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Wen T, Zhang X, Zhu J, Zhang S, Rhaman MS, Zeng W. A SLAF-based high-density genetic map construction and genetic architecture of thermotolerant traits in maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1338086. [PMID: 38384753 PMCID: PMC10880447 DOI: 10.3389/fpls.2024.1338086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
The leaf scorching trait at flowering is a crucial thermosensitive phenotype in maize under high temperature stress (HS), yet the genetic basis of this trait remains poorly understood. In this study, we genotyped a 254 RIL-F2:8 population, derived from the leaf scorch-free parental inbred line Abe2 and the leaf scorching maternal inbred line B73, using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 10,112 polymorphic SLAF markers were developed, and a high-density genetic map with a total length of 1,475.88 cM was constructed. The average sequencing depth of the parents was 55.23X, and that of the progeny was 12.53X. Then, we identified a total of 16 QTLs associated with thermotolerant traits at flowering, of which four QTLs of leaf scorching damage (LS) were distributed on chromosomes 1 (qLS1), 2 (qLS2.1, qLS2.2) and 3 (qLS3), which could explain 19.73% of phenotypic variation. Combining one qLS1 locus with QTL-seq results led to the identification of 6 candidate genes. Expression experiments and sequence variation indicated that Zm00001d033328, encoding N-acetyl-gamma-glutamyl-phosphate reductase, was the most likely candidate gene controlling thermotolerant traits at flowering. In summary, the high-density genetic map and genetic basis of thermotolerant traits lay a critical foundation for mapping other complex traits and identifying the genes associated with thermotolerant traits in maize.
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Affiliation(s)
- Tingting Wen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
- Seed Administration Station of Shandong Province, Jinan, China
| | - Xuefei Zhang
- Taian Daiyue District Bureau of Agriculture and Rural Affairs, Taian, China
| | - Jiaojiao Zhu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Susu Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Mohammad Saidur Rhaman
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Wei Zeng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 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: 0] [Impact Index Per Article: 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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Weldemichael MY, Gebremedhn HM. QTL mapping in sesame (Sesamum indicum L.): A review. J Biotechnol 2023; 376:11-23. [PMID: 37717598 DOI: 10.1016/j.jbiotec.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 09/19/2023]
Abstract
Sesame (Sesamum indicum L.) is an important oilseed crop used for food, feed, medicinal, and industrial applications. Inherently low genetic yield potential and susceptibility to biotic and abiotic stresses contribute to low productivity in sesame. Development of stress resistant varieties coupled with high yield is a viable option to raise the genetic potential of sesame. Conventional phenotype-based breeding methods have made an important role in the last couple of decades by developing several sesame varieties with improved quality, yield, and tolerance to biotic and abiotic stresses. However, due to adverse environmental effects, time consuming to develop new variety, and low genetic gain, conventional phenotype-based approach is not adequate to satisfy the rising population growth. In this context, advanced method of genotype selection via modern techniques of biotechnology plays essential roles in reducing the constraints and boosting sesame production to satisfy the huge demand. In line to this, quantitative trait loci (QTL) mapping is considered as a promising method to address the problems of sesame breeding. Previously, huge data have been generated in the practical use of QTL for sesame improvement. Therefore, this paper aims to review recent advances in the area of QTL mapping for yield and yield related traits in sesame for enhancing and sustaining sesame production. In this section, we present an intensive review on the identification and mapping of the most desirable potential candidate genes/QTLs associated with desirable traits. Moreover, this review focuses on the major QTL regions and/or potential candidate genes and associated molecular markers that could provide potential genetic resources for molecular marker-assisted selection and further cloning of functional genes for yield and yield-related traits as well as various biotic and abiotic stress tolerances. Finally, the summarized QTL mapping data shed light on future directions for enhanced sesame breeding programs.
