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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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Yan W, Ni Y, Zhao H, Liu X, Jia M, Zhao X, Li Y, Miao H, Liu H, Zhang H. Comprehensive analysis of sesame LRR-RLKs: structure, evolution and dynamic expression profiles under Macrophomina phaseolina stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1334189. [PMID: 38410728 PMCID: PMC10895033 DOI: 10.3389/fpls.2024.1334189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
Leucine-rich repeat receptor-like kinases (LRR-RLKs) can participate in the regulation of plant growth and development, immunity and signal transduction. Sesamum indicum, one of the most important oil crops, has a significant role in promoting human health. In this study, 175 SiLRR-RLK genes were identified in S. indicum, and they were subdivided into 12 subfamilies by phylogenetic analysis. Gene duplication analysis showed that the expansion of the SiLRR-RLK family members in the sesame was mainly due to segmental duplication. Moreover, the gene expansion of subfamilies IV and III contributed to the perception of stimuli under M. phaseolina stress in the sesame. The collinearity analysis with other plant species revealed that the duplication of SiLRR-RLK genes occurred after the differentiation of dicotyledons and monocotyledons. The expression profile analysis and functional annotation of SiLRR-RLK genes indicated that they play a vital role in biotic stress. Furthermore, the protein-protein interaction and coexpression networks suggested that SiLRR-RLKs contributed to sesame resistance to Macrophomina phaseolina by acting alone or as a polymer with other SiLRR-RLKs. In conclusion, the comprehensive analysis of the SiLRR-RLK gene family provided a framework for further functional studies on SiLRR-RLK genes.
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Affiliation(s)
- Wenqing Yan
- The Shennong Laboratory, Zhengzhou, Henan, China
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Zhengzhou, Henan, China
| | - Yunxia Ni
- The Shennong Laboratory, Zhengzhou, Henan, China
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Zhengzhou, Henan, China
| | - Hui Zhao
- The Shennong Laboratory, Zhengzhou, Henan, China
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Zhengzhou, Henan, China
| | - Xintao Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Zhengzhou, Henan, China
| | - Min Jia
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Zhengzhou, Henan, China
| | - Xinbei Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Zhengzhou, Henan, China
| | - Yongdong Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Zhengzhou, Henan, China
| | - Hongmei Miao
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Hongyan Liu
- The Shennong Laboratory, Zhengzhou, Henan, China
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Haiyang Zhang
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
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3
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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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Miao H, Wang L, Qu L, Liu H, Sun Y, Le M, Wang Q, Wei S, Zheng Y, Lin W, Duan Y, Cao H, Xiong S, Wang X, Wei L, Li C, Ma Q, Ju M, Zhao R, Li G, Mu C, Tian Q, Mei H, Zhang T, Gao T, Zhang H. Genomic evolution and insights into agronomic trait innovations of Sesamum species. PLANT COMMUNICATIONS 2024; 5:100729. [PMID: 37798879 PMCID: PMC10811377 DOI: 10.1016/j.xplc.2023.100729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/17/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
Sesame is an ancient oilseed crop with high oil content and quality. However, the evolutionary history and genetic mechanisms of its valuable agronomic traits remain unclear. Here, we report chromosome-scale genomes of cultivated sesame (Sesamum indicum L.) and six wild Sesamum species, representing all three karyotypes within this genus. Karyotyping and genome-based phylogenic analysis revealed the evolutionary route of Sesamum species from n = 13 to n = 16 and revealed that allotetraploidization occurred in the wild species Sesamum radiatum. Early divergence of the Sesamum genus (48.5-19.7 million years ago) during the Tertiary period and its ancient phylogenic position within eudicots were observed. Pan-genome analysis revealed 9164 core gene families in the 7 Sesamum species. These families are significantly enriched in various metabolic pathways, including fatty acid (FA) metabolism and FA biosynthesis. Structural variations in SiPT1 and SiDT1 within the phosphatidyl ethanolamine-binding protein gene family lead to the genomic evolution of plant-architecture and inflorescence-development phenotypes in Sesamum. A genome-wide association study (GWAS) of an interspecific population and genome comparisons revealed a long terminal repeat insertion and a sequence deletion in DIR genes of wild Sesamum angustifolium and cultivated sesame, respectively; both variations independently cause high susceptibility to Fusarium wilt disease. A GWAS of 560 sesame accessions combined with an overexpression study confirmed that the NAC1 and PPO genes play an important role in upregulating oil content of sesame. Our study provides high-quality genomic resources for cultivated and wild Sesamum species and insights that can improve molecular breeding strategies for sesame and other oilseed crops.
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Affiliation(s)
- Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Lingbo Qu
- College of Food Science and Technology, Henan Technology University, Zhengzhou 450001, China
| | - Hongyan Liu
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yamin Sun
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Meiwang Le
- Crops Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Qiang Wang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shuangling Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wenchao Lin
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hengchun Cao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Songjin Xiong
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Xuede Wang
- College of Food Science and Technology, Henan Technology University, Zhengzhou 450001, China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ruihong Zhao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Guiting Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Cong Mu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qiuzhen Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hongxian Mei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Tide Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Tongmei Gao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
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Yan W, Hu P, Ni Y, Zhao H, Liu X, Cao H, Jia M, Tian B, Miao H, Liu H. Genome-wide characterization of the wall-associated kinase-like (WAKL) family in sesame (Sesamum indicum) identifies a SiWAKL6 gene involved in resistance to Macrophomina Phaseolina. BMC PLANT BIOLOGY 2023; 23:624. [PMID: 38057720 DOI: 10.1186/s12870-023-04658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Sesame charcoal rot caused by Macrophomina phaseolina is one of the most serious fungal diseases in sesame production, and threatens the yield and quality of sesame. WAKL genes are important in the plant response to biotic stresses by sensing and transmitting external signals to the intracellular receptor. However, there is still a lack about the WAKL gene family and its function in sesame resistance to M. phaseolina. The aim of this study was to interpret the roles of WAKL genes in sesame resistance to M. phaseolina. RESULTS In this study, a comprehensive study of the WAKL gene family was conducted and 31 WAKL genes were identified in the sesame genome. Tandem duplication events were the main factor in expansion of the SiWAKL gene family. Phylogenetic analysis showed that the sesame SiWAKL gene family was divided into 4 groups. SiWAKL genes exhibited different expression patterns in diverse tissues. Under M. phaseolina stress, most SiWAKL genes were significantly induced. Notably, SiWAKL6 was strongly induced in the resistant variety "Zhengzhi 13". Functional analysis showed that SiWAKL6 was induced by salicylic acid but not methyl jasmonate in sesame. Overexpression of SiWAKL6 in transgenic Arabidopsis thaliana plants enhanced their resistance to M. phaseolina by inducing the expression of genes involved in the salicylic acid signaling pathway and reconstructing reactive oxygen species homeostasis. CONCLUSIONS Taken together, the results provide a better understanding of functions about SiWAKL gene family and suggest that manipulation of these SiWAKL genes can improve plant resistance to M. phaseolina. The findings contributed to further understanding of functions of SiWAKL genes in plant immunity.
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Affiliation(s)
- Wenqing Yan
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, Henan, 450002, China
| | - Peilin Hu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, Henan, 450002, China
| | - Yunxia Ni
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, Henan, 450002, China
| | - Hui Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, Henan, 450002, China
| | - Xintao Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, Henan, 450002, China
| | - Hengchun Cao
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Zhengzhou, Henan, 450002, China
| | - Min Jia
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, Henan, 450002, China
| | - Baoming Tian
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, Henan, 450002, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, 450002, China.
| | - Hongmei Miao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, Henan, 450002, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Zhengzhou, Henan, 450002, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, 450002, China.
- The Shennong Laboratory, Zhengzhou, Henan, 450002, China.
| | - Hongyan Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, Henan, 450002, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, 450002, China.
- The Shennong Laboratory, Zhengzhou, Henan, 450002, China.
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Bu M, Fan W, Li R, He B, Cui P. Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies. Metabolites 2023; 13:1170. [PMID: 38132852 PMCID: PMC10744971 DOI: 10.3390/metabo13121170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.
