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Gogoi A, Munda S, Paw M, Begum T, Siddiqui MH, Gaafar ARZ, Kesawat MS, Lal M. Molecular genetic divergence analysis amongst high curcumin lines of Golden Crop (Curcuma longa L.) using SSR marker and use in trait-specific breeding. Sci Rep 2023; 13:19690. [PMID: 37952010 PMCID: PMC10640617 DOI: 10.1038/s41598-023-46779-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 11/04/2023] [Indexed: 11/14/2023] Open
Abstract
Curcuma longa L., is recognized worldwide as a medicinally and economically important plant species due to its curcumin content which is an industrially important compound. In this study, a total of 329 accessions were collected from four states of India and planted in the experimental farm of CSIR-NEIST, Jorhat, India, in augmented design. Among these, 152 high curcumin (> 1.50%) accessions were screened for molecular divergence study using 39 SSR primers. The primers showed the most efficient outcome with 2-8 allele/ loci and a total 163 number of alleles with 100% polymorphism. Cluster analysis revealed the construction of three clusters, out of which one cluster was geographically dependent, and germplasm was particularly from Assam state. Jaccard's pairwise coefficient showed maximum genetic dissimilarity of (0.75) between accession RRLJCL 3 and RRLJCL 126, indicating high variation as it was from two different states viz Arunachal Pradesh and Nagaland respectively and minimum genetic dissimilarity of (0.09) between RRLJCL 58 and RRLJCL 59 indicating significantly less variation as the two accessions were from same state, i.e., Arunachal Pradesh. Analysis of Molecular Variance (AMOVA) revealed high molecular variation within the population (87%) and significantly less variation among the population (13%). Additionally, Neighbour Joining dendrogram, Principal Component Analysis (PCA), and bar plot structure revealed similar clustering of germplasm. This diversity assessment will help in selecting the trait-specific genotypes, crop improvement program, conservation of gene pool, marker-assisted breeding, and quantitative trait loci identification. Moreover, to the best of our knowledge, it is the first molecular diversity report among 152 high curcumin lines of C. longa from North East India using 39 SSR primers.
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Affiliation(s)
- Anindita Gogoi
- Academy of Scientific and Industrial Research, Ghaziabad, UP, 201002, India
- CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Sunita Munda
- CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Manabi Paw
- CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Twahira Begum
- CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India.
| | - Manzer H Siddiqui
- 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
| | - Mahipal Singh Kesawat
- Institute for Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Mohan Lal
- Academy of Scientific and Industrial Research, Ghaziabad, UP, 201002, India.
- CSIR-North East Institute of Science and Technology, Jorhat, Assam, 785006, India.
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Kadoglidou K, Cook C, Boutsika A, Sarrou E, Mellidou I, Aidonidou C, Grigoriadis I, Angeli A, Martens S, Georgiadou V, Moysiadis T, Ralli P, Mylonas I, Tourvas N, Michailidis M, Kalivas A, Maloupa E, Ganopoulos I, Xanthopoulou A. Evaluation of a dill ( Anethum graveolens L.) gene bank germplasm collection using multivariate analysis of morphological traits, molecular genotyping and chemical composition to identify novel genotypes for plant breeding. PeerJ 2023; 11:e15043. [PMID: 37013148 PMCID: PMC10066692 DOI: 10.7717/peerj.15043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/21/2023] [Indexed: 03/31/2023] Open
Abstract
Dill (Anethum graveolens L.) is an aromatic herb widely used in the food industry, with several commercial cultivars available with different qualitative characteristics. Commercial cultivars are usually preferred over landraces due to their higher yield and also the lack of improved landraces than can be commercialized. In Greece, however, traditional dill landraces are cultivated by local communities. Many are conserved in the Greek Gene Bank and the aim here was to investigate and compare the morphological, genetic, and chemical biodiversity of twenty-two Greek landraces and nine modern/commercial cultivars. Multivariate analysis of the morphological descriptors, molecular markers, and essential oil and polyphenol composition revealed that the Greek landraces were clearly distinguished compared with modern cultivars at the level of phenological, molecular and chemical traits. Landraces were typically taller, with larger umbels, denser foliage, and larger leaves. Plant height, density of foliage, density of feathering as well as aroma characteristics were desirable traits observed for some landraces, such as T538/06 and GRC-1348/04, which were similar or superior to those of some commercial cultivars. Polymorphic loci for inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) molecular markers were 76.47% and 72.41% for landraces, and 68.24% and 43.10% for the modern cultivars, respectively. Genetic divergence was shown, but not complete isolation, indicating that some gene flow may have occurred between landraces and cultivars. The major constituent in all dill leaf essential oils was α-phellandrene (54.42–70.25%). Landraces had a higher α-phellandrene and dill ether content than cultivars. Two dill landraces were rich in chlorogenic acid, the main polyphenolic compound determined. The study highlighted for the first-time Greek landraces with desirable characteristics regarding quality, yield, and harvest time suitable for breeding programs to develop new dill cultivars with superior features.
