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Weldemichael MY, Gebremedhn HM. Omics technologies towards sesame improvement: a review. Mol Biol Rep 2023; 50:6885-6899. [PMID: 37326753 DOI: 10.1007/s11033-023-08551-w] [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: 02/20/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023]
Abstract
Genetic improvement of sesame (Sesamum indicum L.), one of the most important oilseed crops providing edible oil, proteins, minerals, and vitamins, is important to ensure a balanced diet for the growing world population. Increasing yield, seed protein, oil, minerals, and vitamins is urgently needed to meet the global demand. The production and productivity of sesame is very low due to various biotic and abiotic stresses. Therefore, various efforts have been made to combat these constraints and increase the production and productivity of sesame through conventional breeding. However, less attention has been paid to the genetic improvement of the crop through modern biotechnological methods, leaving it lagging behind other oilseed crops. Recently, however, the scenario has changed as sesame research has entered the era of "omics" and has made significant progress. Therefore, the purpose of this paper is to provide an overview of the progress made by omics research in improving sesame. This review presents a number of efforts that have been made over past decade using omics technologies to improve various traits of sesame, including seed composition, yield, and biotic and abiotic resistant varieties. It summarizes the advances in genetic improvement of sesame using omics technologies, such as germplasm development (web-based functional databases and germplasm resources), gene discovery (molecular markers and genetic linkage map construction), proteomics, transcriptomics, and metabolomics that have been carried out in the last decade. In conclusion, this review highlights future directions that may be important for omics-assisted breeding in sesame genetic improvement.
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Affiliation(s)
- Micheale Yifter Weldemichael
- Department of Biotechnology, College of Dryland Agriculture and Natural Resources, Mekelle University, P.O. Box 231, Mekelle, Tigrai, Ethiopia.
| | - Hailay Mehari Gebremedhn
- Department of Biotechnology, College of Dryland Agriculture and Natural Resources, Mekelle University, P.O. Box 231, Mekelle, Tigrai, Ethiopia
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Mesfer ALshamrani S, Safhi FA, Alshaya DS, Ibrahim AA, Mansour H, Abd El Moneim D. Genetic diversity using biochemical, physiological, karyological and molecular markers of Sesamum indicum L. Front Genet 2022; 13:1035977. [PMID: 36313443 PMCID: PMC9597450 DOI: 10.3389/fgene.2022.1035977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
The genetic diversity and the relationships among sesame cultivars were investigated using physiological and cyto/molecular analysis. To our information, no studies have yet been conducted on the genetic evaluation of sesame genotypes based on cyto/molecular analysis in Saudi Arabia. This study showed that genotype Bah-312 had the highest values from physiological and biochemical traits (plant height, harvest index, total plant dry matter, seed yield, oil content, and fatty acids content). Using 20 ISSR and 25 SCoT primers, the studied genotypes amplified 233 and 275 alleles, while the average polymorphism percentage (P%) was 65.32% (ISSR) and 77.8% (SCoT) across all the studied genotypes, respectively. To assess the markers efficiency analysis the polymorphism information contents (PIC), Marker Index (MI), Effective Multiplex Ratio (EMR), Resolving Power (Rp) were estimated. In general, primers (ISSR 2 & SCoT 21) and (ISSR 4 & SCoT 3) revealed the highest and lowest values for P %, PIC, MI, and EMR%. Furthermore, 188 positive and negative unique bands were detected, out of which ISSR generated 84, while 104 were amplified by SCoT analysis. In this regard, genotype Bah-312 generated 41 unique amplicons, and Jiz-511 genotype 23 unique amplicons. In the same context, the population genetics parameters, number of different alleles (Na), number of effective alleles (Ne), Shannon’s index (I), expected heterozygosity (He), and Unbiased Expected Heterozygosity (uHe), were calculated. ISSR marker showed the highest values for all the estimated parameters. In this regard, genotype Bah-312 exhibited the highest values (1.35, 1.37, 0.31, 0.21, 0.29) & (1.31, 1.35, 0.30, 0.20, 0.27) while, genotype Ahs-670 revealed the least values (1.29, 1.31, 0.26, 0.16, 0.23) &(1.14, 1.26, 0.22, 0.15, 0.20) for ISSR and SCoT markers respectively. For cytological data, according to the highest asymmetry index (AsK%) and lowest total form percentage (TF%) values, genotype Ahs-670 was the most advanced cultivar, and genotype Bah-312 was the most primitive one. According to the degree of asymmetry of karyotype (A) and intrachromosomal asymmetry index (A1), sesame genotype Ahs-670 was the most asymmetrical, and Bah-312 was the most symmetrical genotype. This study gives some helpful information about the genetic diversity of six sesame landraces. The variation harbored by these landraces could be used in sesame breeding programs.