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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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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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Song S, Dossou SSK, Meng M, Sheng C, Li H, Zhou R, Li D, Xu P, You J, Wang L. Five improved sesame reference genomes and genome resequencing unveil the contribution of structural variants to genetic diversity and yield-related traits variation. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1722-1724. [PMID: 37306179 PMCID: PMC10440982 DOI: 10.1111/pbi.14092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/13/2023]
Affiliation(s)
- Shengnan Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanHubeiChina
| | - Senouwa Segla Koffi Dossou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanHubeiChina
| | - Minghui Meng
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanHubeiChina
| | - Chen Sheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanHubeiChina
| | - Huan Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanHubeiChina
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanHubeiChina
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanHubeiChina
| | - Pan Xu
- State Key Laboratory of Grassland Agro‐ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouGansuChina
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanHubeiChina
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanHubeiChina
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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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Sabag I, Bi Y, Peleg Z, Morota G. Multi-environment analysis enhances genomic prediction accuracy of agronomic traits in sesame. Front Genet 2023; 14:1108416. [PMID: 36992702 PMCID: PMC10040590 DOI: 10.3389/fgene.2023.1108416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/27/2023] [Indexed: 03/16/2023] Open
Abstract
Introduction: Sesame is an ancient oilseed crop containing many valuable nutritional components. The demand for sesame seeds and their products has recently increased worldwide, making it necessary to enhance the development of high-yielding cultivars. One approach to enhance genetic gain in breeding programs is genomic selection. However, studies on genomic selection and genomic prediction in sesame have yet to be conducted.Methods: In this study, we performed genomic prediction for agronomic traits using the phenotypes and genotypes of a sesame diversity panel grown under Mediterranean climatic conditions over two growing seasons. We aimed to assess prediction accuracy for nine important agronomic traits in sesame using single- and multi-environment analyses.Results: In single-environment analysis, genomic best linear unbiased prediction, BayesB, BayesC, and reproducing kernel Hilbert spaces models showed no substantial differences. The average prediction accuracy of the nine traits across these models ranged from 0.39 to 0.79 for both growing seasons. In the multi-environment analysis, the marker-by-environment interaction model, which decomposed the marker effects into components shared across environments and environment-specific deviations, improved the prediction accuracies for all traits by 15%–58% compared to the single-environment model, particularly when borrowing information from other environments was made possible.Discussion: Our results showed that single-environment analysis produced moderate-to-high genomic prediction accuracy for agronomic traits in sesame. The multi-environment analysis further enhanced this accuracy by exploiting marker-by-environment interaction. We concluded that genomic prediction using multi-environmental trial data could improve efforts for breeding cultivars adapted to the semi-arid Mediterranean climate.
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Affiliation(s)
- Idan Sabag
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Ye Bi
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Zvi Peleg, ; Gota Morota,
| | - Gota Morota
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- *Correspondence: Zvi Peleg, ; Gota Morota,
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Wang H, Cui C, Liu Y, Zheng Y, Zhao Y, Chen X, Wang X, Jing B, Mei H, Wang Z. Genetic mapping of QTLs controlling brown seed coat traits by genome resequencing in sesame ( Sesamum indicum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1131975. [PMID: 36909448 PMCID: PMC9995652 DOI: 10.3389/fpls.2023.1131975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Sesame seeds have become an irreplaceable source of edible oils and food products with rich nutrients and a unique flavor, and their metabolite contents and physiological functions vary widely across different seed coat colors. Although the quantitative trait loci (QTLs) for genetic variation in seed coat color have been extensively investigated, the identification of unique genetic loci for intermediate colors such as brown has not been reported due to their complexity. METHODS Here, we crossed the white sesame 'Yuzhi No. 8' (YZ8) and the brown sesame 'Yanzhou Erhongpi' (YZEHP) to construct a recombinant inbred line (RIL) population with consecutive self-fertilization for ten generations. RESULTS The selfed F1 seeds were brown which was controlled by a dominant gene. Based on the genotyping by whole-genome resequencing of the RILs, a major-effect QTL for brown coat color was identified through both bulk segregant analysis (BSA) and genetic linkage mapping in sesame, which was located within a 1.19 Mb interval on chromosome 6 (qBSCchr6). Moreover, we found that the YZEHP seed coat initially became pigmented at 20 days post-anthesis (DPA) and was substantially colored at 30 DPA. We screened 13 possible candidate genes based on the effects of genetic variants on protein coding and predicted gene functions. Furthermore, qRT‒PCR was used to verify the expression patterns of these genes in different post-anthesis developmental periods. We noted that in comparison to YZ8 seeds, YZEHP seeds had expression of SIN_1023239 that was significantly up-regulated 2.5-, 9.41-, 6.0-, and 5.9-fold at 15, 20, 25, and 30 DPA, respectively, which was consistent with the pattern of brown seed coat pigment accumulation. DISCUSSION This study identified the first major-effect QTL for the control of the brown seed coat trait in sesame. This finding lays the foundation for further fine mapping and cloning as well as investigating the regulatory mechanism of seed coat color in sesame.