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Affiliation(s)
- Mengjia Bu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruonan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bing He
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Cui
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Mei H, Cui C, Liu Y, Du Z, Wu K, Jiang X, Zheng Y, Zhang H. QTL analysis of traits related to seed size and shape in sesame (Sesamum indicum L.). PLoS One 2023; 18:e0293155. [PMID: 37917626 PMCID: PMC10621824 DOI: 10.1371/journal.pone.0293155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023] Open
Abstract
Seed size and shape are important traits that determine seed yield in sesame. Understanding the genetic basis of seed size and shape is essential for improving the yield of sesame. In this study, F2 and BC1 populations were developed by crossing the Yuzhi 4 and Bengal small-seed (BS) lines for detecting the quantitative trait loci (QTLs) of traits related to seed size and shape. A total of 52 QTLs, including 13 in F2 and 39 in BC1 populations, for seed length (SL), seed width (SW), and length to width ratio (L/W) were identified, explaining phenotypic variations from 3.68 to 21.64%. Of these QTLs, nine stable major QTLs were identified in the two populations. Notably, three major QTLs qSL-LG3-2, qSW-LG3-2, and qSW-LG3-F2 that accounted for 4.94-16.34% of the phenotypic variations were co-localized in a 2.08 Mb interval on chromosome 1 (chr1) with 279 candidate genes. Three stable major QTLs qSL-LG6-2, qLW-LG6, and qLW-LG6-F2 that explained 8.14-33.74% of the phenotypic variations were co-localized in a 3.27 Mb region on chr9 with 398 candidate genes. In addition, the stable major QTL qSL-LG5 was co-localized with minor QTLs qLW-LG5-3 and qSW-LG5 to a 1.82 Mb region on chr3 with 195 candidate genes. Gene annotation, orthologous gene analysis, and sequence analysis indicated that three genes are likely involved in sesame seed development. These results obtained herein provide valuable in-formation for functional gene cloning and improving the seed yield of sesame.
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Affiliation(s)
- Hongxian Mei
- The Shennong Laboratory, Zhengzhou, Henan, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Chengqi Cui
- The Shennong Laboratory, Zhengzhou, Henan, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Yanyang Liu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Zhenwei Du
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Ke Wu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Xiaolin Jiang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Haiyang Zhang
- The Shennong Laboratory, Zhengzhou, Henan, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
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8
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Wang C, Niu J, Wei L, Li C, Li G, Tian Q, Ju M, Ma Q, Cao H, Duan Y, Guo H, Zhang H, Miao H. A 4.43-Kb deletion of chromosomal segment containing an ovate family protein confers long capsule in sesame (Sesamum indicum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:221. [PMID: 37819543 DOI: 10.1007/s00122-023-04465-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
KEY MESSAGE A 4.43-Kb structural variation in the sesame genome results in the deletion of the Siofp1 gene and induces the long capsule length trait. Capsule length (CL) has a positive effect on seed weight and yield in various agronomically important species; however, the molecular mechanism underlying long capsule trait regulation in sesame remains unknown. The inheritance analysis showed that long capsule traits (CL > 4.0 cm) were dominant over normal length (average CL = 3.0 cm) and were controlled by a single gene pair. Association mapping with a RIL population and 259 natural sesame germplasm accessions indicated that the target interval was 52,830-730,961 bp of SiChr.10 in sesame. Meanwhile, the structural variation (SV) of the association mapping revealed that only SV_414325 on chromosome 10 was significantly associated with the CL trait, with a P value of 1.1135E-19. SV_414325 represents a 4430-bp deletion from 414,325 to 418,756 bp on SiChr.10, covering Sindi_2155000 (named SiOFP1). In the normal length type, Siofp1 encodes 411 amino acids of the ovate family proteins and is highly expressed in the leaf, stem, bud, and capsule tissues of sesame. In accordance with the transcriptional repressor character, Siofp1 overexpression in transgenic Arabidopsis (T0 and T1 generations) induced a 25-39% greater shortening of silique length than the wild type (P < 0.05), as well as round cauline leaves and short carpels. These results confirm that SiOFP1 plays a key role in regulating CL trait in sesame and other flowering plants. These findings provide a theoretical and material basis for sesame capsule development and high-yield breeding research.
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Affiliation(s)
- Cuiying Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Jiaojiao Niu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Guiting Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Qiuzhen Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Hengchun Cao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Hui Guo
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Haiyang Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
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Weldemichael MY, Bitima TD, Abrha GT, Tesfu K, Gebremedhn HM, Kassa AB, Kindeya YB, Mossa MM. Improving desirable agronomic traits of M2 lines on fourteen Ethiopian Sesame (Sesamum indicum L.) genotypes using Ethyl Methane Sulphonate (EMS). PLoS One 2023; 18:e0287246. [PMID: 37751450 PMCID: PMC10522002 DOI: 10.1371/journal.pone.0287246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 06/02/2023] [Indexed: 09/28/2023] Open
Abstract
Sesame is an important oilseed crop cultivated in Ethiopia as a cash crop for small holder farmers. However, low yield is one of the main constraints of its cultivation. Boosting and sustaining production of sesame is thus timely to achieve the global oil demand. This study was, therefore, aimed at identifying mutant genotypes targeted to produce better agronomic traits of M2 lines on fourteen Ethiopian sesame genotypes through seed treatment with chemical mutagens. EMS was used as a chemical mutagen to treat the fourteen sesame genotypes. Quantitative and qualitative data were recorded and analyzed using analysis of variance with GenStat 16 software. Post-ANOVA mean comparisons were made using Duncan's Multiple Range Test (p≤ 0.01). Statistically significant phenotypic changes were observed in both quantitative and qualitative agronomic traits of the M2 lines. All mutant genotypes generated by EMS treatment showed a highly significant variation for the measured quantitative traits, except for the traits LBL and LTL. On the other hand, EMS-treated genotypes showed a significant change for the qualitative traits, except for PGT, BP, SSCS, LC, LH and LA traits. Mutated Baha Necho, Setit 3, and Zeri Tesfay showed the most promising changes in desirable agronomic traits. To the best of our knowledge, this study represents the first report on the treatment of sesame seeds with EMS to generate desirable agronomic traits in Ethiopian sesame genotypes. These findings would deliver an insight into the genetic characteristics and variability of important sesame agronomic traits. Besides, the findings set up a foundation for future genomic studies in sesame agronomic traits, which would serve as genetic resources for sesame improvement.
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Affiliation(s)
| | | | | | - Kalkidan Tesfu
- National Agricultural Biotechnology Research Center, Holleta, Ethiopia
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10
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Cao H, Tian Q, Ju M, Duan Y, Li G, Ma Q, Zhang H, Zhang X, Miao H. Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame ( Sesamum indicum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1261238. [PMID: 37810391 PMCID: PMC10558006 DOI: 10.3389/fpls.2023.1261238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/01/2023] [Indexed: 10/10/2023]
Abstract
Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions.
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Affiliation(s)
- Hengchun Cao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Qiuzhen Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Guiting Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Xianmei Zhang
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- Luohe Academy of Agricultural Sciences, Luohe, Henan, China
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
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11
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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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12
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Zhang Y, Gong H, Cui X, Gao C, Li N, Pu Y, Zhang X, Zhao J. Integrated lipidomic and transcriptomic analyses reveal the mechanism of lipid biosynthesis and accumulation during seed development in sesame. FRONTIERS IN PLANT SCIENCE 2023; 14:1211040. [PMID: 37426956 PMCID: PMC10325577 DOI: 10.3389/fpls.2023.1211040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023]
Abstract
Sesame is one of the most important oilseed crops and attracts significant attention because of its huge nutritional capacity. However, the molecular mechanisms underlying oil accumulation in sesame remains poorly understood. In this study, lipidomic and transcriptomic analyses in different stages of sesame seed (Luzhi No.1, seed oil content 56%) development were performed to gain insight into the regulatory mechanisms that govern differences in lipid composition, content, biosynthesis, and transport. In total, 481 lipids, including fatty acids (FAs, 38 species), triacylglycerol (TAG, 127 species), ceramide (33 species), phosphatidic acid (20 species), and diacylglycerol (17 species), were detected in developing sesame seed using gas and liquid chromatography-mass spectrometry. Most FAs and other lipids accumulated 21-33 days after flowering. RNA-sequence profiling in developing seed highlighted the enhanced expression of genes involved in the biosynthesis and transport of FAs, TAGs, and membrane lipids, which was similar to that seen during lipid accumulation. Through the differential expression analysis of genes involved in lipid biosynthesis and metabolism during seed development, several candidate genes were found to affect the oil content and FA composition of sesame seed, including ACCase, FAD2, DGAT, G3PDH, PEPCase, WRI1 and WRI1-like genes. Our study reveals the patterns of lipid accumulation and biosynthesis-related gene expression and lays an important foundation for the further exploration of sesame seed lipid biosynthesis and accumulation.