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Affiliation(s)
| | - Fatmah Ahmed Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
- *Correspondence: Fatmah Ahmed Safhi,
| | - Dalal Sulaiman Alshaya
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Amira A. Ibrahim
- Botany and Microbiology Department, Faculty of Science, Arish University, El-Arish, Egypt
| | - Hassan Mansour
- Department of Biological Sciences, College of Science & Arts, King Abdulaziz University, Rabigh, Saudi Arabia
- Botany Department, Faculty of Science, Suez Canal University Ismailia, Ismailia, Egypt
| | - Diaa Abd El Moneim
- Department of Plant Production, (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
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Yadav R, Kalia S, Rangan P, Pradheep K, Rao GP, Kaur V, Pandey R, Rai V, Vasimalla CC, Langyan S, Sharma S, Thangavel B, Rana VS, Vishwakarma H, Shah A, Saxena A, Kumar A, Singh K, Siddique KHM. Current Research Trends and Prospects for Yield and Quality Improvement in Sesame, an Important Oilseed Crop. FRONTIERS IN PLANT SCIENCE 2022; 13:863521. [PMID: 35599863 PMCID: PMC9120847 DOI: 10.3389/fpls.2022.863521] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/16/2022] [Indexed: 06/04/2023]
Abstract
Climate change is shifting agricultural production, which could impact the economic and cultural contexts of the oilseed industry, including sesame. Environmental threats (biotic and abiotic stresses) affect sesame production and thus yield (especially oil content). However, few studies have investigated the genetic enhancement, quality improvement, or the underlying mechanisms of stress tolerance in sesame. This study reveals the challenges faced by farmers/researchers growing sesame crops and the potential genetic and genomic resources for addressing the threats, including: (1) developing sesame varieties that tolerate phyllody, root rot disease, and waterlogging; (2) investigating beneficial agro-morphological traits, such as determinate growth, prostrate habit, and delayed response to seed shattering; (3) using wild relatives of sesame for wide hybridization; and (4) advancing existing strategies to maintain sesame production under changing climatic conditions. Future research programs need to add technologies and develop the best research strategies for economic and sustainable development.
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Affiliation(s)
- Rashmi Yadav
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi, India
| | - Parimalan Rangan
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - K. Pradheep
- National Bureau of Plant Genetic Resources, Thrissur, India
| | - Govind Pratap Rao
- Indian Agricultural Research Institute, Pusa Campus, New Delhi, India
| | - Vikender Kaur
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Renu Pandey
- Indian Agricultural Research Institute, Pusa Campus, New Delhi, India
| | - Vandna Rai
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | | | - Sapna Langyan
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Sanjula Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Punjab, India
| | - Boopathi Thangavel
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | | | - Anshuman Shah
- National Institute for Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Abhishek Saxena
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Ashok Kumar
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Kuldeep Singh
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Kadambot H. M. Siddique
- The UWA School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia (UWA), Perth, WA, Australia
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Berhe M, Dossa K, You J, Mboup PA, Diallo IN, Diouf D, Zhang X, Wang L. Genome-wide association study and its applications in the non-model crop Sesamum indicum. BMC PLANT BIOLOGY 2021; 21:283. [PMID: 34157965 PMCID: PMC8218510 DOI: 10.1186/s12870-021-03046-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/17/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sesame is a rare example of non-model and minor crop for which numerous genetic loci and candidate genes underlying features of interest have been disclosed at relatively high resolution. These progresses have been achieved thanks to the applications of the genome-wide association study (GWAS) approach. GWAS has benefited from the availability of high-quality genomes, re-sequencing data from thousands of genotypes, extensive transcriptome sequencing, development of haplotype map and web-based functional databases in sesame. RESULTS In this paper, we reviewed the GWAS methods, the underlying statistical models and the applications for genetic discovery of important traits in sesame. A novel online database SiGeDiD ( http://sigedid.ucad.sn/ ) has been developed to provide access to all genetic and genomic discoveries through GWAS in sesame. We also tested for the first time, applications of various new GWAS multi-locus models in sesame. CONCLUSIONS Collectively, this work portrays steps and provides guidelines for efficient GWAS implementation in sesame, a non-model crop.