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Affiliation(s)
- Han Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Chengqi Cui
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Yanyang Liu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Yiqing Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xiaoqin Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xueqi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Bing Jing
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Hongxian Mei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
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Li H, Tahir ul Qamar M, Yang L, Liang J, You J, Wang L. Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement. Int J Mol Sci 2023; 24:3105. [PMID: 36834516 PMCID: PMC9965044 DOI: 10.3390/ijms24043105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 02/09/2023] Open
Abstract
Sesame is one of the important traditional oil crops in the world, and has high economic and nutritional value. Recently, due to the novel high throughput sequencing techniques and bioinformatical methods, the study of the genomics, methylomics, transcriptomics, proteomics and metabonomics of sesame has developed rapidly. Thus far, the genomes of five sesame accessions have been released, including white and black seed sesame. The genome studies reveal the function and structure of the sesame genome, and facilitate the exploitation of molecular markers, the construction of genetic maps and the study of pan-genomes. Methylomics focus on the study of the molecular level changes under different environmental conditions. Transcriptomics provide a powerful tool to study abiotic/biotic stress, organ development, and noncoding RNAs, and proteomics and metabonomics also provide some support in studying abiotic stress and important traits. In addition, the opportunities and challenges of multi-omics in sesame genetics breeding were also described. This review summarizes the current research status of sesame from the perspectives of multi-omics and hopes to provide help for further in-depth research on sesame.
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Affiliation(s)
- Huan Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Muhammad Tahir ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Junchao Liang
- Jiangxi Province Key Laboratory of Oil Crops Biology, Crop Research Institute, Nanchang Branch of National Center of Oil Crops Improvement, Jiangxi Academy of Agricultural Sciences, Nanchang 330000, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Dutta D, Banerjee S, Pal M, Gangopadhyay G. Validation of determinate ( dt) gene-based DNA marker in inter-specific hybrid sesame and in-silico analysis of the predicted dt protein structures. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:139-152. [PMID: 35221576 PMCID: PMC8847511 DOI: 10.1007/s12298-022-01135-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/04/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED Determinacy is a desirable trait in sesame, an important oilseed crop. We have developed an inter-specific hybrid between basally branched indeterminate cultivated Sesamum indicum genotype and wild S. prostratum with no branching yet synchronous pods on the shoot. The hybrid and a few exotic sesame germplasms were successfully screened with a determinacy (dt) gene-based DNA marker. In-silico translation of the partial coding sequences of the dt gene from the two contrasting parent genotypes revealed an SNP (V159A) in S. prostratum. The predicted cytoplasmic dt protein showed a high resemblance with flowering protein centroradialis. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01135-1.
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Affiliation(s)
- Debabrata Dutta
- Division of Plant Biology, Bose Institute (Main Campus), 93/1 APC Road, Kolkata, 700009 India
| | - Saptadipa Banerjee
- Division of Plant Biology, Bose Institute (Main Campus), 93/1 APC Road, Kolkata, 700009 India
| | - Manisha Pal
- Division of Plant Biology, Bose Institute (Main Campus), 93/1 APC Road, Kolkata, 700009 India
| | - Gaurab Gangopadhyay
- Division of Plant Biology, Bose Institute (Main Campus), 93/1 APC Road, Kolkata, 700009 India
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Sabag I, Morota G, Peleg Z. Genome-wide association analysis uncovers the genetic architecture of tradeoff between flowering date and yield components in sesame. BMC PLANT BIOLOGY 2021; 21:549. [PMID: 34809568 PMCID: PMC8607594 DOI: 10.1186/s12870-021-03328-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/08/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Unrevealing the genetic makeup of crop morpho-agronomic traits is essential for improving yield quality and sustainability. Sesame (Sesamum indicum L.) is one of the oldest oil-crops in the world. Despite its economic and agricultural importance, it is an 'orphan crop-plant' that has undergone limited modern selection, and, as a consequence preserved wide genetic diversity. Here we established a new sesame panel (SCHUJI) that contains 184 genotypes representing wide phenotypic variation and is geographically distributed. We harnessed the natural variation of this panel to perform genome-wide association studies for morpho-agronomic traits under the Mediterranean climate conditions. RESULTS Field-based phenotyping of the SCHUJI panel across two seasons exposed wide phenotypic variation for all traits. Using 20,294 single-nucleotide polymorphism markers, we detected 50 genomic signals associated with these traits. Major genomic region on LG2 was associated with flowering date and yield-related traits, exemplified the key role of the flowering date on productivity. CONCLUSIONS Our results shed light on the genetic architecture of flowering date and its interaction with yield components in sesame and may serve as a basis for future sesame breeding programs in the Mediterranean basin.
