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Takvorian N, Zangui H, Naino Jika AK, Alouane A, Siljak-Yakovlev S. Genome Size Variation in Sesamum indicum L. Germplasm from Niger. Genes (Basel) 2024; 15:711. [PMID: 38927647 PMCID: PMC11203198 DOI: 10.3390/genes15060711] [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: 04/30/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Sesamum indicum L. (Pedaliaceae) is one of the most economically important oil crops in the world, thanks to the high oil content of its seeds and its nutritional value. It is cultivated all over the world, mainly in Asia and Africa. Well adapted to arid environments, sesame offers a good opportunity as an alternative subsistence crop for farmers in Africa, particularly Niger, to cope with climate change. For the first time, the variation in genome size among 75 accessions of the Nigerien germplasm was studied. The sample was collected throughout Niger, revealing various morphological, biochemical and phenological traits. For comparison, an additional accession from Thailand was evaluated as an available Asian representative. In the Niger sample, the 2C DNA value ranged from 0.77 to 1 pg (753 to 978 Mbp), with an average of 0.85 ± 0.037 pg (831 Mbp). Statistical analysis showed a significant difference in 2C DNA values among 58 pairs of Niger accessions (p-value < 0.05). This significant variation indicates the likely genetic diversity of sesame germplasm, offering valuable insights into its possible potential for climate-resilient agriculture. Our results therefore raise a fundamental question: is intraspecific variability in the genome size of Nigerien sesame correlated with specific morphological and physiological traits?
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Affiliation(s)
- Najat Takvorian
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, 91190 Gif-sur-Yvette, France;
- Sorbonne Université, UFR Sciences de la Vie, UFR927, 4 Place Jussieu, F-75005 Paris Cedex 05, France
| | - Hamissou Zangui
- Department of Plant Production, Abdou Moumouni University, BP-10960 Niamey, Niger; (H.Z.); (A.K.N.J.)
| | - Abdel Kader Naino Jika
- Department of Plant Production, Abdou Moumouni University, BP-10960 Niamey, Niger; (H.Z.); (A.K.N.J.)
| | - Aïda Alouane
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, 91190 Gif-sur-Yvette, France;
- Sorbonne Université, UFR Sciences de la Vie, UFR927, 4 Place Jussieu, F-75005 Paris Cedex 05, France
| | - Sonja Siljak-Yakovlev
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, 91190 Gif-sur-Yvette, France;
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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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Feng X, Li G, Wu W, Lyu H, Wang J, Liu C, Zhong C, Shi S, He Z. Expansion and adaptive evolution of the WRKY transcription factor family in Avicennia mangrove trees. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:155-168. [PMID: 37275537 PMCID: PMC10232687 DOI: 10.1007/s42995-023-00177-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 04/26/2023] [Indexed: 06/07/2023]
Abstract
Mangroves are adapted to intertidal zones, which present extreme environmental conditions. WRKYs are among the most prominent transcription factors (TFs) in higher plants and act through various interconnected networks to regulate responses to multiple abiotic stressors. Here, based on omic data, we investigated the landscape and evolutionary patterns of WRKYs in the main mangrove genus Avicennia. We found that both the number and the proportion of TFs and WRKYs in Avicennia species exceeded their inland relatives, indicating a significant expansion of WRKYs in Avicennia. We identified 109 WRKY genes in the representative species Avicennia marina. Comparative genomic analysis showed that two recent whole-genome duplication (WGD) events played a critical role in the expansion of WRKYs, and 88% of Avicennia marina WRKYs (AmWRKYs) have been retained following these WGDs. Applying comparative transcriptomics on roots under experimental salt gradients, we inferred that there is high divergence in the expression of WGD-retained AmWRKYs. Moreover, we found that the expression of 16 AmWRKYs was stable between freshwater and moderately saline water but increased when the trees were exposed to high salinity. In particular, 14 duplicates were retained following the two recent WGD events, indicating potential neo- and sub-functionalization. We also found that WRKYs could interact with other upregulated genes involved in signalling pathways and natural antioxidant biosynthesis to enhance salt tolerance, contributing to the adaptation to intertidal zones. Our omic data of the WRKY family in A. marina broadens the understanding of how a TF family relates to the adaptive evolution of mangroves. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00177-y.
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Affiliation(s)
- Xiao Feng
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458 China
| | - Guohong Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Weihong Wu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Haomin Lyu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Jiexin Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Cong Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100 China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510275 China
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Kefale H, Wang L. Discovering favorable genes, QTLs, and genotypes as a genetic resource for sesame ( Sesamum indicum L.) improvement. Front Genet 2022; 13:1002182. [PMID: 36544489 PMCID: PMC9763032 DOI: 10.3389/fgene.2022.1002182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/03/2022] [Indexed: 12/12/2022] Open
Abstract
Sesame (Sesamum indicum L.) is an ancient diploid oilseed crop with high oil content, quality protein, and antioxidant characteristics that is produced in many countries worldwide. The genes, QTLs, and genetic resources of sesame are utilized by sesame researchers and growers. Researchers have identified the many useful traits of this crop, which are available on different platforms. The genes, genotypes, QTLs, and other genetic diversity data of sesame have been collected and stored in more than nine genomic resources, and five sesame crop marker databases are available online. However, data on phenotypic and genotypic variability, which would contribute to sesame improvements, are limited and not yet accessible. The present study comprehensively reviewed more than 110 original published research papers and scientifically incorporated the results. The candidate genes, genotypes, and QTLs of significantly important traits of sesame were identified. Genetic resources related to grain yield and yield component traits, oil content and quality, drought tolerance, salt tolerance, waterlogging resistance, disease resistance, mineral nutrient, capsule shattering resistance, and other agronomic important traits of sesame were studied. Numerous candidate genotypes, genes, QTLs, and alleles associated with those traits were summarized and discovered. The chromosome regions and linkage groups, maps associated with the best traits, and candidate genes were also included. The variability presented in this paper combined with sesame genetic information will help inform further sesame improvement.
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Affiliation(s)
- Habtamu Kefale
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China,Department of Plant Science, College of Agriculture and Natural Resources, Debre Markos University, Debre Markos, Ethiopia,*Correspondence: Habtamu Kefale,
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Insight into gene regulatory networks involved in sesame (Sesamum indicum L.) drought response. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Andargie M, Congyi Z. Genome-wide analysis of codon usage in sesame ( Sesamum indicum L.). Heliyon 2022; 8:e08687. [PMID: 35106386 PMCID: PMC8789531 DOI: 10.1016/j.heliyon.2021.e08687] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/20/2021] [Accepted: 12/24/2021] [Indexed: 10/28/2022] Open
Abstract
Sesamum indicum is an ancient oil crop grown in tropical and subtropical areas of the world. We have analyzed 23,538 coding sequences (CDS) of S. indicum to understand the factors shaping codon usage in this important oil crop plant. We identified eleven highly preferred codons in S. indicum that have AT-endings. The slope of a neutrality plot was less than one while effective number of codons (ENC) plot showed distribution above and below the standard curve. There is a significant relationship between protein length and relative synonymous codon usage (RSCU) at the primary axis while there is a weak correlation between protein length and Nc values. Correspondence analysis conducted on RSCU values differentiated CDS based on their GC content and their characteristic feature and showed a discrete distribution. Moreover, by determining codon usage, we found out that majority of the lignan biosynthesis related genes showed a weaker codon usage bias. These results provide insights into understanding codon evolution in sesame.
