indonesia (UPI), Bandung, Indonesia
| | - Shahkila Mohd Arif
- Department of Biological Sciences, Universiti Teknologi Malaysia (UTM), Johor Bahru, Malaysia
| | - Azman Abd Samad
- Department of Biological Sciences, Universiti Teknologi Malaysia (UTM), Johor Bahru, Malaysia
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48
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Genetic analysis of diversity within a Chinese local sugarcane germplasm based on start codon targeted polymorphism. BIOMED RESEARCH INTERNATIONAL 2014; 2014:468375. [PMID: 24779012 PMCID: PMC3980922 DOI: 10.1155/2014/468375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/14/2013] [Accepted: 01/03/2014] [Indexed: 11/17/2022]
Abstract
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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Zhao M, Huang C, Chen Q, Wu X, Qu J, Zhang J. Genetic variability and population structure of the mushroom Pleurotus eryngii var. tuoliensis. PLoS One 2013; 8:e83253. [PMID: 24349475 PMCID: PMC3861475 DOI: 10.1371/journal.pone.0083253] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 10/30/2013] [Indexed: 11/20/2022] Open
Abstract
The genetic diversity of 123 wild strains of Pleurotus eryngii var. tuoliensis, which were collected from nine geographical locations in Yumin, Tuoli, and Qinghe counties in the Xinjiang Autonomous Region of China, was analysed using two molecular marker systems (inter-simple sequence repeat and start codon targeted). At the variety level, the percentage of polymorphic loci and Nei’s gene diversity index for P. eryngii var. tuoliensis was 96.32% and 0.238, respectively. At the population level, Nei’s gene diversity index ranged from 0.149 to 0.218 with an average of 0.186, and Shannon's information index ranged from 0.213 to 0.339 with an average of 0.284. These results revealed the abundant genetic variability in the wild resources of P. eryngii var. tuoliensis. Nei’s gene diversity analysis indicated that the genetic variance was mainly found within individual geographical populations, and the analysis of molecular variance revealed low but significant genetic differentiation among local and regional populations. The limited gene flow (Nm = 1.794) was inferred as a major reason for the extent of genetic differentiation of P. eryngii var. tuoliensis. The results of Mantel tests showed that the genetic distance among geographical populations of P. eryngii var. tuoliensis was positively correlated with the geographical distance and the longitudinal distances (rGo = 0.789 and rLn = 0.873, respectively), which indicates that geographical isolation is an important factor for the observed genetic differentiation. Nine geographical populations of P. eryngii var. tuoliensis were divided into three groups according to their geographical origins, which revealed that the genetic diversity was closely related to the geographical distribution of this wild fungus.
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Affiliation(s)
- Mengran Zhao
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Chenyang Huang
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Qiang Chen
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Xiangli Wu
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Jibin Qu
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Jinxia Zhang
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
- * E-mail:
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50
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Mulpuri S, Muddanuru T, Francis G. Start codon targeted (SCoT) polymorphism in toxic and non-toxic accessions of Jatropha curcas L. and development of a codominant SCAR marker. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 207:117-27. [PMID: 23602106 DOI: 10.1016/j.plantsci.2013.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 02/20/2013] [Accepted: 02/24/2013] [Indexed: 05/11/2023]
Abstract
Thirty six start codon targeted (SCoT) primers were used for characterization of 48 accessions of Jatropha curcas from different countries and include material with genetic variation for levels of phorbol esters, yield, seed oil content, test weight and plant type. SCoT analysis revealed high polymorphism and 74% of the primers generated polymorphic profiles. The SCoT6 primer discriminated edible and toxic accessions in a single reaction while the SCoT26 and 27 primers produced amplicons specific to toxic and non-toxic accessions, respectively. The polymorphic SCoT markers obtained with these three primers were converted to sequence characterized amplicon regions (SCARs) which resulted in codominant SCARs with SCoT6 primer and dominant SCARs with SCoT 26 and 27 primers. The codominant nature of SCoT6 primer and the resultant SCAR6 primer were validated on intraspecific hybrids derived from a cross between non-toxic and toxic accessions. The accession JP38 from Madagascar was found to be distinct and showed accession specific bands with 9 different SCoT primers. Sequence analysis of polymorphic amplicons obtained with SCoT6 primer showed a 65 bp deletion in accessions with low/zero phorbol esters. Diversity analysis separated the toxic and non-toxic accessions into two groups and the accessions JP29 and JP48 from Mexico formed a third cluster.
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Affiliation(s)
- Sujatha Mulpuri
- Crop Improvement Section, Directorate of Oilseeds Research, Rajendranagar, Hyderabad 500030, India.
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