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Affiliation(s)
- Kalliopi Kadoglidou
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Catherine Cook
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Anastasia Boutsika
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Eirini Sarrou
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Ifigeneia Mellidou
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Christina Aidonidou
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Ioannis Grigoriadis
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Andrea Angeli
- Fondazione Edmund Mach, Center of Research and Innovation, San Michele all’Adige, Trento, Italy
| | - Stefan Martens
- Fondazione Edmund Mach, Center of Research and Innovation, San Michele all’Adige, Trento, Italy
| | - Vasiliki Georgiadou
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Theodoros Moysiadis
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
- Department of Computer Science, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
| | - Parthenopi Ralli
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Ioannis Mylonas
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Nikolaos Tourvas
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Michail Michailidis
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Apostolos Kalivas
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Eleni Maloupa
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Ioannis Ganopoulos
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
| | - Aliki Xanthopoulou
- ELGO DIMITRA, Institute of Plant Breeding and Genetic Resources, Thessaloniki, Greece
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Zhu Y, Liang D, Song Z, Tan Y, Guo X, Wang D. Genetic Diversity Analysis and Core Germplasm Collection Construction of Camellia oleifera Based on Fruit Phenotype and SSR Data. Genes (Basel) 2022; 13:genes13122351. [PMID: 36553618 PMCID: PMC9777545 DOI: 10.3390/genes13122351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Many Camellia oleifera germplasm resources were collected from Guizhou Province, but the fruit morphological variation and genetic diversity of C. oleifera germplasm resources remain unclear. The genetic diversity of C. oleifera germplasms resources in Guizhou was studied based on fruit traits and simple sequence repeat (SSR) molecular markers to build a core collection. This paper aims to provide a scientific basis for the collection, management, development, and utilization of C. oleifera resources in Guizhou province. The variation coefficients among and within varieties of seven fruit phenotypic traits of C. oleifera ranged from 11.79% to 61.76% and from 8.15% to 42.31%, respectively, showing rich phenotypic variation. Furthermore, 12 SSR markers were used to analyze the genetic diversity. These primers generated 214 polymorphic bands, and the average number was 17.833. The average number of effective alleles (Ne), Shannon's information index (I), observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), and major allele frequency (MAF) were 8.999, 2.301, 0.965, 0.50, 0.836, and 0.238, respectively. The results showed that 12 SSR markers had high polymorphism, and the genetic diversity of 167 C. oleifera germplasm resources was high. Based on SSR molecular marker information and fruit traits clustering, 167 C. oleifera germplasm resources were divided into three groups. When constructing core collections based on fruit traits and molecular marker information, the PowerCore-25 of core collections greatly preserves fruit traits and improves genetic diversity. This paper can provide a reference for the genetic diversity and fruit traits variation of C. camellia germplasm resources in Guizhou Province. It is significant for establishing a core collection, thus promoting germplasm innovation and the development of the oil tea industry in Guizhou.
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Affiliation(s)
- Yunzheng Zhu
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Deyang Liang
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Zejun Song
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Yi Tan
- College of Forestry, Guizhou University, Guiyang 550025, China
| | - Xiaolan Guo
- College of Life Sciences, Huizhou University, Huizhou 516007, China
| | - Delu Wang
- College of Forestry, Guizhou University, Guiyang 550025, China
- Correspondence:
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Safhi FA, ALshamrani SM, Jalal AS, El-Moneim DA, Alyamani AA, Ibrahim AA. Genetic Characterization of Some Saudi Arabia's Accessions from Commiphora gileadensis Using Physio-Biochemical Parameters, Molecular Markers, DNA Barcoding Analysis and Relative Gene Expression. Genes (Basel) 2022; 13:2099. [PMID: 36421774 PMCID: PMC9690626 DOI: 10.3390/genes13112099] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/29/2022] [Accepted: 11/07/2022] [Indexed: 09/02/2023] Open
Abstract
Commiphora gileadensis L. is a medicinal plant, known as balsam, with pharmaceutical potential for its phytochemical activities and chemical constituents. Genetic diversity is a genetic tool used in medicinal plant evolution and conservation. Three accessions from C. gileadensis were collected from three localities in Saudi Arabia (Jeddah, Jizan and Riyadh). Genetic characterization was carried out using physio-biochemical parameters, molecular markers (inter-simple sequence repeat (ISSR) and start codon targeted (SCoT)), DNA barcoding (18 S rRNA and ITS rDNA regions), relative gene expressions (phenylalanine ammonia-lyase 1 (PAL1), defensin (PR-12)) and pathogenesis-related protein (AFPRT). The results of this study showed that C. gileadensis accession C3, collected from Riyadh, had the highest content from the physio-biochemical parameters perspective, with values of 92.54 mg/g and 77.13 mg/g for total phenolic content (TPC) and total flavonoid content (TFC), respectively. Furthermore, the highest content of antioxidant enzyme activity was present in accession C3 with values of 16.87, 60.87, 35.76 and 27.98 U mg-1 for superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) (mol/min/mg FW) and ascorbate peroxidase (APX) (U mg-1 protein), respectively. The highest total number of bands and number of unique bands were 138 and 59, respectively, for the SCoT marker. The SCoT marker was the most efficient for the genetic diversity of C. gileadensis by producing the highest polymorphism (75.63%). DNA barcoding using 18 S and ITS showed the nearby Commiphora genus and clustered C. gileadensis accessions from Jeddah and Jizan in one clade and the C. gileadensis accession from Ryiadh in a separate cluster. Moreover, relative gene expression of the PAL1, defensin (PR-12) and AFPRT (PR1) genes was upregulated in the C. gileadensis accession from Ryiadh. In conclusion, ecological and environmental conditions in each locality affect the genomic expression and genetic diversity, which can help the evolution of important medicinal plants and improve breeding and conservation systems.
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Affiliation(s)
- Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | | | - Areej Saud Jalal
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production(Genetic Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Amal A. Alyamani
- Department of Biotechnology, Faculty of Science, Taif University, Taif 21974, Saudi Arabia
| | - Amira A. Ibrahim
- Botany and Microbiology Department, Faculty of Science, Arish University, El-Arish 45511, Egypt
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