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Affiliation(s)
- Mebeaselassie Andargie
- University of Goettingen, Molecular Phytopathology and Mycotoxin Research, Grisebachstrasse 6, 37077 Goettingen, Germany
| | - Zhu Congyi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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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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Dutta D, Prasad R, Gangopadhyay G. Inter-specific hybrid sesame with high lignan content in oil reveals increased expression of sesamin synthase gene. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00354-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Garewal N, Goyal N, Pathania S, Kaur J, Singh K. Gauging the trends of pseudogenes in plants. Crit Rev Biotechnol 2021; 41:1114-1129. [PMID: 33993808 DOI: 10.1080/07388551.2021.1901648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pseudogenes, the debilitated parts of ancient genes, were previously scrapped off as junk or discarded genes with no functional significance. Pseudogenes have come under scrutiny for their functionality, since recent studies have unveiled their importance in the regulation of their corresponding parent genes and various biological mechanisms. Despite the enormous occurrence of pseudogenes in plants, the lack of experimental validation has contributed toward their unresolved roles in gene regulation. Contrarily, most of the studies associated with gene regulation have been mainly reported for humans, mice, and other mammalian genomes. Consequently, in order to present a cumulative report on plant-based pseudogenes research, an attempt has been made to assemble multiple studies presenting the pseudogene classification, the prediction and the determination of comparative accuracies of various computational pipelines, and recent trends in analyzing their biological functions, and regulatory mechanisms. This review represents the classical, as well as the recent advances on pseudogene identification and their potential roles in transcriptional regulation, which could possibly invigorate the quality of genome annotation, evolutionary analysis, and complexity surrounding the regulatory pathways in plants. Thus, when the ambiguous boundary girdling the pseudogenes eventually recedes on account of their explicit orchestration role, research in flora would no longer saunter compared to that on fauna.
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Affiliation(s)
- Naina Garewal
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Neetu Goyal
- Department of Biotechnology, Panjab University, Chandigarh, India
| | | | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
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Asekova S, Oh E, Kulkarni KP, Siddique MI, Lee MH, Kim JI, Lee JD, Kim M, Oh KW, Ha TJ, Kim SU, Cho KS. An Integrated Approach of QTL Mapping and Genome-Wide Association Analysis Identifies Candidate Genes for Phytophthora Blight Resistance in Sesame ( Sesamum indicum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:604709. [PMID: 33664756 PMCID: PMC7920980 DOI: 10.3389/fpls.2021.604709] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/11/2021] [Indexed: 05/05/2023]
Abstract
Phytophthora blight (PB) caused by Phytophthora nicotianae is a highly destructive disease in sesame (Sesamum indicum L.). In this study, we used linkage mapping and genome-wide association study (GWAS) to identify quantitative trait loci (QTL) and candidate genes associated with PB resistance. The QTL mapping in 90 RILs of the Goenbaek × Osan cross using genotyping-by-sequencing detected significant QTLs for PB resistance on chromosome 10, explaining 12.79%-13.34% of phenotypic variation. Association of this locus to PB resistance was also revealed through bulked segregant analysis in second RIL population (Goenbaek × Milsung cross) comprising 188 RILs. The GWAS of 87 sesame accessions evaluated against three P. nicotianae isolates identified 29 SNPs on chromosome 10 significantly associated with PB resistance. These SNPs were located within a 0.79 Mb region, which co-located with the QTL intervals identified in RIL populations, and hence scanned for identifying candidate genes. This region contained several defense-related candidate R genes, five of which were selected for quantitative expression analysis. One of these genes, SIN_1019016 was found to show significantly higher expression in the resistant parent compared to that in the susceptible parents and selected RILs. Paired-end sequencing of the gene SIN_1019016 in parental cultivars revealed two synonymous SNPs between Goenbaek and Osan in exon 2 of coding DNA sequence. These results suggested SIN_1019016 as one of the candidate gene conferring PB resistance in sesame. The findings from this study will be useful in the marker-assisted selection as well as the functional analysis of PB resistance candidate gene(s) in sesame.
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Affiliation(s)
- Sovetgul Asekova
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang-si, South Korea
| | - Eunyoung Oh
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang-si, South Korea
| | | | - Muhammad Irfan Siddique
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Myoung Hee Lee
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang-si, South Korea
| | - Jung In Kim
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang-si, South Korea
| | - Jeong-Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Minsu Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Ki-Won Oh
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang-si, South Korea
| | - Tae-Joung Ha
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang-si, South Korea
| | - Sung-Up Kim
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang-si, South Korea
| | - Kwang-Soo Cho
- Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang-si, South Korea
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Wang L, Yu J, Zhang Y, You J, Zhang X, Wang L. Sinbase 2.0: An Updated Database to Study Multi-Omics in Sesamum indicum. PLANTS 2021; 10:plants10020272. [PMID: 33573226 PMCID: PMC7911383 DOI: 10.3390/plants10020272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 11/16/2022]
Abstract
Sesame is one of the oldest oil crops in the world and is widely grown in the tropical and subtropical areas of Asia, Africa and America. Upon the completion of the sesame reference genome version 1.0, we launched Sinbase 1.0 as an integrated database for genomic and bioinformatics analyses. Recently, an upgraded version (version 2.0) of the genome sequence was released. In addition, large numbers of multi-omics data have been generated on sesame, but a comprehensive database that integrates these resources for the community has been lacking until now. Here, we developed an interactive and comprehensive sesame multi-omics database, Sinbase 2.0, which provides information of the sesame updated genome containing 13 chromosomes, 3 genetic linkage maps, 5 intra- and 6 inter-species comparative genomics, 1 genomic variation analysis, 5 transcriptome data, 1 proteome, 31 functional markers, 175 putative functional genes, and 54 QTLs detected for important agronomic traits. Moreover, Sinbase 2.0 has been enriched with novel user-friendly computational tools. All datasets of Sinbase 2.0 can be downloaded online conveniently. Sinbase 2.0 will be updated regularly with new available sesame multi-omics data and can be accessed freely via Sinbase 2.—Sesame Muti-Omics Database. We expect that Sinbase 2.0, similarly to the previous version, will continue to make a major contribution to advance sesame research towards a better understanding of its biology and genetic improvement, as well as comparative genomics and evolutionary biology.
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Affiliation(s)
- Liwen Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, No.2 Xudong Second Road, Wuhan 430062, China; (L.W.); (J.Y.); (Y.Z.); (J.Y.); (X.Z.)
- Shandong Luyan Agricultural Co., LTC, Jinan 250100, China
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, No.2 Xudong Second Road, Wuhan 430062, China; (L.W.); (J.Y.); (Y.Z.); (J.Y.); (X.Z.)
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, No.2 Xudong Second Road, Wuhan 430062, China; (L.W.); (J.Y.); (Y.Z.); (J.Y.); (X.Z.)
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, No.2 Xudong Second Road, Wuhan 430062, China; (L.W.); (J.Y.); (Y.Z.); (J.Y.); (X.Z.)
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, No.2 Xudong Second Road, Wuhan 430062, China; (L.W.); (J.Y.); (Y.Z.); (J.Y.); (X.Z.)
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, No.2 Xudong Second Road, Wuhan 430062, China; (L.W.); (J.Y.); (Y.Z.); (J.Y.); (X.Z.)