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Affiliation(s)
- Yujuan Zhang
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Huihui Gong
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xinxiao Cui
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chunhua Gao
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Nana Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yanyan Pu
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiurong Zhang
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Junsheng Zhao
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
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13
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Wang ML, Tonnis B, Li X, Morris JB. Generation of Sesame Mutant Population by Mutagenesis and Identification of High Oleate Mutants by GC Analysis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1294. [PMID: 36986984 PMCID: PMC10055875 DOI: 10.3390/plants12061294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/31/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Sesame is one of the important oilseed crops in the world. Natural genetic variation exists in the sesame germplasm collection. Mining and utilizing the genetic allele variation from the germplasm collection is an important approach for seed quality improvement. The sesame germplasm accession, PI 263470, which has a significantly higher level of oleic acid (54.0%) than the average (39.5%), was identified by screening the entire USDA germplasm collection. The seeds from this accession were planted in a greenhouse. Leaf tissues and seeds were harvested from individual plants. DNA sequencing of the coding region of the fatty acid desaturase gene (FAD2) confirmed that this accession contained a natural mutation of G425A which may correspond to the deduced amino acid substitution of R142H leading to the high level of oleic acid, but it was a mixed accession with three genotypes (G/G, G/A, and A/A at the position). The genotype with A/A was selected and self-crossed for three generations. The purified seeds were used for EMS-induced mutagenesis to further enhance the level of oleic acid. A total of 635 M2 plants were generated from mutagenesis. Some mutant plants had significant morphological changes including leafy flat stems and others. M3 seeds were used for fatty acid composition analysis by gas chromatography (GC). Several mutant lines were identified with high oleic acid (70%). Six M3 mutant lines plus one control line were advanced to M7 or M8 generations. Their high oleate traits from M7 or M8 seeds harvested from M6 or M7 plants were further confirmed. The level of oleic acid from one mutant line (M7 915-2) was over 75%. The coding region of FAD2 was sequenced from these six mutants, but no mutation was identified. Additional loci may contribute to the high level of oleic acid. The mutants identified in this study can be used as breeding materials for sesame improvement and as genetic materials for forward genetic studies.
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Affiliation(s)
- Ming Li Wang
- Plant Genetic Resources Conservation Unit, USDA-ARS, 1109 Experiment Street, Griffin, GA 30223, USA
| | - Brandon Tonnis
- Plant Genetic Resources Conservation Unit, USDA-ARS, 1109 Experiment Street, Griffin, GA 30223, USA
| | - Xianran Li
- Wheat Health, Genetics, and Quality Research, USDA-ARS, 291 Clark Hall, Pullman, WA 99164, USA
| | - John Bradly Morris
- Plant Genetic Resources Conservation Unit, USDA-ARS, 1109 Experiment Street, Griffin, GA 30223, USA
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14
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Sinha S, Navathe S, Singh S, Gupta DK, Kharwar RN, Chand R. Genome sequencing and annotation of Cercospora sesami, a fungal pathogen causing leaf spot to Sesamum indicum. 3 Biotech 2023; 13:55. [PMID: 36685323 PMCID: PMC9852405 DOI: 10.1007/s13205-023-03468-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Cercospora sesami is a plant pathogen that causes leaf spot disease in sesame plants worldwide. In this study, genome sequence assembly of C. sesami isolate Cers 52-10 (MCC 9069) was generated using native paired-end and mate-pair DNA sequencing based on the Illumina HiSeq 2500 platform. The genome assembly of C. sesami is 34.3 Mb in size with an N50 of 26,222 bp and an average GC content of 53.02%. A total number of 10,872 genes were predicted in this study, out of which 9,712 genes were functionally annotated. Genes assigned to carbohydrate-active enzyme classes were also identified during the study. A total of 80 putative effector candidates were predicted and functionally annotated. The C. sesami genome sequence is available at DDBJ/ENA/GenBank, and other associated information is submitted to Mendeley's data. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03468-4.
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Affiliation(s)
- Shagun Sinha
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
- Center of Advanced Studies in Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - Sudhir Navathe
- Agharkar Research Institute, G. G. Agarkar Road, Pune, Maharashtra 411004 India
| | - Sakshi Singh
- Core Unit for Molecular Tumor Diagnostics, National Center for Tumor Diseases, German Cancer Research Center (DKFZ), Dresden, 01307 Germany
| | - Deepak K. Gupta
- Neogen Informatics Inc, Office 101, First Floor, A-121, Vikas Marg, New Delhi, 110092 India
| | - Ravindra Nath Kharwar
- Center of Advanced Studies in Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - Ramesh Chand
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
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15
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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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16
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Sirany T, Tadele E. Economics of Sesame and Its Use Dynamics in Ethiopia. ScientificWorldJournal 2022; 2022:1263079. [PMID: 36081605 PMCID: PMC9448608 DOI: 10.1155/2022/1263079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022] Open
Abstract
Ethiopia's oilseed industry makes a major contribution to foreign exchange revenues. Ethiopia's three main oilseed crops (sesame, soybean, and Niger seed) account for about 20% of the country's total agricultural export profits, second only to coffee. Even though Ethiopia is one of the world's largest producers and exporters of sesame seeds, the country is facing increasing supply and demand restrictions. This paper begins with an examination of one of the most prominent oil crops in the country. It is a highly adaptable crop that may be used for anything from subsistence to commercial output. We established a comprehensive scientific understanding of the crop using a systematic review of the current literature and deductive logical reasoning that can be used to inform future research and policies. Various exclusion and inclusion criteria were used to filter the most notable findings. Millions of growers and other market participants are employed throughout the oilseed value chain. Reduced sesame productivity, pests and diseases, and limited access to modern technologies are all severe supply-side constraints. On the demand side, traders and market distortion, as well as an artificially higher home price and the ease with which unskilled labor can enter the market, are all factors. Other demand-side constraints include worldwide price volatility, a highly concentrated export market, and intense global competition. Ethiopia's sesame seed development potential is being severely hampered by these restrictions. If farmers, dealers, and the government do not address these issues strategically, the country may soon lose its competitiveness in the global sesame seed market. This will contribute to Ethiopia's ongoing discussion about how to better inform private and public sector policies and investments to increase sesame production, transform agriculture, improve nutrition and food systems, and be able to ease supply- and demand-side restrictions. In a nutshell, an increased area under cultivation combined with best agronomic practices could boost sesame production. Farmers, policymakers, researchers, and other stakeholders must thus intervene to enhance sesame production. Future studies should concentrate on how to boost sesame output in farmers' fields while following appropriate sesame production technology and agronomic principles.
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Affiliation(s)
- Teshome Sirany
- Department of Rural Development, Debre Markos University, Debre Marqos, Ethiopia
| | - Esubalew Tadele
- Department of Agricultural Economics, Debre Markos University, Debre Marqos, Ethiopia
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17
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Jia KH, Liu H, Zhang RG, Xu J, Zhou SS, Jiao SQ, Yan XM, Tian XC, Shi TL, Luo H, Li ZC, Bao YT, Nie S, Guo JF, Porth I, El-Kassaby YA, Wang XR, Chen C, Van de Peer Y, Zhao W, Mao JF. Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome. HORTICULTURE RESEARCH 2021; 8:177. [PMID: 34465761 PMCID: PMC8408255 DOI: 10.1038/s41438-021-00614-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 05/11/2023]
Abstract
Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.
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Affiliation(s)
- Kai-Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hui Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, 261000, Shandong, China
| | - Jie Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shan-Shan Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Mei Yan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Chan Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Tian-Le Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hang Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhi-Chao Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yu-Tao Bao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jing-Fang Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xiao-Ru Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87, Umeå, Sweden.
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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18
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Gupta P, Geniza M, Naithani S, Phillips JL, Haq E, Jaiswal P. Chia ( Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:667678. [PMID: 34354718 PMCID: PMC8330693 DOI: 10.3389/fpls.2021.667678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/09/2021] [Indexed: 06/12/2023]
Abstract
Chia (Salvia hispanica L.), now a popular superfood and a pseudocereal, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids (PUFAs). At present, the genomic and genetic information available in the public domain for this crop are scanty, which hinders an understanding of its growth and development and genetic improvement. We report an RNA-sequencing (RNA-Seq)-based comprehensive transcriptome atlas of Chia sampled from 13 tissue types covering vegetative and reproductive growth stages. We used ~355 million high-quality reads of total ~394 million raw reads from transcriptome sequencing to generate de novo reference transcriptome assembly and the tissue-specific transcript assemblies. After the quality assessment of the merged assemblies and implementing redundancy reduction methods, 82,663 reference transcripts were identified. About 65,587 of 82,663 transcripts were translated into 99,307 peptides, and we were successful in assigning InterPro annotations to 45,209 peptides and gene ontology (GO) terms to 32,638 peptides. The assembled transcriptome is estimated to have the complete sequence information for ~86% of the genes found in the Chia genome. Furthermore, the analysis of 53,200 differentially expressed transcripts (DETs) revealed their distinct expression patterns in Chia's vegetative and reproductive tissues; tissue-specific networks and developmental stage-specific networks of transcription factors (TFs); and the regulation of the expression of enzyme-coding genes associated with important metabolic pathways. In addition, we identified 2,411 simple sequence repeats (SSRs) as potential genetic markers from the transcripts. Overall, this study provides a comprehensive transcriptome atlas, and SSRs, contributing to building essential genomic resources to support basic research, genome annotation, functional genomics, and molecular breeding of Chia.
