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Elshafei AA, Ibrahim EI, Abdellatif KF, Salem AEAK, Moustafa KA, Al-Doss AA, Migdadi HM, Hussien AM, Soufan W, Abd El Rahman T, Eldemery SM. Molecular and agro-morphological characterization of new barley genotypes in arid environments. BMC Biotechnol 2024; 24:41. [PMID: 38862994 PMCID: PMC11167802 DOI: 10.1186/s12896-024-00861-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Genetic diversity, population structure, agro-morphological traits, and molecular characteristics, are crucial for either preserving genetic resources or developing new cultivars. Due to climate change, water availability for agricultural use is progressively diminishing. This study used 100 molecular markers (25 TRAP, 22 SRAP, 23 ISTR, and 30 SSR). Additionally, 15 morphological characteristics were utilized to evaluate the optimal agronomic traits of 12 different barley genotypes under arid conditions. RESULTS Substantial variations, ranging from significant to highly significant, were observed in the 15 agromorphological parameters evaluated among the 12 genotypes. The KSU-B101 barley genotype demonstrated superior performance in five specific traits: spike number per plant, 100-grain weight, spike number per square meter, harvest index, and grain yield. These results indicate its potential for achieving high yields in arid regions. The Sahrawy barley genotype exhibited the highest values across five parameters, namely leaf area, spike weight per plant, spike length, spike weight per square meter, and biological yield, making it a promising candidate for animal feed. The KSU-B105 genotype exhibited early maturity and a high grain count per spike, which reflects its early maturity and ability to produce a high number of grains per spike. This suggests its suitability for both animal feed and human food in arid areas. Based on marker data, the molecular study found that the similarity coefficients between the barley genotypes ranged from 0.48 to 0.80, with an average of 0.64. The dendrogram constructed from these data revealed three distinct clusters with a similarity coefficient of 0.80. Notably, the correlation between the dendrogram and its similarity matrix was high (0.903), indicating its accuracy in depicting the genetic relationships. The combined analysis revealed a moderate correlation between the morphological and molecular analysis, suggesting alignment between the two characterization methods. CONCLUSIONS The morphological and molecular analyses of the 12 barley genotypes in this study effectively revealed the varied genetic characteristics of their agro-performance in arid conditions. KSU-B101, Sahrawy, and KSU-B105 have emerged as promising candidates for different agricultural applications in arid regions. Further research on these genotypes could reveal their full potential for breeding programs.
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Affiliation(s)
- Adel A Elshafei
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Research Institute, National Research Center, Dokki, Giza, 12622, Egypt.
| | - Eid I Ibrahim
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Kamal F Abdellatif
- Plant Biotechnology Department, Genetic Engineering & Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat, Egypt
| | - Abd El-Azeem K Salem
- Field Crops Research Department, Agricultural and Biological Research Institute, National Research Center, Dokki, Giza, 12622, Egypt
| | - Khaled A Moustafa
- Barley Research Department, Field Crops Research Institute, Agricultural Research Center, Giza, 12619, Egypt
| | - Abdullah A Al-Doss
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Hussein M Migdadi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Amal M Hussien
- Genetic Resources Research Department, Field Crops Research Institute, Agricultural Research Center, Giza, 12619, Egypt
| | - Walid Soufan
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Taha Abd El Rahman
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Samah M Eldemery
- Molecular Biology Department, Genetic Engineering & Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat, Egypt
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Bokaei AS, Sofalian O, Sorkhilalehloo B, Asghari A, Pour-Aboughadareh A. Deciphering the level of genetic diversity in some aegilops species using CAAT box-derived polymorphism (CBDP) and start codon target polymorphism (SCoT) markers. Mol Biol Rep 2023:10.1007/s11033-023-08488-0. [PMID: 37219668 DOI: 10.1007/s11033-023-08488-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Maintaining genetic diversity is of the most essential principle for a long-term conservation of plant genetic resources and could play a crucial role in their management. The genus Aegilops is one important member of wheat germplasm, and there are evidences that novel genes of this genus' species can be studied/utilized as ideal sources for the wheat cultivar improvement. The objective of this study was to dissect the genetic diversity and population structure among a set of Iranian Aegilops using two gene-based molecular markers. METHODS AND RESULTS This study investigated the level of genetic diversity among 157 Aegilops accessions consisting of Ae. tauschii Coss. (DD genome), Ae. crassa Boiss. (DDMM genome), and Ae. cylindrica Host. (CCDD genome) belonging to NPGBI using two sets of CBDP and SCoT markers. The SCoT and CBDP primers yielded 171 and 174 fragments, out of which 145 (90.23%) and 167 (97.66%) fragments were polymorphic, respectively. The average of polymorphism information content (PIC)/ marker index (MI)/resolving power (Rp) for SCoT and CBDP markers were 0.32/3.59/16.03 and 0.29/3.01/16.26, respectively. Results of AMOVA revealed the genetic variability within species was greater than the variation observed among them (SCoT: 88% vs. 12%; CBDP: 72% vs. 28%; SCoT + CBDP: 80% vs. 20%). Based on the information obtained from both markers, the higher level of genetic diversity was found in Ae. tauschii as compared to other species. The grouping patterns obtained by Neighbor-joining algorithms, principal coordinate analysis (PCoA), and Bayesian-model-based structure were consistent with each other and resulted in grouping all studied accessions according to their genomic constitutions. CONCLUSION The results of this study revealed a high level of genetic diversity among Iranian Aegilops germplasm. Moreover, SCoT and CBDP marker systems were efficient in deciphering DNA polymorphism and classification of Aegilops germplasm.
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Affiliation(s)
- Ali Sajjad Bokaei
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Omid Sofalian
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Behzad Sorkhilalehloo
- Seed and Plant Improvement Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Ali Asghari
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Alireza Pour-Aboughadareh
- Seed and Plant Improvement Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.
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Salah A, El-Khateeb EA, Gaafar RM, Mohamed Atia MA. Genome-wide in silico and in vitro mining to develop a novel cyclotide-based marker system in plants. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2023.2176175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Affiliation(s)
- Arwa Salah
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | | | | | - Mohamed Atia Mohamed Atia
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
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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] [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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