- Correspondence:
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Kazemitabar SK, Faraji S, Najafi-Zarrini H. Identification and in silico evaluation of bHLH genes in the Sesamum indicum genome: Growth regulation and stress dealing specially through the metal ions homeostasis and flavonoid biosynthesis. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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13
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Rong S, Wu Z, Cheng Z, Zhang S, Liu H, Huang Q. Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive ( Olea europaea L.). Genes (Basel) 2020; 11:genes11050510. [PMID: 32380769 PMCID: PMC7288668 DOI: 10.3390/genes11050510] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/25/2020] [Accepted: 05/01/2020] [Indexed: 12/17/2022] Open
Abstract
Olive (Olea europaea.L) is an economically important oleaginous crop and its fruit cold-pressed oil is used for edible oil all over the world. The basic region-leucine zipper (bZIP) family is one of the largest transcription factors families among eukaryotic organisms; its members play vital roles in environmental signaling, stress response, plant growth, seed maturation, and fruit development. However, a comprehensive report on the bZIP gene family in olive is lacking. In this study, 103 OebZIP genes from the olive genome were identified and divided into 12 subfamilies according to their genetic relationship with 78 bZIPs of A. thaliana. Most OebZIP genes are clustered in the subgroup that has a similar gene structure and conserved motif distribution. According to the characteristics of the leucine zipper region, the dimerization characteristics of 103 OebZIP proteins were predicted. Gene duplication analyses revealed that 22 OebZIP genes were involved in the expansion of the bZIP family. To evaluate the expression patterns of OebZIP genes, RNA-seq data available in public databases were analyzed. The highly expressed OebZIP genes and several lipid synthesis genes (LPGs) in fruits of two varieties with different oil contents during the fast oil accumulation stage were examined via qRT-PCR. By comparing the dynamic changes of oil accumulation, OebZIP1, OebZIP7, OebZIP22, and OebZIP99 were shown to have a close relationship with fruit development and lipid synthesis. Additionally, some OebZIP had a significant positive correlation with various LPG genes. This study gives insights into the structural features, evolutionary patterns, and expression analysis, laying a foundation to further reveal the function of the 103 OebZIP genes in olive.
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Sustainable Sesame (Sesamum indicum L.) Production through Improved Technology: An Overview of Production, Challenges, and Opportunities in Myanmar. SUSTAINABILITY 2020. [DOI: 10.3390/su12093515] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This paper aims to review the research achievements concerning sustainable sesame (Sesamum indicum L.) production and outlook on the production constraints and future perspectives for Myanmar sesame. Sesame is an economically and nutritionally important crop, and it is prized for oil. The global sesame market demand is rising with increasing health awareness. Meanwhile, there is high competition in the market among producing countries for an international trade. Smallholder farmers in developing countries cultivate sesame as a cash crop on marginal soils. The edible oilseed sectors currently face several challenges, including ones affecting sesame crops. For sustainable production of sesame, an integrated approach is needed to overcome these challenges and the critical limiting factors should be identified. In recent years, sesame genomic resources, including molecular markers, genetic maps, genome sequences, and online functional databases, are available for sesame genetic improvement programs. Since ancient times, sesame has been cultivated in Myanmar, but productivity is still lower than that of other sesame producing countries. Myanmar sesame production is limited by many factors, including production technology, research and development, etc. With integration of these genomic resources, crop production and protection techniques, postharvest practices, crop improvement programs, and capacity building will play a crucial role for improving sesame production in Myanmar.
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15
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Ono E, Waki T, Oikawa D, Murata J, Shiraishi A, Toyonaga H, Kato M, Ogata N, Takahashi S, Yamaguchi MA, Horikawa M, Nakayama T. Glycoside-specific glycosyltransferases catalyze regio-selective sequential glucosylations for a sesame lignan, sesaminol triglucoside. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1221-1233. [PMID: 31654577 DOI: 10.1111/tpj.14586] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/07/2019] [Accepted: 10/16/2019] [Indexed: 05/10/2023]
Abstract
Sesame (Sesamum indicum) seeds contain a large number of lignans, phenylpropanoid-related plant specialized metabolites. (+)-Sesamin and (+)-sesamolin are major hydrophobic lignans, whereas (+)-sesaminol primarily accumulates as a water-soluble sesaminol triglucoside (STG) with a sugar chain branched via β1→2 and β1→6-O-glucosidic linkages [i.e. (+)-sesaminol 2-O-β-d-glucosyl-(1→2)-O-β-d-glucoside-(1→6)-O-β-d-glucoside]. We previously reported that the 2-O-glucosylation of (+)-sesaminol aglycon and β1→6-O-glucosylation of (+)-sesaminol 2-O-β-d-glucoside (SMG) are mediated by UDP-sugar-dependent glucosyltransferases (UGT), UGT71A9 and UGT94D1, respectively. Here we identified a distinct UGT, UGT94AG1, that specifically catalyzes the β1→2-O-glucosylation of SMG and (+)-sesaminol 2-O-β-d-glucosyl-(1→6)-O-β-d-glucoside [termed SDG(β1→6)]. UGT94AG1 was phylogenetically related to glycoside-specific glycosyltransferases (GGTs) and co-ordinately expressed with UGT71A9 and UGT94D1 in the seeds. The role of UGT94AG1 in STG biosynthesis was further confirmed by identification of a STG-deficient sesame mutant that predominantly accumulates SDG(β1→6) due to a destructive insertion in the coding sequence of UGT94AG1. We also identified UGT94AA2 as an alternative UGT potentially involved in sugar-sugar β1→6-O-glucosylation, in addition to UGT94D1, during STG biosynthesis. Yeast two-hybrid assays showed that UGT71A9, UGT94AG1, and UGT94AA2 were found to interact with a membrane-associated P450 enzyme, CYP81Q1 (piperitol/sesamin synthase), suggesting that these UGTs are components of a membrane-bound metabolon for STG biosynthesis. A comparison of kinetic parameters of these UGTs further suggested that the main β-O-glucosylation sequence of STG biosynthesis is β1→2-O-glucosylation of SMG by UGT94AG1 followed by UGT94AA2-mediated β1→6-O-glucosylation. These findings together establish the complete biosynthetic pathway of STG and shed light on the evolvability of regio-selectivity of sequential glucosylations catalyzed by GGTs.
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Affiliation(s)
- Eiichiro Ono
- Suntory Global Innovation Center (SIC) Ltd., Research Institute, Soraku-gun, Kyoto, 619-0284, Japan
| | - Toshiyuki Waki
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Daiki Oikawa
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Jun Murata
- Suntory Bioorganic Research Institute (SUNBOR), Suntory Foundation for Life Sciences, Soraku-gun, Kyoto, 619-0284, Japan
| | - Akira Shiraishi
- Suntory Bioorganic Research Institute (SUNBOR), Suntory Foundation for Life Sciences, Soraku-gun, Kyoto, 619-0284, Japan
| | - Hiromi Toyonaga
- Suntory Global Innovation Center (SIC) Ltd., Research Institute, Soraku-gun, Kyoto, 619-0284, Japan
| | - Masako Kato
- National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8517, Japan
| | - Naoki Ogata
- National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8517, Japan
| | - Seiji Takahashi
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | | | - Manabu Horikawa
- Suntory Bioorganic Research Institute (SUNBOR), Suntory Foundation for Life Sciences, Soraku-gun, Kyoto, 619-0284, Japan
| | - Toru Nakayama
- Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
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Dossa K, Mmadi MA, Zhou R, Liu A, Yang Y, Diouf D, You J, Zhang X. Ectopic expression of the sesame MYB transcription factor SiMYB305 promotes root growth and modulates ABA-mediated tolerance to drought and salt stresses in Arabidopsis. AOB PLANTS 2020; 12:plz081. [PMID: 32099638 PMCID: PMC7019004 DOI: 10.1093/aobpla/plz081] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/21/2019] [Indexed: 05/02/2023]
Abstract
An increasing number of candidate genes related to abiotic stress tolerance are being discovered and proposed to improve the existing cultivars of the high oil-bearing crop sesame (Sesamum indicum L.). However, the in planta functional validation of these genes is remarkably lacking. In this study, we cloned a novel sesame R2-R3 MYB gene SiMYB75 which is strongly induced by drought, sodium chloride (NaCl), abscisic acid (ABA) and mannitol. SiMYB75 is expressed in various sesame tissues, especially in root and its protein is predicted to be located in the nucleus. Ectopic over-expression of SiMYB75 in Arabidopsis notably promoted root growth and improved plant tolerance to drought, NaCl and mannitol treatments. Furthermore, SiMYB75 over-expressing lines accumulated higher content of ABA than wild-type plants under stresses and also increased sensitivity to ABA. Physiological analyses revealed that SiMYB75 confers abiotic stress tolerance by promoting stomatal closure to reduce water loss; inducing a strong reactive oxygen species scavenging activity to alleviate cell damage and apoptosis; and also, up-regulating the expression levels of various stress-marker genes in the ABA-dependent pathways. Our data suggested that SiMYB75 positively modulates drought, salt and osmotic stresses responses through ABA-mediated pathways. Thus, SiMYB75 could be a promising candidate gene for the improvement of abiotic stress tolerance in crop species including sesame.