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Affiliation(s)
- Idan Sabag
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, 7610001, Rehovot, Israel
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061, USA
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061, USA.
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, 7610001, Rehovot, Israel.
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12
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Li C, Duan Y, Miao H, Ju M, Wei L, Zhang H. Identification of Candidate Genes Regulating the Seed Coat Color Trait in Sesame ( Sesamum indicum L.) Using an Integrated Approach of QTL Mapping and Transcriptome Analysis. Front Genet 2021; 12:700469. [PMID: 34422002 PMCID: PMC8371934 DOI: 10.3389/fgene.2021.700469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
Seed coat color is an important seed quality trait in sesame. However, the genetic mechanism of seed coat color variation remains elusive in sesame. We conducted a QTL mapping of the seed coat color trait in sesame using an F2 mapping population. With the aid of the newly constructed superdense genetic linkage map comprised of 22,375 bins distributed in 13 linkage groups (LGs), 17 QTLs of the three indices (i.e., L, a, and b values) of seed coat color were detected in seven intervals on four LGs, with a phenotype variance explanation rate of 4.46-41.53%. A new QTL qSCa6.1 on LG 6 and a QTL hotspot containing at least four QTLs on LG 9 were further identified. Variants screening of the target intervals showed that there were 84 genes which possessed the variants that were high-impact and co-segregating with the seed coat color trait. Meanwhile, we performed the transcriptome comparison of the developing seeds of a white- and a black-seeded variety, and found that the differentially expressed genes were significantly enriched in 37 pathways, including three pigment biosynthesis related pathways. Integration of variants screening and transcriptome comparison results suggested that 28 candidate genes probably participated in the regulation of the seed coat color in sesame; of which, 10 genes had been proved or suggested to be involved in pigments biosynthesis or accumulation during seed formation. The findings gave the basis for the mechanism of seed coat color regulation in sesame, and exhibited the effects of the integrated approach of genome resequencing and transcriptome analysis on the genetics analysis of the complex traits.
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Affiliation(s)
- Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Henan Key Laboratory of Specific Oilseed Crops Genomics, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Henan Key Laboratory of Specific Oilseed Crops Genomics, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Henan Key Laboratory of Specific Oilseed Crops Genomics, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Henan Key Laboratory of Specific Oilseed Crops Genomics, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Henan Key Laboratory of Specific Oilseed Crops Genomics, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, China
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13
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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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14
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Cui C, Liu Y, Liu Y, Cui X, Sun Z, Du Z, Wu K, Jiang X, Mei H, Zheng Y. Genome-wide association study of seed coat color in sesame (Sesamum indicum L.). PLoS One 2021; 16:e0251526. [PMID: 34019554 PMCID: PMC8139513 DOI: 10.1371/journal.pone.0251526] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/27/2021] [Indexed: 11/19/2022] Open
Abstract
Sesame (Sesamum indicum L.) is an important and ancient oilseed crop. Sesame seed coat color is related to biochemical functions involved in protein and oil metabolism, and antioxidant content. Because of its complication, the genetic basis of sesame seed coat color remains poorly understood. To elucidate the factors affecting the genetic architecture of seed coat color, 366 sesame germplasm lines were evaluated for seed coat color in 12 environments. The genome-wide association studies (GWAS) for three seed coat color space values, best linear unbiased prediction (BLUP) values from a multi-environment trial analysis and principal component scores (PCs) of three seed coat color space values were conducted. GWAS for three seed coat color space values identified a total of 224 significant single nucleotide polymorphisms (SNPs, P < 2.34×10-7), with phenotypic variation explained (PVE) ranging from 1.01% to 22.10%, and 35 significant SNPs were detected in more than 6 environments. Based on BLUP values, 119 significant SNPs were identified, with PVE ranging from 8.83 to 31.98%. Comparing the results of the GWAS using phenotypic data from different environments and the BLUP values, all significant SNPs detected in more than 6 environments were also detected using the BLUP values. GWAS for PCs identified 197 significant SNPs, and 30 were detected in more than 6 environments. GWAS results for PCs were consistent with those for three color space values. Out of 224 significant SNPs, 22 were located in the confidence intervals of previous reported quantitative trait loci (QTLs). Finally, 92 candidate genes were identified in the vicinity of the 4 SNPs that were most significantly associated with sesame seed coat color. The results in this paper will provide new insights into the genetic basis of sesame seed coat color, and should be useful for molecular breeding in sesame.