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Affiliation(s)
- Muez Berhe
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
- Humera Agricultural Research Center of Tigray Agricultural Research Institute, Humera, Tigray, Ethiopia
| | - Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China.
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal.
- Laboratory of Genetics, Horticulture and Seed Sciences, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526, Cotonou, Republic of Benin.
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Pape Adama Mboup
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Idrissa Navel Diallo
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, 10700, Dakar, Senegal
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, and Rural Affairs, No.2 Xudong 2nd Road, Wuhan, 430062, China.
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Basak M, Uzun B, Yol E. Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq. PLoS One 2019; 14:e0223757. [PMID: 31600316 PMCID: PMC6786593 DOI: 10.1371/journal.pone.0223757] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022] Open
Abstract
The Mediterranean sesame core collection contains agro-morphologically superior sesame accessions from geographically diverse regions in four continents. In the present investigation, the genetic diversity and population structure of this collection was analyzed with 5292 high-quality SNPs discovered by double-digest restriction site associated DNA (ddRAD) sequencing, a cost-effective and flexible next-generation sequencing method. The genetic distance between pairs of accessions varied from 0.023 to 0.524. The gene diversity was higher in accessions from Asia than from America, Africa, and Europe. The highest genetic differentiation was observed between accessions collected from America and Europe. Structure analysis showed the presence of three subpopulations among the sesame accessions, and only six accessions were placed in an admixture group. Phylogenetic tree and principal coordinate analysis clustered the accessions based on their countries of origin. However, no clear division was evident among the sesame accessions with regard to their continental locations. This result was supported by an AMOVA analysis, which revealed a genetic variation among continental groups of 5.53% of the total variation. The large number of SNPs clearly indicated that the Mediterranean sesame core collection is a highly diverse genetic resource. The collection can be exploited by breeders to select appropriate accessions that will provide high genetic gain in sesame improvement programs. The high-quality SNP data generated here should also be used in genome-wide association studies to explore qualitative trait loci and SNPs related to economically and agronomically important traits in sesame.
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Affiliation(s)
- Merve Basak
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Bulent Uzun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Engin Yol
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
- * E-mail:
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Genetic diversity and population structure of Cucumis sativus L. by using SSR markers. 3 Biotech 2017; 7:307. [PMID: 28955604 DOI: 10.1007/s13205-017-0944-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022] Open
Abstract
The genetic variation, marker attributes and population structure was assessed in 104 genotypes of cucumber using 23 SSR primer pairs. The total number of alleles produced was 67 with an average of 2.91 per locus. Allele frequency was in the range of 0.215 to 0.561 with mean value of 0.403, polymorphic information content ranged from 0.158 to 0.495 with the mean of 0.333, marker index ranged from 0.316 to 1.54 with an average value of 0.954 and resolving power ranged from 0.346 to 2.692 with mean of 1.392. The maximum allele frequency was reported with primer SSR65, whereas the maximum value of polymorphic information content and resolving power was found with SSR61 and the maximum value of marker index was reported with SSR60. Jaccard's similarity coefficient ranged from 0.07 to 0.897 with maximum similarity between genotype G40 and G41 and minimum between G16 and G20, and G16 and G100. Clustering and PCA grouped the genotypes in two clusters, and majority of them were found in cluster B. The population structure analysis also showed two major populations, in which 47 genotypes were found in population 1, 39 genotypes in population 2, whereas remaining 18 genotypes were admixtures. The study provides researchers a valuable information for genotype identification, gene mapping, molecular breeding, and future exploration of cucumber germplasm in India and other major cucumber growing countries.
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