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Affiliation(s)
- 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, No.2 Xudong 2nd Road, Wuhan, China
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Dakar, Sénégal
- Corresponding authors’ e-mail addresses: ;
| | - Marie A Mmadi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, China
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Dakar, Sénégal
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, China
| | - Aili Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, China
| | - Yuanxiao Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, Wuhan, China
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Dakar, Sénégal
| | - 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, No.2 Xudong 2nd Road, Wuhan, China
| | - 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, No.2 Xudong 2nd Road, Wuhan, China
- Corresponding authors’ e-mail addresses: ;
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Wei M, Liu A, Zhang Y, Zhou Y, Li D, Dossa K, Zhou R, Zhang X, You J. Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame. BMC Genomics 2019; 20:748. [PMID: 31619177 PMCID: PMC6796446 DOI: 10.1186/s12864-019-6091-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/10/2019] [Indexed: 01/19/2023] Open
Abstract
Background The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas. Results In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame. Conclusions This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.
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Affiliation(s)
- Mengyuan Wei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yujuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.,Special Economic Crop Research Center of Shandon Academy of Agricultural Sciences, Shandong Cotton Research Center, Jinan, 250100, China
| | - Yong Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Zhou R, Liu P, Li D, Zhang X, Wei X. Photoperiod response-related gene SiCOL1 contributes to flowering in sesame. BMC PLANT BIOLOGY 2018; 18:343. [PMID: 30526484 PMCID: PMC6288898 DOI: 10.1186/s12870-018-1583-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/30/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sesame is a major oilseed crop which is widely cultivated all around the world. Flowering, the timing of transition from vegetative to reproductive growth, is one of the most important events in the life cycle of sesame. Sesame is a typical short-day (SD) plant and its flowering is largely affected by photoperiod. However, the flowering mechanism in sesame at the molecular level is still not very clear. Previous studies showed that the CONSTANS (CO) gene is the crucial photoperiod response gene which plays a center role in duration of the plant vegetative growth. RESULTS In this study, the CO-like (COL) genes were identified and characterized in the sesame genome. Two homologs of the CO gene in the SiCOLs, SiCOL1 and SiCOL2, were recognized and comprehensively analyzed. However, sequence analysis showed that SiCOL2 lacked one of the B-box motifs. In addition, the flowering time of the transgenic Arabidopsis lines with overexpressed SiCOL2 were longer than that of SiCOL1, indicating that SiCOL1 was more likely to be the potential functional homologue of CO in sesame. Expression analysis revealed that SiCOL1 had high expressed levels before flowering in leaves and exhibited diurnal rhythmic expression in both SD and long-day (LD) conditions. In total, 16 haplotypes of SiCOL1 were discovered in the sesame collections from Asia. However, the mutated haplotypes did not express under both SD and LD conditions and was regarded as a nonfunctional allele. Notably, the sesame landraces from high-latitude regions harboring nonfunctional alleles of SiCOL1 flowered much earlier than landraces from low-latitude regions under LD condition, and adapted to the northernmost regions of sesame cultivation. The result indicated that sesame landraces from high-latitude regions might have undergone artificial selection to adapt to the LD environment. CONCLUSIONS Our results suggested that SiCOL1 might contribute to regulation of flowering in sesame and natural variations in SiCOL1 were probably related to the expansion of sesame cultivation to high-latitude regions. The results could be used in sesame breeding and in broadening adaptation of sesame varieties to new regions.
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Affiliation(s)
- Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Pan Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
| | - Xin Wei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062 China
- College of Life Sciences, Shanghai Normal University, Shanghai, 200234 China
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Liu H, Zhou F, Zhou T, Yang Y, Zhao Y. Cytological characterization and molecular mapping of a novel recessive genic male sterility in sesame (Sesamum indicum L.). PLoS One 2018; 13:e0204034. [PMID: 30235259 PMCID: PMC6147451 DOI: 10.1371/journal.pone.0204034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 09/02/2018] [Indexed: 11/18/2022] Open
Abstract
Recessive genic male sterility (RGMS) has great potential for F1 hybrid seeds production in sesame (Sesamum indicum L.). However, it is not yet widely used in practice due to poor understanding of the underlying mechanism in RGMS. Previously, we have developed a novel sesame RGMS line (D248A) controlled by a single recessive gene. To elucidate its cytological mechanism, histological observations were carried out in sterile and fertile buds. The results indicated that abnormality in D248A began at microspore mother cell stage and persisted until microspore stage. The microsporocytes had less cytoplasm and no obvious nucleus. Normal meiosis failed in microspore mother cells. Cytoplasm condensation and vacuolation frequently occurred in tetrads, leading to the production of crumpled and abortive microspores. To develop molecular markers for breeding of hybrid lines, InDel and SSR markers were analyzed in a fertility segregating NIL population constructed by sib-mating D248A with D248B. Five markers were identified for the male sterile gene (Ms), with a respective genetic distance of 1.47 and 5.17 cM for the two closest markers (SB2993 and LG1-170) on both sides. The Ms gene was further anchored into a 108-kb interval in the downstream of chromosome 1, within which 15 genes were predicted and four were likely to be responsible for male sterility. These findings provide a deeper understanding of the mechanism underlying RGMS in sesame.
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Affiliation(s)
- Hongyan Liu
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute, CAAS, Wuhan, China
| | - Fang Zhou
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute, CAAS, Wuhan, China
| | - Ting Zhou
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute, CAAS, Wuhan, China
| | - Yuanxiao Yang
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute, CAAS, Wuhan, China
| | - Yingzhong Zhao
- Key Laboratory of Oil Crops Biology and Genetic Improvement, Ministry of Agriculture, Oil Crops Research Institute, CAAS, Wuhan, China
- * E-mail:
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20
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Wang Y, Zhang Y, Zhou R, Dossa K, Yu J, Li D, Liu A, Mmadi MA, Zhang X, You J. Identification and characterization of the bZIP transcription factor family and its expression in response to abiotic stresses in sesame. PLoS One 2018; 13:e0200850. [PMID: 30011333 PMCID: PMC6047817 DOI: 10.1371/journal.pone.0200850] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/03/2018] [Indexed: 11/18/2022] Open
Abstract
Basic leucine zipper (bZIP) gene family is one of the largest transcription factor families in plants, and members of this family play important roles in multiple biological processes such as light signaling, seed maturation, flower development as well as abiotic and biotic stress responses. Nonetheless, genome-wide comprehensive analysis of the bZIP family is lacking in the important oil crop sesame. In the present study, 63 bZIP genes distributed on 14 linkage groups were identified in sesame, and denominated as SibZIP01-SibZIP63. Besides, all members of SibZIP family were divided into nine groups based on the phylogenetic relationship of Arabidopsis bZIPs, which was further supported by the analysis of their conserved motifs and gene structures. Promoter analysis showed that all SibZIP genes harbor cis-elements related to stress responsiveness in their promoter regions. Expression analyses of SibZIP genes based on transcriptome data showed that these genes have different expression patterns in different tissues. Additionally, we showed that a majority of SibZIPs (85.71%) exhibited significant transcriptional changes in responses to abiotic stresses, including drought, waterlogging, osmotic, salt, and cold, suggesting that SibZIPs may play a cardinal role in the regulation of stress responses in sesame. Together, these results provide new insights into stress-responsive SibZIP genes and pave the way for future studies of SibZIPs-mediated abiotic stress response in sesame.