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Affiliation(s)
- Chengqi Cui
- 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
| | - Yan Liu
- Nanyang Academy of Agricultural Sciences, Nanyang, Henan, China
| | - Xianghua Cui
- Zhumadian Academy of Agricultural Sciences, Zhumadian, Henan, China
| | - Zhiyu Sun
- College of Life Sciences, South China Normal University, Guangzhou, Guangdong, 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
| | - Hongxian Mei
- 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
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15
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Lee E, Yang X, Ha J, Kim MY, Park KY, Lee SH. Identification of a Locus Controlling Compound Raceme Inflorescence in Mungbean [ Vigna radiata (L.) R. Wilczek]. Front Genet 2021; 12:642518. [PMID: 33763121 PMCID: PMC7982598 DOI: 10.3389/fgene.2021.642518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
Mungbean [Vigna radiata (L.) R. Wilczek] produces a compound raceme inflorescence that branches into secondary inflorescences, which produce flowers. This architecture results in the less-domesticated traits of asynchronous pod maturity and multiple harvest times. This study identified the genetic factors responsible for the compound raceme of mungbean, providing a unique biological opportunity to improve simultaneous flowering. Using a recombinant inbred line (RIL) population derived from VC1973A, an elite cultivar with a compound raceme type, and IT208075, a natural mutant with a simple raceme type, a single locus that determined the inflorescence type was identified based on 1:1 segregation ratio in the F8 generation, and designated Comraceme. Linkage map analysis showed Comraceme was located on chromosome 4 within a marker interval spanning 520 kb and containing 64 genes. RILs carrying heterozygous fragments around Comraceme produced compound racemes, indicating this form was dominant to the simple raceme type. Quantitative trait loci related to plant architecture and inflorescence have been identified in genomic regions of soybean syntenic to Comraceme. In IT208075, 15 genes were present as distinct variants not observed in other landrace varieties or wild mungbean. These genes included Vradi04g00002481, a development-related gene encoding a B3 transcriptional factor. The upstream region of Vradi04g00002481 differed between lines producing the simple and compound types of raceme. Expression of Vradi04g00002481 was significantly lower at the early vegetative stage and higher at the early reproductive stage, in IT208075 than in VC1973A. Vradi04g00002481 was therefore likely to determine inflorescence type in mungbean. Although further study is required to determine the functional mechanism, this finding provides valuable genetic information for understanding the architecture of the compound raceme in mungbean.
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Affiliation(s)
- Eunsoo Lee
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Xuefei Yang
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, South Korea
| | - Moon Young Kim
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Keum Yong Park
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Suk-Ha Lee
- Department of Agriculture, Forestry and Bioresources and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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16
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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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17
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Genome-Wide Discovery of InDel Markers in Sesame ( Sesamum indicum L.) Using ddRADSeq. PLANTS 2020; 9:plants9101262. [PMID: 32987937 PMCID: PMC7599716 DOI: 10.3390/plants9101262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 01/15/2023]
Abstract
The development and validation of different types of molecular markers is crucial to conducting marker-assisted sesame breeding. Insertion-deletion (InDel) markers are highly polymorphic and suitable for low-cost gel-based genotyping. From this perspective, this study aimed to discover and develop InDel markers through bioinformatic analysis of double digest restriction site-associated DNA sequencing (ddRADSeq) data from 95 accessions belonging to the Mediterranean sesame core collection. Bioinformatic analysis indicated the presence of 7477 InDel positions genome wide. Deletions accounted for 61% of the InDels and short deletions (1-2 bp) were the most abundant type (94.9%). On average, InDels of at least 2 bp in length had a frequency of 2.99 InDels/Mb. The 86 InDel sites having length ≥8 bp were detected in genome-wide analysis. These regions can be used for the development of InDel markers considering low-cost genotyping with agarose gels. In order to validate these InDels, a total of 38 InDel regions were selected and primers were successfully amplified. About 13% of these InDels were in the coding sequences (CDSs) and in the 3'- and 5'- untranslated regions (UTRs). Furthermore, the efficiencies of these 16 InDel markers were assessed on 32 sesame accessions. The polymorphic information content (PIC) of these 16 markers ranged from 0.06 to 0.62 (average: 0.33). These results demonstrated the success of InDel identification and marker development for sesame with the use of ddRADSeq data. These agarose-resolvable InDel markers are expected to be useful for sesame breeders.