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Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeremy L. Phillips
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Ebaad Haq
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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19
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Mei H, Liu Y, Cui C, Hu C, Xie F, Zheng L, Du Z, Wu K, Jiang X, Zheng Y, Ma Q. QTL mapping of yield-related traits in sesame. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:43. [PMID: 37309387 PMCID: PMC10236103 DOI: 10.1007/s11032-021-01236-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 05/27/2021] [Indexed: 06/14/2023]
Abstract
Improving yield is one of the most important targets of sesame breeding. Identifying quantitative trait loci (QTLs) of yield-related traits is a prerequisite for marker-assisted selection (MAS) and QTL/gene cloning. In this study, a BC1 population was developed and genotyped with the specific-locus amplified fragment (SLAF) sequencing technology, and a high-density genetic map was constructed. The map consisted of 13 linkage groups, contained 3528 SLAF markers, and covered a total of 1312.52 cM genetic distance, with an average distance of 0.37 cM between adjacent markers. Based on the map, 46 significant QTLs were identified for seven yield-related traits across three environments. These QTLs distributed on 11 linkage groups, each explaining 2.34-71.41% of the phenotypic variation. Of the QTLs, 23 were stable QTLs that were detected in more than one environment, and 20 were major QTLs that explained more than 10% of the corresponding phenotypic variation in at least one environment. Favorable alleles of 38 QTLs originated from the locally adapted variety, Yuzhi 4; the exotic germplasm line, BS, contributed favorable alleles to only 8 QTLs. The results should provide useful information for future molecular breeding and functional gene cloning. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01236-x.
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Affiliation(s)
- Hongxian Mei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450008 People’s Republic of China
| | - Yanyang Liu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450008 People’s Republic of China
| | - Chengqi Cui
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450008 People’s Republic of China
| | - Chengda Hu
- Henan Institute of Meteorological Science, Zhengzhou, 450003 People’s Republic of China
| | - Fuxin Xie
- Nanyang Academy of Agricultural Sciences, Nanyang, 473085 People’s Republic of China
| | - Lei Zheng
- Luohe Academy of Agricultural Sciences, Luohe, 462300 People’s Republic of China
| | - Zhenwei Du
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450008 People’s Republic of China
| | - Ke Wu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450008 People’s Republic of China
| | - Xiaolin Jiang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450008 People’s Republic of China
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450008 People’s Republic of China
| | - Qingrong Ma
- Henan Institute of Meteorological Science, Zhengzhou, 450003 People’s Republic of China
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20
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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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Weldemichael MY, Baryatsion YT, Sbhatu DB, Gebresamuel Abraha G, Juhar HM, Kassa AB, Baraki Sibhatu F, Gebremedhn HM, Gebrelibanos TS, Mebrahtu Mossa M, Gebru MM, Meresa BK, Teklay M, Berhe BD, Gebru HA. Effect of Sodium Azide on Quantitative and Qualitative Stem Traits in the M2 Generation of Ethiopian Sesame ( Sesamum indicum L.) Genotypes. ScientificWorldJournal 2021; 2021:6660711. [PMID: 34007247 PMCID: PMC8110370 DOI: 10.1155/2021/6660711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/15/2021] [Accepted: 04/24/2021] [Indexed: 11/17/2022] Open
Abstract
The emerging oilseed crop Sesamum indicum, also known as the queen of oilseeds, is being grown globally for its oil content for medicinal and nutritional values. One of the key challenges of sesame cultivation is its low productivity. In the present study, sodium azide (NaN3) was used as a chemical mutagen. The aim of this study was to examine the effect of NaN3 on quantitative and qualitative stem traits in the M2 generation of Ethiopian sesame (Sesamum indicum L.) genotypes. Seeds of fourteen sesame genotypes were used in this study and germinated and grown under greenhouse conditions. Different qualitative and quantitative data were collected and analyzed. Traits such as plant height, ground distance to first distance, and internode length were significantly affected by NaN3 treatment. The highest plant height was recorded in the control on Humera 1 and Baha Necho genotypes, while the lowest was observed on Setit 2 and Hirhir treated with the chemical. The highest ground distance to the first branch was observed in Gumero, while the least ground distance was recorded in Setit 1 in the treated and control genotypes, respectively. The best internode length was recorded on Setit 2 and ADI in the control, while the lowest internode length was observed in Setit 1 genotype treated with sodium azide. Genotypes such as ACC44, ADI, Baha Necho, Borkena, Gonder 1, and Setit 1 treated with NaN3 have showed glabrous type of stem hairiness. All the fourteen genotypes (both treated and control) were clustered into four groups. In conclusion, we observed a highly significant variation among the genotypes due the effect of the chemical and genotypes themselves. Hence, this report would create more genetic diversity for further sesame genetic research improvements.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Medhin Teklay
- Tigrai Biotechnology Center Pvt. Ltd. Co., P.O. Box 223, Mekelle, Tigrai, Ethiopia
| | | | - Haftay Abadi Gebru
- Tigrai Biotechnology Center Pvt. Ltd. Co., P.O. Box 223, Mekelle, Tigrai, Ethiopia
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22
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Yan W, Ni Y, Liu X, Zhao H, Chen Y, Jia M, Liu M, Liu H, Tian B. The mechanism of sesame resistance against Macrophomina phaseolina was revealed via a comparison of transcriptomes of resistant and susceptible sesame genotypes. BMC PLANT BIOLOGY 2021; 21:159. [PMID: 33781203 PMCID: PMC8008628 DOI: 10.1186/s12870-021-02927-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/15/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum) charcoal rot, a destructive fungal disease caused by Macrophomina phaseolina (Tassi) Goid (MP), is a great threat to the yield and quality of sesame. However, there is a lack of information about the gene-for-gene relationship between sesame and MP, and the molecular mechanism behind the interaction is not yet clear. The aim of this study was to interpret the molecular mechanism of sesame resistance against MP in disease-resistant (DR) and disease-susceptible (DS) genotypes based on transcriptomics. This is the first report of the interaction between sesame and MP using this method. RESULTS A set of core genes that response to MP were revealed by comparative transcriptomics and they were preferentially associated with GO terms such as ribosome-related processes, fruit ripening and regulation of jasmonic acid mediated signalling pathway. It is also exhibited that translational mechanism and transcriptional mechanism could co-activate in DR so that it can initiate the immunity to MP more rapidly. According to weighted gene co-expression network analysis (WGCNA) of differentially expressed gene sets between two genotypes, we found that leucine-rich repeat receptor-like kinase (LRR-RLK) proteins may assume an important job in sesame resistance against MP. Notably, compared with DS, most key genes were induced in DR such as pattern recognition receptors (PRRs) and resistance genes, indicating that DR initiated stronger pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Finally, the study showed that JA/ET and SA signalling pathways all play an important role in sesame resistance to MP. CONCLUSIONS The defence response to MP of sesame, a complex bioprocess involving many phytohormones and disease resistance-related genes, was illustrated at the transcriptional level in our investigation. The findings shed more light on further understanding of different responses to MP in resistant and susceptible sesame.
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Affiliation(s)
- Wenqing Yan
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yunxia Ni
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, Henan, China
| | - Xintao Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, Henan, China
| | - Hui Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, Henan, China
| | - Yanhua Chen
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Min Jia
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Mingming Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Hongyan Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, Henan, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Baoming Tian
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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Liang J, Sun J, Ye Y, Yan X, Yan T, Rao Y, Zhou H, Le M. QTL mapping of PEG-induced drought tolerance at the early seedling stage in sesame using whole genome re-sequencing. PLoS One 2021; 16:e0247681. [PMID: 33626101 PMCID: PMC7904189 DOI: 10.1371/journal.pone.0247681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 02/10/2021] [Indexed: 11/19/2022] Open
Abstract
Improvement in sesame drought tolerance at seedling stage is important for yield stability. Genetic approaches combing with conventional breeding is the most effective way to develop drought-tolerant cultivars. In this study, three traits and their relative values, including seedling weight (SW), shoot length (SL) and root length (RL), were evaluated under control and osmotic conditions in a recombinant inbred line (RIL) population derived from cross of Zhushanbai and Jinhuangma. Significant variation and high broad sense heritability were observed for all traits except SW under stress condition in the population. With this population, a high-density linkage map with 1354 bin markers was constructed through whole genome re-sequencing (WGS) strategy. Quantitative trait loci (QTL) mapping was performed for all the traits. A total of 34 QTLs were detected on 10 chromosomes. Among them, 13 stable QTLs were revealed in two independent experiments, eight of them were associated with traits under water stress condition. One region on chromosome 12 related to RL under osmotic condition and relative RL had the highest LOD value and explained the largest phenotypic variation among all the QTLs detected under water stress condition. These findings will provide new genetic resources for molecular improvement of drought tolerance and candidate gene identification in sesame.