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Affiliation(s)
- Yanyan Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yujuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Cotton Research Center, Cotton Research Center, Shandong Academy of Agricultural Sciences, Huanghuaihai Key Laboratory of Cotton Genetic Improvement and Cultivation Physiology of the Ministry of Agriculture, Jinan, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Thiès, Sénégal
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Marie Ali Mmadi
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Thiès, Sénégal
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- * E-mail:
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21
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You J, Wang Y, Zhang Y, Dossa K, Li D, Zhou R, Wang L, Zhang X. Genome-wide identification and expression analyses of genes involved in raffinose accumulation in sesame. Sci Rep 2018. [PMID: 29531231 PMCID: PMC5847563 DOI: 10.1038/s41598-018-22585-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Sesame (Sesamum indicum L.) is an important oilseed crop. However, multiple abiotic stresses severely affect sesame growth and production. Raffinose family oligosaccharides (RFOs), such as raffinose and stachyose, play an important role in desiccation tolerance of plants and developing seeds. In the present study, three types of key enzymes, galactinol synthase (GolS), raffinose synthase (RafS) and stachyose synthase (StaS), responsible for the biosynthesis of RFOs were identified at the genome-wide scale in sesame. A total of 7 SiGolS and 15 SiRS genes were identified in the sesame genome. Transcriptome analyses showed that SiGolS and SiRS genes exhibited distinct expression profiles in different tissues and seed developmental stages. Comparative expression analyses under various abiotic stresses indicated that most of SiGolS and SiRS genes were significantly regulated by drought, osmotic, salt, and waterlogging stresses, but slightly affected by cold stress. The up-regulation of several SiGolS and SiRS genes by multiple abiotic stresses suggested their active implication in sesame abiotic stress responses. Taken together, these results shed light on the RFOs-mediated abiotic stress resistance in sesame and provide a useful framework for improving abiotic stress resistance of sesame through genetic engineering.
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Affiliation(s)
- Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yanyan Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yujuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.,Special Economic Crop Research Center of Shandon Academy of Agricultural Sciences, Shandong Cotton Research Center, Jinan, 250100, China
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.,Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Senegal
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Mmadi MA, Dossa K, Wang L, Zhou R, Wang Y, Cisse N, Sy MO, Zhang X. Functional Characterization of the Versatile MYB Gene Family Uncovered Their Important Roles in Plant Development and Responses to Drought and Waterlogging in Sesame. Genes (Basel) 2017; 8:genes8120362. [PMID: 29231869 PMCID: PMC5748680 DOI: 10.3390/genes8120362] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/22/2017] [Accepted: 11/29/2017] [Indexed: 12/02/2022] Open
Abstract
The MYB gene family constitutes one of the largest transcription factors (TFs) modulating various biological processes in plants. Although genome-wide analysis of this gene family has been carried out in some species, only three MYB members have been functionally characterized heretofore in sesame (Sesamum indicum L.). Here, we identified a relatively high number (287) of sesame MYB genes (SIMYBs) with an uncommon overrepresentation of the 1R-subfamily. A total of 95% of SIMYBs was mapped unevenly onto the 16 linkage groups of the sesame genome with 55 SIMYBs tandemly duplicated. In addition, molecular characterization, gene structure, and evolutionary relationships of SIMYBs were established. Based on the close relationship between sesame and Arabidopsis thaliana, we uncovered that the functions of SIMYBs are highly diverse. A total of 65% of SIMYBs were commonly detected in five tissues, suggesting that they represent key TFs modulating sesame growth and development. Moreover, we found that SIMYBs regulate sesame responses to drought and waterlogging, which highlights the potential of SIMYBs towards improving stress tolerance in sesame. This work presents a comprehensive picture of the MYB gene family in sesame and paves the way for further functional validation of the members of this versatile gene family.
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Affiliation(s)
- Marie Ali Mmadi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320, Thiès, Senegal.
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, 107000 Dakar, Senegal.
| | - 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, Wuhan 430062, China.
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320, Thiès, Senegal.
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, 107000 Dakar, Senegal.
| | - 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, Wuhan 430062, China.
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| | - Yanyan 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, Wuhan 430062, China.
| | - Ndiaga Cisse
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320, Thiès, Senegal.
| | - Mame Oureye Sy
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, 107000 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, Wuhan 430062, China.
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Phloem-Conducting Cells in Haustoria of the Root-Parasitic Plant Phelipanche aegyptiaca Retain Nuclei and Are Not Mature Sieve Elements. PLANTS 2017; 6:plants6040060. [PMID: 29206147 PMCID: PMC5750636 DOI: 10.3390/plants6040060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/29/2017] [Accepted: 12/03/2017] [Indexed: 12/12/2022]
Abstract
Phelipanche aegyptiaca parasitizes a wide range of plants, including important crops, and causes serious damage to their production. P. aegyptiaca develops a specialized intrusive organ called a haustorium that establishes connections to the host’s xylem and phloem. In parallel with the development of xylem vessels, the differentiation of phloem-conducting cells has been demonstrated by the translocation of symplasmic tracers from the host to the parasite. However, it is unclear yet whether haustorial phloem-conducting cells are sieve elements. In this study, we identified phloem-conducting cells in haustoria by the host-to-parasite translocation of green fluorescent protein (GFP) from AtSUC2pro::GFP tomato sieve tubes. Haustorial GFP-conducting cells contained nuclei but not callose-rich sieve plates, indicating that phloem-conducting cells in haustoria differ from conventional sieve elements. To ascertain why the nuclei were not degenerated, expression of the P. aegyptiaca homologs NAC-domain containing transcription factor (NAC45), NAC45/86-dependent exonuclease-domain protein 1 (NEN1), and NEN4 was examined. However, these genes were more highly expressed in the haustorium than in tubercle protrusion, implying that nuclear degradation in haustoria may not be exclusively controlled by the NAC45/86-NEN regulatory pathway. Our results also suggest that the formation of plasmodesmata with large size exclusion limits is independent of nuclear degradation and callose deposition.