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18
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Gadri Y, Eshed Williams L, Peleg Z. Tradeoffs between yield components promote crop stability in sesame. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 295:110105. [PMID: 32534624 DOI: 10.1016/j.plantsci.2019.03.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/20/2019] [Accepted: 03/25/2019] [Indexed: 06/11/2023]
Abstract
Sesame is an important oil-crop worldwide. Complex tradeoffs between various yield components significantly affect the outcome yield. Our aims were to characterize the effect of genotype, environment and management, and their interactions, on yield components. Wild-type line, bearing a bicarpellate-capsule and three capsules per leaf axil, and its derived mutant-line, featuring one tetracarpellate-capsule per leaf axil, were analyzed under two irrigation regimes and three sowing-stands. Dissection of flower meristems and capsules showed larger placenta size and final capsule diameter in the mutant-line. Allelic segregation of F2 population revealed that the number of carpels per capsule demonstrates monogenic inheritance, whereas the number of capsules per leaf axil is a polygenic trait. A significant effect of genotype, irrigation and stand was observed on most yield components. While wild-type had more capsules per plant, the mutant-line compensated by increased seed number per capsule and consequently accumulated the same number of seeds per plant. Under either high intra-row or inter-row density, the branches number was reduced; however, the outcome yield was compensated by number of plants per area. While some yield components showed phenotypic-plasticity (branching), other traits were genetically stable (number of capsules per leaf axil and number of carpels per capsule). Our result shed-light on tradeoffs between yield components and on their underlying mechanisms.
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Affiliation(s)
- Yaron Gadri
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Leor Eshed Williams
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
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19
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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: 33] [Impact Index Per Article: 8.3] [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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20
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Wang F, Zhang J, Chen Y, Zhang C, Gong J, Song Z, Zhou J, Wang J, Zhao C, Jiao M, Liu A, Du Z, Yuan Y, Fan S, Zhang J. Identification of candidate genes for key fibre-related QTLs and derivation of favourable alleles in Gossypium hirsutum recombinant inbred lines with G. barbadense introgressions. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:707-720. [PMID: 31446669 PMCID: PMC7004909 DOI: 10.1111/pbi.13237] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/15/2019] [Indexed: 05/02/2023]
Abstract
Fine mapping QTLs and identifying candidate genes for cotton fibre-quality and yield traits would be beneficial to cotton breeding. Here, we constructed a high-density genetic map by specific-locus amplified fragment sequencing (SLAF-seq) to identify QTLs associated with fibre-quality and yield traits using 239 recombinant inbred lines (RILs), which was developed from LMY22 (a high-yield Gossypium hirsutumL. cultivar) × LY343 (a superior fibre-quality germplasm with G. barbadenseL. introgressions). The genetic map spanned 3426.57 cM, including 3556 SLAF-based SNPs and 199 SSR marker loci. A total of 104 QTLs, including 67 QTLs for fibre quality and 37 QTLs for yield traits, were identified with phenotypic data collected from 7 environments. Among these, 66 QTLs were co-located in 19 QTL clusters on 12 chromosomes, and 24 QTLs were detected in three or more environments and determined to be stable. We also investigated the genomic components of LY343 and their contributions to fibre-related traits by deep sequencing the whole genome of LY343, and we found that genomic components from G. hirsutum races (which entered LY343 via its G. barbadense parent) contributed more favourable alleles than those from G. barbadense. We further identified six putative candidate genes for stable QTLs, including Gh_A03G1147 (GhPEL6), Gh_D07G1598 (GhCSLC6) and Gh_D13G1921 (GhTBL5) for fibre-length QTLs and Gh_D03G0919 (GhCOBL4), Gh_D09G1659 (GhMYB4) and Gh_D09G1690 (GhMYB85) for lint-percentage QTLs. Our results provide comprehensive insight into the genetic basis of the formation of fibre-related traits and would be helpful for cloning fibre-development-related genes as well as for marker-assisted genetic improvement in cotton.