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Affiliation(s)
- Junchao Liang
- Crop Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- Nanchang Branch of National Center of Oilcrops Improvement, Nanchang, China
- Jiangxi Province Key Laboratory of Oilcrops Biology, Nanchang, China
| | - Jian Sun
- Crop Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- Nanchang Branch of National Center of Oilcrops Improvement, Nanchang, China
- Jiangxi Province Key Laboratory of Oilcrops Biology, Nanchang, China
- * E-mail: (JS); (ML)
| | - Yanying Ye
- Crop Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- Nanchang Branch of National Center of Oilcrops Improvement, Nanchang, China
- Jiangxi Province Key Laboratory of Oilcrops Biology, Nanchang, China
| | - Xiaowen Yan
- Crop Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- Nanchang Branch of National Center of Oilcrops Improvement, Nanchang, China
- Jiangxi Province Key Laboratory of Oilcrops Biology, Nanchang, China
| | - Tingxian Yan
- Crop Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- Nanchang Branch of National Center of Oilcrops Improvement, Nanchang, China
- Jiangxi Province Key Laboratory of Oilcrops Biology, Nanchang, China
| | - Yueliang Rao
- Crop Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- Nanchang Branch of National Center of Oilcrops Improvement, Nanchang, China
- Jiangxi Province Key Laboratory of Oilcrops Biology, Nanchang, China
| | - Hongying Zhou
- Crop Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- Nanchang Branch of National Center of Oilcrops Improvement, Nanchang, China
- Jiangxi Province Key Laboratory of Oilcrops Biology, Nanchang, China
| | - Meiwang Le
- Nanchang Branch of National Center of Oilcrops Improvement, Nanchang, China
- Jiangxi Province Key Laboratory of Oilcrops Biology, Nanchang, China
- Horticulture Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
- * E-mail: (JS); (ML)
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24
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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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Ma Y, Cui G, Chen T, Ma X, Wang R, Jin B, Yang J, Kang L, Tang J, Lai C, Wang Y, Zhao Y, Shen Y, Zeng W, Peters RJ, Qi X, Guo J, Huang L. Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza. Nat Commun 2021; 12:685. [PMID: 33514704 PMCID: PMC7846762 DOI: 10.1038/s41467-021-20959-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/01/2021] [Indexed: 11/09/2022] Open
Abstract
Tanshinones are the bioactive nor-diterpenoid constituents of the Chinese medicinal herb Danshen (Salvia miltiorrhiza). These groups of chemicals have the characteristic furan D-ring, which differentiates them from the phenolic abietane-type diterpenoids frequently found in the Lamiaceae family. However, how the 14,16-epoxy is formed has not been elucidated. Here, we report an improved genome assembly of Danshen using a highly homozygous genotype. We identify a cytochrome P450 (CYP71D) tandem gene array through gene expansion analysis. We show that CYP71D373 and CYP71D375 catalyze hydroxylation at carbon-16 (C16) and 14,16-ether (hetero)cyclization to form the D-ring, whereas CYP71D411 catalyzes upstream hydroxylation at C20. In addition, we discover a large biosynthetic gene cluster associated with tanshinone production. Collinearity analysis indicates a more specific origin of tanshinones in Salvia genus. It illustrates the evolutionary origin of abietane-type diterpenoids and those with a furan D-ring in Lamiaceae.
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Affiliation(s)
- Ying Ma
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guanghong Cui
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Tong Chen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaohui Ma
- College of Pharmaceutical Science, Yunnan University of Traditional Chinese Medicine, Kunming, China
| | - Ruishan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Baolong Jin
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jian Yang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Liping Kang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jinfu Tang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Changjiangsheng Lai
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yanan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yujun Zhao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ye Shen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wen Zeng
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Reuben J Peters
- Roy J. Carver Dep. of Biochem., Biophys. & Mol. Biol., Iowa State University, Ames, IA, USA
| | - Xiaoquan Qi
- Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
| | - Juan Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
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Martínez Arbas S, Narayanasamy S, Herold M, Lebrun LA, Hoopmann MR, Li S, Lam TJ, Kunath BJ, Hicks ND, Liu CM, Price LB, Laczny CC, Gillece JD, Schupp JM, Keim PS, Moritz RL, Faust K, Tang H, Ye Y, Skupin A, May P, Muller EEL, Wilmes P. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nat Microbiol 2021; 6:123-135. [PMID: 33139880 PMCID: PMC7752763 DOI: 10.1038/s41564-020-00794-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 09/11/2020] [Indexed: 02/07/2023]
Abstract
Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE-host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR-Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid-host and phage-host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant 'Candidatus Microthrix parvicella' population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes.
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Affiliation(s)
- Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Megeno S.A., Esch-sur-Alzette, Luxembourg
| | - Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura A Lebrun
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Sujun Li
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Tony J Lam
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Benoît J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nathan D Hicks
- TGen North, Flagstaff, AZ, USA
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Cindy M Liu
- TGen North, Flagstaff, AZ, USA
- Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Lance B Price
- TGen North, Flagstaff, AZ, USA
- Department of Environmental and Occupational Health, Miken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | | | - Paul S Keim
- TGen North, Flagstaff, AZ, USA
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Karoline Faust
- Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Haixu Tang
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Yuzhen Ye
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Neuroscience, University of California, La Jolla, CA, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emilie E L Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Microbiology, Genomics and the Environment, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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27
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Nagarajan MB, Tentori AM, Zhang WC, Slack FJ, Doyle PS. Spatially resolved and multiplexed MicroRNA quantification from tissue using nanoliter well arrays. MICROSYSTEMS & NANOENGINEERING 2020; 6:51. [PMID: 32419951 PMCID: PMC7211184 DOI: 10.1038/s41378-020-0169-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 05/27/2023]
Abstract
Spatially resolved gene expression patterns are emerging as a key component of medical studies, including companion diagnostics, but technologies for quantification and multiplexing are limited. We present a method to perform spatially resolved and multiplexed microRNA (miRNA) measurements from formalin-fixed, paraffin-embedded (FFPE) tissue. Using nanoliter well arrays to pixelate the tissue section and photopatterned hydrogels to quantify miRNA, we identified differentially expressed miRNAs in tumors from a genetically engineered mouse model for non-small cell lung cancer (K-rasLSL-G12D/+; p53fl/fl). This technology could be used to quantify heterogeneities in tissue samples and lead to informed, biomarker-based diagnostics.
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Affiliation(s)
- Maxwell B. Nagarajan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Augusto M. Tentori
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Wen Cai Zhang
- HMS Initiative for RNA Medicine, Department of Pathology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215 USA
| | - Frank J. Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215 USA
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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Li C, Li X, Liu H, Wang X, Li W, Chen MS, Niu LJ. Chromatin Architectures Are Associated with Response to Dark Treatment in the Oil Crop Sesamum indicum, Based on a High-Quality Genome Assembly. PLANT & CELL PHYSIOLOGY 2020; 61:978-987. [PMID: 32154879 DOI: 10.1093/pcp/pcaa026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/01/2020] [Indexed: 05/21/2023]
Abstract
Eukaryotic chromatin is tightly packed into hierarchical structures, allowing appropriate gene transcription in response to environmental and developmental cues. Here, we provide a chromosome-scale de novo genome assembly of sesame with a total length of 292.3 Mb and a scaffold N50 of 20.5 Mb, containing estimated 28,406 coding genes using Pacific Biosciences long reads combined with a genome-wide chromosome conformation capture (Hi-C) approach. Based on this high-quality reference genome, we detected changes in chromatin architectures between normal growth and dark-treated sesame seedlings. Gene expression level was significantly higher in 'A' compartment and topologically associated domain (TAD) boundary regions than in 'B' compartment and TAD interior regions, which is coincident with the enrichment of H4K3me3 modification in these regions. Moreover, differentially expressed genes (DEGs) induced by dark treated were enriched in the changed TAD-related regions and genomic differential contact regions. Gene Ontology (GO) enrichment analysis of DEGs showed that genes related to 'response to stress' and 'photosynthesis' functional categories were enriched, which corresponds to dark treatment. These results suggested that chromatin organization is associated with gene transcription in response to dark treatment in sesame. Our results will facilitate the understanding of regulatory mechanisms in response to environmental cues in plants.
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Affiliation(s)
- Chaoqiong Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Xiaoli Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Hongzhan Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Xueqin Wang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan 466001, China
| | - Weifeng Li
- Sesame Experiment Station, Zhoukou Academy of Agricultural Sciences, Zhoukou, Henan 466001, China
| | - Mao-Sheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Long-Jian Niu
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Department of Biology, Nankai University, Tianjin 660885, China
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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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Miao H, Li C, Duan Y, Wei L, Ju M, Zhang H. Identification of a Sidwf1 gene controlling short internode length trait in the sesame dwarf mutant dw607. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:73-86. [PMID: 31686114 DOI: 10.1007/s00122-019-03441-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
SiDWF1 encodes a gibberellin receptor GID1B-like protein controlling the internode length and plant height in sesame. Sesame is a high-height crop. Here we systematically analyzed the morphological and genetic characters of the sesame dwarf mutant dw607 (dwf1 type). The plant height and the internode length of dw607 significantly declined, while the thousand seed weight (TSW) significantly increased (P < 0.01). The cell size of stem parenchyma and pith tissue reduced, and vascular bundle cells and parenchyma tissue arranged much tighter in the dwarf mutant. Based on the cross-population association mapping of a RIL population of the cross 'dw607 (dwf1) × 15N41 (wt type),' the target interval linked to the short internode length was located on C9.scaffold2 of SiChr.4 in sesame. We further screened the 58 variants using the genomic variant data of 824 germplasm and BSA DNA pools and determined the target gene Sidwf1. The SNP mutation of C1057 to T1057 resulted in the amino acid change of P150 (proline) to S150 (serine) in SiDWF1. SiDWF1 gene allele is 1,638 bp and encodes a gibberellin receptor GID1B-like protein. Transcription profile assay reflected that Sidwf1 is highly expressed in leaf, stem, bud, and capsule tissues. The dynamic variation in endogenous GA3 content in dw607 and the wild type was also monitored in this study. The results revealed the molecular genetic mechanism of the internode length and plant height trait in sesame for the first time. The findings supply the theoretical and material basis for developing the marker-assisted selection (MAS) breeding in sesame.