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Dossa K, Yu J, Liao B, Cisse N, Zhang X. Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase. FRONTIERS IN PLANT SCIENCE 2017; 8:1470. [PMID: 28878802 PMCID: PMC5572293 DOI: 10.3389/fpls.2017.01470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/08/2017] [Indexed: 05/21/2023]
Abstract
The sequencing of the full nuclear genome of sesame (Sesamum indicum L.) provides the platform for functional analyses of genome components and their application in breeding programs. Although the importance of microsatellites markers or simple sequence repeats (SSR) in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning SSRs at the whole genome level in sesame. In addition, SSRs represent a suitable marker type for sesame molecular breeding in developing countries where it is mainly grown. In this study, we identified 138,194 genome-wide SSRs of which 76.5% were physically mapped onto the 13 pseudo-chromosomes. Among these SSRs, up to three primers pairs were supplied for 101,930 SSRs and used to in silico amplify the reference genome together with two newly sequenced sesame accessions. A total of 79,957 SSRs (78%) were polymorphic between the three genomes thereby suggesting their promising use in different genomics-assisted breeding applications. From these polymorphic SSRs, 23 were selected and validated to have high polymorphic potential in 48 sesame accessions from different growing areas of Africa. Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/), which provides free access to SSRs data as well as an integrated platform for functional analyses. Altogether, the reference SSR and SisatBase would serve as useful resources for genetic assessment, genomic studies, and breeding advancement in sesame, especially in developing countries.
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Affiliation(s)
- Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la SécheresseThiès, Senegal
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Ndiaga Cisse
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la SécheresseThiès, Senegal
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
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Development of an SSR-based genetic map in sesame and identification of quantitative trait loci associated with charcoal rot resistance. Sci Rep 2017; 7:8349. [PMID: 28827730 PMCID: PMC5566338 DOI: 10.1038/s41598-017-08858-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/19/2017] [Indexed: 12/17/2022] Open
Abstract
Sesame is prized for its oil. Genetic improvement of sesame can be enhanced through marker-assisted breeding. However, few simple sequence repeat (SSR) markers and SSR-based genetic maps were available in sesame. In this study, 7,357 SSR markers were developed from the sesame genome and transcriptomes, and a genetic map was constructed by generating 424 novel polymorphic markers and using a cross population with 548 recombinant inbred lines (RIL). The genetic map had 13 linkage groups, equalling the number of sesame chromosomes. The linkage groups ranged in size from 113.6 to 179.9 centimorgans (cM), with a mean value of 143.8 cM over a total length of 1869.8 cM. Fourteen quantitative trait loci (QTL) for sesame charcoal rot disease resistance were detected, with contribution rates of 3–14.16% in four field environments; ~60% of the QTL were located within 5 cM at 95% confidence interval. The QTL with the highest phenotype contribution rate (qCRR12.2) and those detected in different environments (qCRR8.2 and qCRR8.3) were used to predict candidate disease response genes. The new SSR-based genetic map and 14 novel QTLs for charcoal rot disease resistance will facilitate the mapping of agronomic traits and marker-assisted selection breeding in sesame.
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Dossa K, Diouf D, Wang L, Wei X, Zhang Y, Niang M, Fonceka D, Yu J, Mmadi MA, Yehouessi LW, Liao B, Zhang X, Cisse N. The Emerging Oilseed Crop Sesamum indicum Enters the "Omics" Era. FRONTIERS IN PLANT SCIENCE 2017; 8:1154. [PMID: 28713412 PMCID: PMC5492763 DOI: 10.3389/fpls.2017.01154] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/15/2017] [Indexed: 05/18/2023]
Abstract
Sesame (Sesamum indicum L.) is one of the oldest oilseed crops widely grown in Africa and Asia for its high-quality nutritional seeds. It is well adapted to harsh environments and constitutes an alternative cash crop for smallholders in developing countries. Despite its economic and nutritional importance, sesame is considered as an orphan crop because it has received very little attention from science. As a consequence, it lags behind the other major oil crops as far as genetic improvement is concerned. In recent years, the scenario has considerably changed with the decoding of the sesame nuclear genome leading to the development of various genomic resources including molecular markers, comprehensive genetic maps, high-quality transcriptome assemblies, web-based functional databases and diverse daft genome sequences. The availability of these tools in association with the discovery of candidate genes and quantitative trait locis for key agronomic traits including high oil content and quality, waterlogging and drought tolerance, disease resistance, cytoplasmic male sterility, high yield, pave the way to the development of some new strategies for sesame genetic improvement. As a result, sesame has graduated from an "orphan crop" to a "genomic resource-rich crop." With the limited research teams working on sesame worldwide, more synergic efforts are needed to integrate these resources in sesame breeding for productivity upsurge, ensuring food security and improved livelihood in developing countries. This review retraces the evolution of sesame research by highlighting the recent advances in the "Omics" area and also critically discusses the future prospects for a further genetic improvement and a better expansion of this crop.
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Affiliation(s)
- Komivi Dossa
- Centre d’Etudes Régional Pour l’Amélioration de l’Adaptation à la SécheresseThiès, Sénégal
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DiopDakar, Sénégal
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DiopDakar, Sénégal
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Xin Wei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Mareme Niang
- Centre d’Etudes Régional Pour l’Amélioration de l’Adaptation à la SécheresseThiès, Sénégal
| | - Daniel Fonceka
- Centre d’Etudes Régional Pour l’Amélioration de l’Adaptation à la SécheresseThiès, Sénégal
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, UMR AGAPMontpellier, France
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Marie A. Mmadi
- Centre d’Etudes Régional Pour l’Amélioration de l’Adaptation à la SécheresseThiès, Sénégal
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DiopDakar, Sénégal
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Louis W. Yehouessi
- Centre d’Etudes Régional Pour l’Amélioration de l’Adaptation à la SécheresseThiès, Sénégal
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of AgricultureWuhan, China
| | - Ndiaga Cisse
- Centre d’Etudes Régional Pour l’Amélioration de l’Adaptation à la SécheresseThiès, Sénégal
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Wei X, Gong H, Yu J, Liu P, Wang L, Zhang Y, Zhang X. SesameFG: an integrated database for the functional genomics of sesame. Sci Rep 2017; 7:2342. [PMID: 28539606 PMCID: PMC5443765 DOI: 10.1038/s41598-017-02586-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/12/2017] [Indexed: 11/09/2022] Open
Abstract
Sesame (Sesamum indicum L.) has high oil content, a small diploid genome and a short growth period, making it an attractive species for genetic studies on oilseed crops. With the advancement of next-generation sequencing technology, genomics and functional genomics research of sesame has developed quickly in the last few years, and large amounts of data have been generated. However, these results are distributed in many different publications, and there is a lack of integration. To promote functional genomics research of sesame, we collected genetic information combined with comprehensive phenotypic information and integrated them in the web-based database named SesameFG. The current version of SesameFG contains phenotypic information on agronomic traits of 705 sesame accessions, de novo assembled genomes of three sesame varieties, massive numbers of identified SNPs, gene expression profiles of five tissues, gene families, candidate genes for the important agronomic traits and genomic-SSR markers. All phenotypic and genotypic information in SesameFG is available for online queries and can be downloaded freely. SesameFG provides useful search functions and data mining tools, including Genome Browser and local BLAST services. SesameFG is freely accessible at http://ncgr.ac.cn/SesameFG/. SesameFG provides valuable resources and tools for functional genomics research and the molecular breeding of sesame.
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Affiliation(s)
- Xin Wei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Hao Gong
- National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Pan Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Yu J, Wang L, Guo H, Liao B, King G, Zhang X. Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome. BMC Genomics 2017; 18:257. [PMID: 28340563 PMCID: PMC5364699 DOI: 10.1186/s12864-017-3599-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 02/21/2017] [Indexed: 12/26/2022] Open
Abstract
Background Whole genome duplication (WGD) and tandem duplication (TD) provide two critical sources of raw genetic material for genome complexity and evolutionary novelty. Little is known about the complexity of the Sesamum indicum genome after it diverged from a common ancestor with the paleodiploid Vitis vinifera and further experienced WGD and TD events. Results Here, we analyzed the functional divergence of different classes of inter- and intra-genome gene pairs from ancestral events to uncover multiple-layers of evolutionary dynamics acting during the process of forming the modern S. indicum genome. Comprehensive inter-genome analyses revealed that 60% and 70% of syntenic orthologous gene pairs were retained among the two subgenomes in S. indicum compared to V. vinifera, although there was no evidence of significant differences under selection pressure. For the intra-genomic analyses, 5,932 duplicated gene pairs experienced fractionation, with the remaining 1,236 duplicated gene pairs having undergone functional divergence under diversifying selection. Analysis of the TD events indicated that 2,945 paralogous gene pairs, from 1,089 tandem arrays of 2–16 genes, experienced functional divergence under diversifying selection. Sequence diversification of different classes of gene pairs revealed that most of TD events occurred after the WGD event, with others following the ancestral gene order indicating ancient TD events at some time prior to the WGD event. Our comparison-of-function analyses for different classes of gene pairs indicated that the WGD and TD evolutionary events were both responsible for introducing genes that enabled exploration of novel and complementary functionalities, whilst maintaining individual plant ruggedness. Conclusions In this study, we first investigated functional divergence of different classes of gene pairs to characterize the dynamic processes associated with each evolutionary event in S. indicum. The data demonstrated massive and distinct functional divergence among different classes of gene pairs, and provided a genome-scale view of gene function diversification explaining the complexity of the S. indicum genome. We hope this provides a biological model to study the mechanism of plant species formation, particularly in the context of the evolutionary history of flowering plants, and offers novel insights for the study of angiosperm genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3599-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingyin Yu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Linhai Wang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Hui Guo
- Plant Genome Mapping Laboratory, the University of Georgia, Athens, GA, 30605, USA
| | - Boshou Liao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Graham King
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia. .,The Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
| | - Xiurong Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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Liu H, Tan M, Yu H, Li L, Zhou F, Yang M, Zhou T, Zhao Y. Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.). BMC PLANT BIOLOGY 2016; 16:250. [PMID: 27832742 PMCID: PMC5105256 DOI: 10.1186/s12870-016-0934-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/27/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum L.) is a globally important oilseed crop with highly-valued oil. Strong hybrid vigor is frequently observed within this crop, which can be exploited by the means of genic male sterility (GMS). We have previously developed a dominant GMS (DGMS) line W1098A that has great potential for the breeding of F1 hybrids. Although it has been genetically and anatomically characterized, the underlying molecular mechanism for male sterility remains unclear and therefore limits the full utilization of such GMS line. In this study, RNA-seq based transcriptome profiling was carried out in two near-isogenic DGMS lines (W1098A and its fertile counterpart, W1098B) to identify differentially expressed genes (DEGs) related to male sterility. RESULTS A total of 1,502 significant DEGs were detected, among which 751 were up-regulated and 751 were down-regulated in sterile flower buds. A number of DEGs were implicated in both ethylene and JA synthesis & signaling pathway; the expression of which were either up- or down-regulated in the sterile buds, respectively. Moreover, the majority of NAC and WRKY transcription factors implicated from the DEGs were up-regulated in sterile buds. By querying the Plant Male Reproduction Database, 49 sesame homologous genes were obtained; several of these encode transcription factors (bHLH089, MYB99, and AMS) that showed reduced expression in sterile buds, thus implying the possible role in specifying or determining tapetal fate and development. The predicted effect of allelic variants on the function of their corresponding DEGs highlighted several Insertions/Deletions (InDels), which might be responsible for the phenotype of sterility/fertility in DGMS lines. CONCLUSION The present comparative transcriptome study suggested that both hormone signaling pathway and transcription factors control the male sterility of DGMS in sesame. The results also revealed that several InDels located in DEGs prone to cause loss of function, which might contribute to male sterility. These findings provide valuable genomic resources for a deeper insight into the molecular mechanism underlying DGMS.
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Affiliation(s)
- Hongyan Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062 China
| | - Mingpu Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Haijuan Yu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Liang Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095 China
| | - Fang Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062 China
| | - Minmin Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062 China
| | - Ting Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062 China
| | - Yingzhong Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, Hubei 430062 China
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30
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Dossa K. A physical map of important QTLs, functional markers and genes available for sesame breeding programs. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:613-619. [PMID: 27924134 PMCID: PMC5120042 DOI: 10.1007/s12298-016-0385-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/28/2016] [Accepted: 10/04/2016] [Indexed: 05/29/2023]
Abstract
Sesame is one of the oldest oilseed crops grown mainly in Africa and Asia. Although genetic and genomic studies on sesame have started late, the past 5 years have witnessed extensive progresses in these areas on this crop. Important genomic sequence resources such as functional markers, genes and QTLs linked to agronomically important traits, have been generated through linkage mapping and association analysis to assist sesame improvement programs. However, most of these data are scattered in different maps making them hard to be exploited efficiently in breeding programs. In this study, we report a comprehensive physical map gathering 151 published genomic sequence resources which highlighted some hotspot functional regions in the sesame genome. Moreover, 83,135 non-redundant SSRs have been supplied along with their physical position and motif composition. This will assist future research in fine mapping or pinpointing more functional genes based on the already published QTLs and functional markers. This physical map represents a good landmark for further non-overlapping genetic and genomic studies working towards sesame improvement.
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Affiliation(s)
- Komivi Dossa
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), BP 3320, Route de Khombole, Thiès, Senegal
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31
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Dossa K, Wei X, Li D, Fonceka D, Zhang Y, Wang L, Yu J, Boshou L, Diouf D, Cissé N, Zhang X. Insight into the AP2/ERF transcription factor superfamily in sesame and expression profiling of DREB subfamily under drought stress. BMC PLANT BIOLOGY 2016; 16:171. [PMID: 27475988 PMCID: PMC4967514 DOI: 10.1186/s12870-016-0859-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/21/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sesame is an important oilseed crop mainly grown in inclement areas with high temperatures and frequent drought. Thus, drought constitutes one of the major constraints of its production. The AP2/ERF is a large family of transcription factors known to play significant roles in various plant processes including biotic and abiotic stress responses. Despite their importance, little is known about sesame AP2/ERF genes. This constitutes a limitation for drought-tolerance candidate genes discovery and breeding for tolerance to water deficit. RESULTS One hundred thirty-two AP2/ERF genes were identified in the sesame genome. Based on the number of domains, conserved motifs, genes structure and phylogenetic analysis including 5 relatives species, they were classified into 24 AP2, 41 DREB, 61 ERF, 4 RAV and 2 Soloist. The number of sesame AP2/ERF genes was relatively few compared to that of other relatives, probably due to gene loss in ERF and DREB subfamilies during evolutionary process. In general, the AP2/ERF genes were expressed differently in different tissues but exhibited the highest expression levels in the root. Mostly all DREB genes were responsive to drought stress. Regulation by drought is not specific to one DREB group but depends on the genes and the group A6 and A1 appeared to be more actively expressed to cope with drought. CONCLUSIONS This study provides insights into the classification, evolution and basic functional analysis of AP2/ERF genes in sesame which revealed their putative involvement in multiple tissue-/developmental stages. Out of 20 genes which were significantly up- /down-regulated under drought stress, the gene AP2si16 may be considered as potential candidate gene for further functional validation as well for utilization in sesame improvement programs for drought stress tolerance.