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Affiliation(s)
- Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, People's Republic of China.
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31
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Du H, Zhang H, Wei L, Li C, Duan Y, Wang H. A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.). BMC PLANT BIOLOGY 2019; 19:588. [PMID: 31881840 PMCID: PMC6935206 DOI: 10.1186/s12870-019-2172-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/28/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. RESULTS The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. CONCLUSIONS This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.
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Affiliation(s)
- Hua Du
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Huili Wang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
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A SNP Mutation of SiCRC Regulates Seed Number Per Capsule and Capsule Length of cs1 Mutant in Sesame. Int J Mol Sci 2019; 20:ijms20164056. [PMID: 31434218 PMCID: PMC6720709 DOI: 10.3390/ijms20164056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/12/2019] [Accepted: 08/15/2019] [Indexed: 11/16/2022] Open
Abstract
Seed number per capsule (SNC) is a major factor influencing seed yield and is an important trait with complex gene interaction effects. We first performed genetic analysis, gene cloning, and molecular mechanism study for an EMS-induced sesame mutant cs1 with fewer SNC and shorter capsule length (CL). The mutant traits were due to the pleiotropism of a regressive gene (Sics1). Capsule hormone determination showed that five out of 12 hormones, including auxin indole-3-acetic acid (IAA), had significantly different levels between wild type (WT) and mutant type (MT). KEGG pathway analysis showed that plant hormone signal transduction, especially the auxin signal transduction pathway, was the most abundant differentially expressed signaling pathway. After the cross-population association and regional genome screening, we found that three homozygous loci were retained in cs1. Further analysis of these three loci resulted in the identification of SiCRC as the candidate gene for cs1. SiCRC consists of seven exons and six introns encoding 163 amino acids. The SiCRC in cs1 showed a point mutation at intron 5 and exon 6 junction, resulting in the splice site being frame-shifted eight nucleotides further downstream, causing incorrect splicing. Taken together, we assumed the SNP mutation in SiCRC disrupted the function of the transcription factor, which might act downstream of the CRC-auxin signal transduction pathway, resulting in a shorter CL and less SNC mutation of cs1 in sesame. Our results highlight the molecular framework underlying the transcription factor CRC-mediated role of auxin transduction in SNC and CL development.
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33
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Zhao Q, Yang J, Cui MY, Liu J, Fang Y, Yan M, Qiu W, Shang H, Xu Z, Yidiresi R, Weng JK, Pluskal T, Vigouroux M, Steuernagel B, Wei Y, Yang L, Hu Y, Chen XY, Martin C. The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis. MOLECULAR PLANT 2019; 12:935-950. [PMID: 30999079 DOI: 10.1016/j.molp.2019.04.002] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/20/2019] [Accepted: 04/07/2019] [Indexed: 05/19/2023]
Abstract
Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, "Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed that a specialized metabolic pathway for the synthesis of 4'-deoxyflavone bioactives evolved in the genus Scutellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its new function following recent mutations, and that four genes encoding enzymes in the 4'-deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo- and subfunctionalizations were involved in the evolution of 4'-deoxyflavone synthesis in the genus Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants.
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Affiliation(s)
- Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Meng-Ying Cui
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yumin Fang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wenqing Qiu
- Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Huiwen Shang
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhicheng Xu
- Novogene Bioinformatics Institute, Beijing, China
| | | | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | | | | | - Yukun Wei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yonghong Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Ya Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Cathie Martin
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; John Innes Centre, Norwich NR4 7UH, UK.
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Michailidis D, Angelis A, Aligiannis N, Mitakou S, Skaltsounis L. Recovery of Sesamin, Sesamolin, and Minor Lignans From Sesame Oil Using Solid Support-Free Liquid-Liquid Extraction and Chromatography Techniques and Evaluation of Their Enzymatic Inhibition Properties. Front Pharmacol 2019; 10:723. [PMID: 31316384 PMCID: PMC6610769 DOI: 10.3389/fphar.2019.00723] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/05/2019] [Indexed: 12/14/2022] Open
Abstract
In this study, an integrated process for the recovery of sesamin and sesamolin, two high added-value lignans of sesame oil (SO) was developed, using synchronous extraction and chromatography techniques. The extraction of SO phenolic content was studied using two different extraction techniques: Annular centrifugal extraction (ACE) and centrifugal partition extraction (CPE). The derived data of each experiment were compared in terms of revealing the yields, time, and solvents consumption showing that CPE is the most effective technique, concerning the solvent consumption. The isolation of lignans was achieved using centrifugal partition chromatography (CPC) both on semi-preparative and preparative scale. The biphasic system used for this purpose consisted of the following solvents: n-Hex/EtOAc/EtOH/H2O in proportion 2:3:3:2 (v/v/v/v) and direct recovery of the two major lignans sesamin and sesamolin was achieved. In parallel the CPC analysis resulted in the isolation of four minor lignans of sesame oil, i.e., samin, sesamol, sesaminol, and episesaminol. Structure elucidation of isolated lignans was based on HRMS/MS and NMR experiments. High-performance liquid chromatography (HPLC) was employed for quantitative analysis of the obtained extracts to determine the purity of the isolated compounds as well. The results of this study demonstrated that sesamin and sesamolin were recovered in purity higher than 95%, verifying the effectiveness of the purposed separation methodology. Finally, due to the general application of sesame oil in cosmetic industry, all the pure compounds were evaluated for their tyrosinase, elastase, collagenase, and hyaluronidase inhibition activity.
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Affiliation(s)
- Dimitris Michailidis
- Faculty of Pharmacy, Department of Pharmacognosy and Natural Products Chemistry, University of Athens, Athens, Greece
| | - Apostolis Angelis
- Faculty of Pharmacy, Department of Pharmacognosy and Natural Products Chemistry, University of Athens, Athens, Greece
| | - Nektarios Aligiannis
- Faculty of Pharmacy, Department of Pharmacognosy and Natural Products Chemistry, University of Athens, Athens, Greece
| | - Sofia Mitakou
- Faculty of Pharmacy, Department of Pharmacognosy and Natural Products Chemistry, University of Athens, Athens, Greece
| | - Léandros Skaltsounis
- Faculty of Pharmacy, Department of Pharmacognosy and Natural Products Chemistry, University of Athens, Athens, Greece
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Genome-wide association study of vitamin E using genotyping by sequencing in sesame (Sesamum indicum). Genes Genomics 2019; 41:1085-1093. [PMID: 31197567 DOI: 10.1007/s13258-019-00837-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/31/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND At least eight structurally related forms of vitamin E occur in nature, four tocopherols and four tocotrienols, all of which are potent membrane-soluble antioxidants. In this study, we detected two major isoforms in sesame (Sesamum indicum L.) seed: γ-tocopherol and β-tocotrienol. The objective of this study is to investigate the genetic basis of these vitamin E isoforms. METHODS We conducted a genome-wide association study (GWAS) using 5962 genome-wide markers, acquired from 96 core sesame accessions. The GWAS was performed using generalized linear (GLM) and mixed linear (MLM) models. RESULTS LG08_6621957, on chromosome 8, was detected as having a significant association with γ-tocopherol in both models. It explained 20.9% of γ-tocopherol variation in sesame. For β-tocotrienol, no significant loci were detected according to the two models, but one locus, SLG03_13104062, explained 17.8% of the phenotypic variation. Based on structure and phylogenetic studies, the 96 accessions were clearly clustered into two subpopulations. CONCLUSION This study on sesame demonstrates and provides an evidence that genotyping by sequencing (GBS) based GWAS can be used to identifying important loci for small growing crops. The significant SNPs or genes could be useful for improving the vitamin E content in sesame breeding programs.
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Yu J, Golicz AA, Lu K, Dossa K, Zhang Y, Chen J, Wang L, You J, Fan D, Edwards D, Zhang X. Insight into the evolution and functional characteristics of the pan-genome assembly from sesame landraces and modern cultivars. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:881-892. [PMID: 30315621 PMCID: PMC6587448 DOI: 10.1111/pbi.13022] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/28/2018] [Accepted: 10/10/2018] [Indexed: 05/08/2023]
Abstract
Sesame (Sesamum indicum L.) is an important oil crop renowned for its high oil content and quality. Recently, genome assemblies for five sesame varieties including two landraces (S. indicum cv. Baizhima and Mishuozhima) and three modern cultivars (S. indicum var. Zhongzhi13, Yuzhi11 and Swetha), have become available providing a rich resource for comparative genomic analyses and gene discovery. Here, we employed a reference-assisted assembly approach to improve the draft assemblies of four of the sesame varieties. We then constructed a sesame pan-genome of 554.05 Mb. The pan-genome contained 26 472 orthologous gene clusters; 15 409 (58.21%) of them were core (present across all five sesame genomes), whereas the remaining 41.79% (11 063) clusters and the 15 890 variety-specific genes were dispensable. Comparisons between varieties suggest that modern cultivars from China and India display significant genomic variation. The gene families unique to the sesame modern cultivars contain genes mainly related to yield and quality, while those unique to the landraces contain genes involved in environmental adaptation. Comparative evolutionary analysis indicates that several genes involved in plant-pathogen interaction and lipid metabolism are under positive selection, which may be associated with sesame environmental adaption and selection for high seed oil content. This study of the sesame pan-genome provides insights into the evolution and genomic characteristics of this important oilseed and constitutes a resource for further sesame crop improvement.
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Affiliation(s)
- Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleMelbourneVicAustralia
| | - Kun Lu
- College of Agronomy and Biotechnology, and Academy of Agricultural SciencesSouthwest UniversityBeibeiChongqingChina
| | - Komivi Dossa
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
- Centre d'Etudes Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS)ThièsSenegal
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
| | - Jinfeng Chen
- Department of Plant Pathology & MicrobiologyUniversity of CaliforniaRiversideCAUSA
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
| | | | - David Edwards
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research InstituteThe Chinese Academy of Agricultural SciencesWuhanChina
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Dar AA, Kancharla PK, Chandra K, Sodhi YS, Arumugam N. Assessment of variability in lignan and fatty acid content in the germplasm of Sesamum indicum L. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2019; 56:976-986. [PMID: 30906055 PMCID: PMC6400779 DOI: 10.1007/s13197-018-03564-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/17/2018] [Accepted: 12/26/2018] [Indexed: 10/27/2022]
Abstract
Information on the variability available in lignan and fatty acid content in the oilseed crop of Sesamum indicum has been limited. This article presents and discusses the composition, quantity, and variability available for the two traits in the sesame germplasm that are grown in diverse agro climatic regions of India. HPLC and GC analysis of sesame seeds harvested over a period of three crop seasons revealed a considerable amount of variability in lignan and fatty acids. The antioxidant lignans sesamol, sesamin and sesamolin were observed to be in the range of 0.16-3.24, 2.10-5.98 and 1.52-3.76 mg/g of seed, respectively. Similarly oleic and linoleic acids, respectively, have ranged from 34.71 to 45.61% and 38.49 to 49.60%. The black sesame seeds were found rich in sesamin, sesamolin, total lignan content and oleic acid and are thus identified nutritionally and pharmaceutically more important than white and brown seeds. Pearson statistics showed a strong correlation between the components within a particular trait and also some correlation was found between the traits. The study revealed promising cultivars for use in sesame breeding aimed at improving lignan and fatty acid contents, and can be thus directly used in human foods, nutrition, health and welfare.
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Affiliation(s)
- Aejaz Ahmad Dar
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605 014 India
| | - Pavan Kumar Kancharla
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605 014 India
| | - Kishan Chandra
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605 014 India
| | - Yaspal Singh Sodhi
- Department of Genetics, Centre for Genetic Manipulation of Crop Plants, University of Delhi, South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Neelakantan Arumugam
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605 014 India
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Nock CJ, Hardner CM, Montenegro JD, Ahmad Termizi AA, Hayashi S, Playford J, Edwards D, Batley J. Wild Origins of Macadamia Domestication Identified Through Intraspecific Chloroplast Genome Sequencing. FRONTIERS IN PLANT SCIENCE 2019; 10:334. [PMID: 30949191 PMCID: PMC6438079 DOI: 10.3389/fpls.2019.00334] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 03/04/2019] [Indexed: 05/13/2023]
Abstract
Identifying the geographic origins of crops is important for the conservation and utilization of novel genetic variation. Even so, the origins of many food crops remain elusive. The tree nut crop macadamia has a remarkable domestication history, from subtropical rain forests in Australia through Hawaii to global cultivation all within the last century. The industry is based primarily on Macadamia integrifolia and M. integrifolia-M. tetraphylla hybrid cultivars with Hawaiian cultivars the main contributors to world production. Sequence data from the chloroplast genome assembled using a genome skimming strategy was used to determine population structure among remnant populations of the main progenitor species, M. integrifolia. Phylogenetic analysis of a 506 bp chloroplast SNP alignment from 64 wild and cultivated accessions identified phylogeographic structure and deep divergences between clades providing evidence for historical barriers to seed dispersal. High levels of variation were detected among wild accessions. Most Hawaiian cultivars, however, shared a single chlorotype that was also present at two wild sites at Mooloo and Mt Bauple from the northernmost distribution of the species in south-east Queensland. Our results provide evidence for a maternal genetic bottleneck during early macadamia domestication, and pinpoint the likely source of seed used to develop the Hawaiian cultivars. The extensive variability and structuring of M. integrifolia chloroplast genomic variation detected in this study suggests much unexploited genetic diversity is available for improvement of this recently domesticated crop.
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Affiliation(s)
- Catherine J. Nock
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
- *Correspondence: Catherine J. Nock,
| | - Craig M. Hardner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | | | - Ainnatul A. Ahmad Termizi
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Satomi Hayashi
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Julia Playford
- Queensland Department of Environment and Science, Brisbane, QLD, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
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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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Zhang H, Miao H, Wei L, Li C, Duan Y, Xu F, Qu W, Zhao R, Ju M, Chang S. Identification of a SiCL1 gene controlling leaf curling and capsule indehiscence in sesame via cross-population association mapping and genomic variants screening. BMC PLANT BIOLOGY 2018; 18:296. [PMID: 30466401 PMCID: PMC6251216 DOI: 10.1186/s12870-018-1503-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 10/26/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Leaf shape can affect plantlet development and seed yield in sesame. The morphological, histological and genetic analyses of a sesame mutant cl1 (cl) with curly leaf and indehiscent capsule traits were performed in this study. In order to clone the cl1 gene for breeding selection, genome re-sequencing of the 130 individuals of cl1 × USA (0)-26 F2 population and a bulked segregation analysis (BSA) pool was carried out. The genome re-sequencing data of the 822 germplasm with normal leaf shape were applied. RESULTS For cl1 mutant, the adaxial/abaxial character of the parenchyma cells in the leaf blades is reduced. Results proved that the leaf curling trait is controlled by a recessive gene (Sicl1). Cross- population association of the F2 population of cl1 × USA (0)-26 indicated that the target cl locus was located on the interval C29 between C29_6522236 and C29_6918901 of SiChr. 1. Further regional genome variants screening determined the 6 candidate variants using genomic variants data of 822 natural germplasm and a BSA pool data. Of which, 5 markers C29_6717525, C29_6721553, C29_6721558, C29_6721563, and C29_6721565 existed in the same gene (C29.460). With the aid of the validation in the test F2 population of cl1 × Yuzhi 11 and natural germplasm, the integrated marker SiCLInDel1 (C29: 6721553-6721572) was determined as the target marker, and C29.460 was the target gene SiCL1 in sesame. SiCL1 is a KAN1 homolog with the full length of 6835 bp. In cl1, the 20 nucleic acids (CAGGTAGCTATGTATATGCA) of SiCLInDel1 marker were mutagenized into 6 nucleic acids (TCTTTG). The deletion led to a frameshift mutation and resulted in the earlier translation termination of the CL gene. The Sicl1 allele was shortened to 1829 bp. SiCL1 gene was expressed mainly in the tissues of stem, leaf, bud, capsule and seed. CONCLUSIONS SiCL1 encodes a transcription repressor KAN1 protein and controls leaf curling and capsule indehiscence in sesame. The findings provided an example of high-efficient gene cloning in sesame. The SiCL1 gene and the cl1 mutant supply the opportunity to explore the development regulation of leaf and capsule, and would improve the new variety breeding with high harvest mechanization adaption in sesame.
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Affiliation(s)
- Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Fangfang Xu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Wenwen Qu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Ruihong Zhao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Shuxian Chang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
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Marakli S. Identification and functional analyses of new sesame miRNAs (Sesamum indicum L.) and their targets. Mol Biol Rep 2018; 45:2145-2155. [PMID: 30209739 DOI: 10.1007/s11033-018-4373-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
Abstract
Plant microRNAs (miRNAs) have been commonly investigated during many years. Hundreds of miRNAs have been identified in many different plant species but there is very little information about the function of sesame (Sesamum indicum L.) miRNAs. For this purpose, in silico prediction of novel sesame miRNAs based on BLAST searches of the expressed sequence tag database was performed, using stringent criterias for miRNA annotation. The secondary structures of their precursor sequences, potential target genes of conserved and novel miRNAs were predicted and subjected to Gene Ontology (GO) annotation. mir447 and mir8140 were reported for the first time in sesame. Enrichment analysis of the GO with biological processes, cellular component and molecular functions revealed that these target genes were potentially involved in different metabolic pathways such as transcription factors, metabolism, growth and development, stress-related and even plant hormones. Results are valuable for figure out the gene regulation mechanism in sesame, using in the medicinal aspect of this plant species. Furthermore, these miRNAs and their profiled targets could provide the improvement of regulation and management, and even development of desirable traits in this plant.