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Affiliation(s)
- 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, No.2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Sénégal
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 107000, Dakar, Sénégal
| | - Xin Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Daniel Fonceka
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Sénégal
- CIRAD, UMR AGAP, F-34398, Montpellier, France
| | - Yanxin 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, No.2 Xudong 2nd Road, 430062, Wuhan, Hubei, 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, No.2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Jingyin Yu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Liao Boshou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Road, 430062, Wuhan, Hubei, China
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, BP 5005 Dakar-Fann, Code postal 107000, Dakar, Sénégal
| | - Ndiaga Cissé
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), BP 3320 Route de Khombole, Thiès, Sénégal
| | - 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, No.2 Xudong 2nd Road, 430062, Wuhan, Hubei, China.
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Tolerant and Susceptible Sesame Genotypes Reveal Waterlogging Stress Response Patterns. PLoS One 2016; 11:e0149912. [PMID: 26934874 PMCID: PMC4774966 DOI: 10.1371/journal.pone.0149912] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 02/06/2016] [Indexed: 02/07/2023] Open
Abstract
Waterlogging is a common adverse environmental condition that limits plant growth. Sesame (Sesamum indicum) is considered a drought-tolerant oil crop but is typically susceptible to harmful effects from waterlogging. The present study used comparative analysis to explore the waterlogging stress response associated with two sesame genotypes. The RNA-seq dataset generated during a time course of 0, 3, 9 and 15 h of waterlogging as well as 20 h post-drainage indicated that stress gradually suppressed the expression of sesame genes, with 9 h as the critical time point for the response of sesame to waterlogging stress. Of the 19,316 genes expressed during waterlogging, 72.1% were affected significantly. Sesame of both tolerant and susceptible genotypes showed decreased numbers of upregulated differentially expressed genes (DEGs) but increased numbers of downregulated DEGs at the onset of waterlogging. However, the tolerant-genotype sesame exhibited 25.5% more upregulated DEGs and 29.7% fewer downregulated DEGs than those of the susceptible-genotype strain between 3 and 15 h. The results indicated that the tolerant sesame displayed a more positive gene response to waterlogging. A total of 1,379 genes were significantly induced and commonly expressed in sesame under waterlogging conditions from 3 to 15 h regardless of tolerance level; of these genes, 98 are known homologous stress responsive genes, while the remaining 1,281 are newly reported here. This gene set may represent the core genes that function in response to waterlogging, including those related mainly to energy metabolism and phenylpropanoid biosynthesis. Furthermore, a set of 3,016 genes functioning in energy supply and cell repair or formation was activated in sesame recovery from waterlogging stress. A comparative analysis between sesame of the tolerant and susceptible genotypes revealed 66 genes that may be candidates for improving sesame tolerance to waterlogging. This study provided a comprehensive picture of the sesame gene expression pattern in response to waterlogging stress. These results will help dissect the mechanism of the sesame response to waterlogging and identify candidate genes to improve its tolerance.
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Wang L, Xia Q, Zhang Y, Zhu X, Zhu X, Li D, Ni X, Gao Y, Xiang H, Wei X, Yu J, Quan Z, Zhang X. Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map. BMC Genomics 2016; 17:31. [PMID: 26732604 PMCID: PMC4702397 DOI: 10.1186/s12864-015-2316-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/15/2015] [Indexed: 12/23/2022] Open
Abstract
Background Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 2014 (version 1.0); however, the number of anchored pseudomolecules was higher than the chromosome number (2n = 2x = 26) due to the lack of a high-density genetic map with 13 linkage groups. Results We resequenced a permanent population consisting of 430 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 13 pseudomolecules. The new genome assembly (version 2.0) included 97.5 % of the scaffolds greater than 150 kb in size present in assembly version 1.0 and increased the total pseudomolecule length from 233.7 to 258.4 Mb with 94.3 % of the genome assembled and 97.2 % of the predicted gene models anchored. Based on the new genome assembly, a bin map including 1,522 bins spanning 1090.99 cM was generated and used to identified 41 quantitative trait loci (QTLs) for sesame plant height and 9 for seed coat color. The plant height-related QTLs explained 3–24 % the phenotypic variation (mean value, 8 %), and 29 of them were detected in at least two field trials. Two major loci (qPH-8.2 and qPH-3.3) that contributed 23 and 18 % of the plant height were located in 350 and 928-kb spaces on Chr8 and Chr3, respectively. qPH-3.3, is predicted to be responsible for the semi-dwarf sesame plant phenotype and contains 102 candidate genes. This is the first report of a sesame semi-dwarf locus and provides an interesting opportunity for a plant architecture study of the sesame. For the sesame seed coat color, the QTLs of the color spaces L*, a*, and b* were detected with contribution rates of 3–46 %. qSCb-4.1 contributed approximately 39 % of the b* value and was located on Chr4 in a 199.9-kb space. A list of 32 candidate genes for the locus, including a predicted black seed coat-related gene, was determined by screening the newly anchored genome. Conclusions This study offers a high-density genetic map and an improved assembly of the sesame genome. The number of linkage groups and pseudomolecules in this assembly equals the number of sesame chromosomes for the first time. The map and updated genome assembly are expected to serve as a platform for future comparative genomics and genetic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2316-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Qiuju Xia
- Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China.
| | - Yanxin Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Xiaodong Zhu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Xiaofeng Zhu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Xuemei Ni
- Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China.
| | - Yuan Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Haitao Xiang
- Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China.
| | - Xin Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Jingyin Yu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
| | - Zhiwu Quan
- Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China.
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan, 430062, China.
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Dossa K, Diouf D, Cissé N. Genome-Wide Investigation of Hsf Genes in Sesame Reveals Their Segmental Duplication Expansion and Their Active Role in Drought Stress Response. FRONTIERS IN PLANT SCIENCE 2016; 7:1522. [PMID: 27790233 PMCID: PMC5061811 DOI: 10.3389/fpls.2016.01522] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/27/2016] [Indexed: 05/05/2023]
Abstract
Sesame is a survivor crop cultivated for ages in arid areas under high temperatures and limited water conditions. Since its entire genome has been sequenced, revealing evolution, and functional characterization of its abiotic stress genes became a hot topic. In this study, we performed a whole-genome identification and analysis of Hsf gene family in sesame. Thirty genes encoding Hsf domain were found and classified into 3 major classes A, B, and C. The class A members were the most representative one and Hsf genes were distributed in 12 of the 16 linkage groups (except the LG 8, 9, 13, and 16). Evolutionary analysis revealed that, segmental duplication events which occurred around 67 MYA, were the primary force underlying Hsf genes expansion in sesame. Comparative analysis also suggested that sesame has retained most of its Hsf genes while its relatives viz. tomato and potato underwent extensive gene losses during evolution. Continuous purifying selection has played a key role in the maintenance of Hsf genes in sesame. Expression analysis of the Hsf genes in sesame revealed their putative involvement in multiple tissue-/developmental stages. Time-course expression profiling of Hsf genes in response to drought stress showed that 90% Hsfs are drought responsive. We infer that classes B-Hsfs might be the primary regulators of drought response in sesame by cooperating with some class A genes. This is the first insight into this gene family and the results provide some gene resources for future gene cloning and functional studies toward the improvement in stress tolerance of sesame.
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Affiliation(s)
- Komivi Dossa
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la SécheresseSénégal
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DiopDakar, Sénégal
- *Correspondence: Komivi Dossa
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DiopDakar, Sénégal
| | - Ndiaga Cissé
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la SécheresseSénégal
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Ohyanagi H, Obayashi T, Yano K. Editorial: Plant and Cell Physiology's 2015 database issue. PLANT & CELL PHYSIOLOGY 2015; 56:4-6. [PMID: 25756138 DOI: 10.1093/pcp/pcu206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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