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Affiliation(s)
- Sevgi Marakli
- Faculty of Arts and Sciences, Department of Biology, Amasya University, Ipekkoy, 05100, Amasya, Turkey.
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Purru S, Sahu S, Rai S, Rao AR, Bhat KV. GinMicrosatDb: a genome-wide microsatellite markers database for sesame ( Sesamum indicum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:929-937. [PMID: 30150867 PMCID: PMC6103941 DOI: 10.1007/s12298-018-0558-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 03/08/2018] [Accepted: 05/21/2018] [Indexed: 06/08/2023]
Abstract
Molecular breeding in sesame is still at infancy due to limited number of microsatellite markers available and the low level of polymorphism exhibited by them. Therefore, whole genome sequencing was used for development of microsatellite markers so as to ensure availability of substantial number of polymorphic markers for use in marker assisted breeding programs. Whole genome sequencing of sesame variety 'Swetha' was done using Illumina paired-end sequencing and Roche 454 shotgun sequencing technologies (GCA_000975565.1 in GenBank). 'GinMicrosatDb', a genome-wide microsatellite marker database has been developed using the whole genome sequence data of sesame variety 'Swetha'. The database consists of microsatellites localized on both linkage groups and scaffolds with their genomic co-ordinates. It provides five sets of forward and reverse primers for each of the microsatellite loci along with the flanking sequences, primer GC content, product size and melting temperature etc. The distribution of microsatellites can be viewed and selected through a genome browser as well as through a physical map. The newly identified microsatellite markers are expected to help sesame breeders in developing marker tags for traits of economic importance thereby bringing about greater efficiency in marker-assisted selection programs.
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Affiliation(s)
- Supriya Purru
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Sahu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Saurabh Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A. R. Rao
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - K. V. Bhat
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012 India
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Zhao R, Miao H, Song W, Chen C, Zhang H. Identification of sesame (Sesamum indicum L.) chromosomes using the BAC-FISH system. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:85-92. [PMID: 29030920 DOI: 10.1111/plb.12647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/09/2017] [Indexed: 05/16/2023]
Abstract
Sesame (Sesamum indicum L.; Pedaliaceae) is a commercially valuable oilseed crop with high oil content. Its small genome size favours the genomic analysis of key biological processes, such as oil synthesis and metabolism. However, the 13 chromosome pairs of sesame have not been characterised because of technological limitations and their small size. We constructed a BAC library comprising 57,600 BAC clones for sesame. The estimated genome coverage of the sesame BAC library was 13.8×. The successive double colour fluorescence in situ hybridisation (FISH) with bacterial artificial chromosomes (BACs) for sesame was established in this study. Subsequently, the 13 sesame chromosome pairs were individually differentiated using 17 specific BACs for the first time. The schematic of the sesame chromosome set was drawn according to the chromosome relative length and relative position of the BAC signal. The cytogenetic characteristics of sesame chromosomes were also explored. The results provide the technical background required for further cytogenetic map construction, genome assembly and localisation of the DNA sequence in sesame.
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Affiliation(s)
- R Zhao
- College of Life Science, Nankai University, Tianjin, China
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - H Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - W Song
- College of Life Science, Nankai University, Tianjin, China
| | - C Chen
- College of Life Science, Nankai University, Tianjin, China
| | - H Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
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Biotrophy-necrotrophy switch in pathogen evoke differential response in resistant and susceptible sesame involving multiple signaling pathways at different phases. Sci Rep 2017; 7:17251. [PMID: 29222513 PMCID: PMC5722813 DOI: 10.1038/s41598-017-17248-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/23/2017] [Indexed: 12/16/2022] Open
Abstract
Infection stages of charcoal rot fungus Macrophomina phaseolina in sesame revealed for the first time a transition from biotrophy via BNS (biotrophy-to-necrotrophy switch) to necrotrophy as confirmed by transcriptional studies. Microscopy using normal and GFP-expressing pathogen showed typical constricted thick intercellular bitrophic hyphae which gave rise to thin intracellular necrotrophic hyphae during BNS and this stage was delayed in a resistant host. Results also show that as the pathogen switched its strategy of infection, the host tailored its defense strategy to meet the changing situation. Less ROS accumulation, upregulation of ROS signaling genes and higher antioxidant enzyme activities post BNS resulted in resistance. There was greater accumulation of secondary metabolites and upregulation of secondary metabolite-related genes after BNS. A total of twenty genes functioning in different aspects of plant defense that were monitored over a time course during the changing infection phases showed a coordinated response. Experiments using phytohormone priming and phytohormone inhibitors showed that resistance resulted from activation of JA-ET signaling pathway. Most importantly this defense response was more prompt in the resistant than the susceptible host indicating that a resistant host makes different choices from a susceptible host during infection which ultimately influences the severity of the disease.
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Majdalawieh AF, Massri M, Nasrallah GK. A comprehensive review on the anti-cancer properties and mechanisms of action of sesamin, a lignan in sesame seeds (Sesamum indicum). Eur J Pharmacol 2017; 815:512-521. [DOI: 10.1016/j.ejphar.2017.10.020] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/15/2017] [Accepted: 10/11/2017] [Indexed: 01/17/2023]
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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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Dar AA, Mudigunda S, Mittal PK, Arumugam N. Comparative assessment of genetic diversity in Sesamum indicum L. using RAPD and SSR markers. 3 Biotech 2017; 7:10. [PMID: 28391476 PMCID: PMC5385169 DOI: 10.1007/s13205-016-0578-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/30/2016] [Indexed: 11/26/2022] Open
Abstract
Sesame (Sesamum indicum L.) is an ancient oilseed crop known for its nutty seeds and high-quality edible oil. It is an unexplored crop with a great economic potential. The present study deals with assessment of genetic diversity in the crop. Twenty two RAPD and 18 SSR primers were used for analysis of the 47 different sesame accessions grown in different agroclimatic zones of India. A total of 256 bands were obtained with RAPD primers, of which 191 were polymorphic. SSR primers gave 64 DNA bands, of which all of were polymorphic. The Jaccard's similarity coefficient of RAPD, SSR, and pooled RAPD and SSR data ranged from 0.510 to 0.885, 0.167 to 0.867, and 0.505 to 0.853, respectively. Maximum polymorphic information content was reported with SSRs (0.194) compared to RAPDs (0.186). Higher marker index was observed with RAPDs (1.426) than with SSRs (0.621). Similarly, maximum resolving power was found with RAPD (4.012) primers than with SSRs (0.884). The RAPD primer RPI-B11 and SSR primer S16 were the most informative in terms of describing genetic variability among the varieties under study. At a molecular level, the seed coat colour was distinguishable by the presence and absence of a group of marker amplicon/s. White and brown seeded varieties clustered close to each other, while black seeded varieties remained distanced from the cluster. In the present study, we found higher variability in Sesamum indicum L. using RAPD and SSR markers and these could assist in DNA finger printing, conservation of germplasm, and crop improvement.
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Affiliation(s)
- Aejaz Ahmad Dar
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
| | - Sushma Mudigunda
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Pramod Kumar Mittal
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Neelakantan Arumugam
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
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Chowdhury S, Basu A, Kundu S. Overexpression of a New Osmotin-Like Protein Gene ( SindOLP) Confers Tolerance against Biotic and Abiotic Stresses in Sesame. FRONTIERS IN PLANT SCIENCE 2017; 8:410. [PMID: 28400780 PMCID: PMC5368222 DOI: 10.3389/fpls.2017.00410] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/10/2017] [Indexed: 05/07/2023]
Abstract
Osmotin-like proteins (OLPs), of PR-5 family, mediate defense against abiotic, and biotic stresses in plants. Overexpression in sesame of an OLP gene (SindOLP), enhanced tolerance against drought, salinity, oxidative stress, and the charcoal rot pathogen. SindOLP was expressed in all parts and localized to the cytosol. The transgenic plants recovered after prolonged drought and salinity stress, showing less electrolyte leakage, more water content, longer roots, and smaller stomatal aperture compared to control plants. There was an increase in osmolytes, ROS-scavenging enzymes, chlorophyll content, proline, secondary metabolites, and reduced lipid peroxidation in the transgenic sesame under multiple stresses. The OLP gene imparted increased tolerance through the increased expression of three genes coding for ROS scavenging enzymes and five defense-related marker genes functioning in the JA/ET and SA pathways, namely Si-Apetala2, Si-Ethylene-responsive factor, Si-Defensin, Si-Chitinase, and Si-Thaumatin-like protein were monitored. The transgenic lines showed greater survival under different stresses compared to control through the integrated activation of multiple components of the defense signaling cascade. This is the first report of transgenic sesame and first of any study done on defense-related genes in sesame. This is also the first attempt at understanding the molecular mechanism underlying multi-stress tolerance imparted by an OLP.
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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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