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Affiliation(s)
- Furong Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Chuanyun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Juwu Gong
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhangqiang Song
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Juan Zhou
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Jingjing Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Chengjie Zhao
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Mengjia Jiao
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Aiying Liu
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhaohai Du
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Youlu Yuan
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Shoujin Fan
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
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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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Core set construction and association analysis of Pinus massoniana from Guangdong province in southern China using SLAF-seq. Sci Rep 2019; 9:13157. [PMID: 31511632 PMCID: PMC6739479 DOI: 10.1038/s41598-019-49737-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/31/2019] [Indexed: 12/31/2022] Open
Abstract
Germplasm resource collection and utilization are important in forestry species breeding. High-through sequencing technologies have been playing increasing roles in forestry breeding. In this study, specific-locus amplified fragment sequencing (SLAF-seq) was employed to analyze 149 masson pine (Pinus massoniana) accessions collected from Guangdong in China. A large number of 471,660 SNPs in the total collection were identified from 599,164 polymorphic SLAF tags. Population structure analysis showed that 149 masson pines could not be obviously divided into subpopulations. Two core sets, containing 29 masson pine accessions for increasing resin and wood yield respectively, were obtained from the total collection. Phenotypic analyses of five traits showed abundant variations, 25 suggestive and 9 significant SNPs were associated with the resin-yielding capacity (RYC') and volume of wood (VW) using EMMAX and FaST-LMM; 22 suggestive and 11 significant SNPs were associated with RYC' and VW using mrMLM and FASTmrMLM. Moreover, a large number of associated SNPs were detected in trait HT, DBH, RW and RYC using mrMLM, FASTmrMLM, FASTmrEMMA and ISIS EM-BLASSO. The core germplasm sets would be a valuable resource for masson pine improvement and breeding. In addition, the associated SNP markers would be meaningful for masson pine resource selection.
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Wang Y, Wang C, Han H, Luo Y, Wang Z, Yan C, Xu W, Qu S. Construction of a High-Density Genetic Map and Analysis of Seed-Related Traits Using Specific Length Amplified Fragment Sequencing for Cucurbita maxima. FRONTIERS IN PLANT SCIENCE 2019; 10:1782. [PMID: 32153597 PMCID: PMC7046561 DOI: 10.3389/fpls.2019.01782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/20/2019] [Indexed: 05/03/2023]
Abstract
Seed traits are agronomically important for Cucurbita breeding, but the genes controlling seed size, seed weight and seed number have not been mapped in Cucurbita maxima (C. maxima). In this study, 100 F2 individual derived from two parental lines, "2013-12" and "9-6", were applied to construct a 3,376.87-cM genetic map containing 20 linkage groups (LGs) with an average genetic distance of 0.47 cM using a total of 8,406 specific length amplified fragment (SLAF) markers in C. maxima. Ten quantitative trait loci (QTLs) of seed width (SW), seed length (SL) and hundred-seed weight (HSW) were identified using the composite interval mapping (CIM) method. The QTLs affecting SW, SL and HSW explained a maximum of 38.6%, 28.9% and 17.2% of the phenotypic variation and were detected in LG6, LG6 and LG17, respectively. To validate these results, an additional 150 F2 individuals were used for QTL mapping of SW and SL with cleaved amplified polymorphic sequence (CAPS) markers. We found that two major QTLs, SL6-1 and SW6-1, could be detected in both SLAF-seq and CAPS markers in an overlapped region. Based on gene annotation and non-synonymous single-nucleotide polymorphisms (SNPs) in the major SWand SL-associated regions, we found that two genes encoding a VQ motif and an E3 ubiquitin-protein ligase may be candidate genes influencing SL, while an F-box and leucinerich repeat (LRR) domain-containing protein is the potential regulator for SW in C. maxima. This study provides the first high-density linkage map of C. maxima using SNPs developed by SLAF-seq technology, which is a powerful tool for associated mapping of important agronomic traits, map-based gene cloning and marker-assisted selection (MAS)-based breeding in C. maxima.
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Affiliation(s)
- Yunli Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Chaojie Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Hongyu Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yusong Luo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Zhichao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Chundong Yan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Wenlong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Shuping Qu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- *Correspondence: Shuping Qu,
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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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Yang Y, Xuan L, Yu C, Wang Z, Xu J, Fan W, Guo J, Yin Y. High-density genetic map construction and quantitative trait loci identification for growth traits in (Taxodium distichum var. distichum × T. mucronatum) × T. mucronatum. BMC PLANT BIOLOGY 2018; 18:263. [PMID: 30382825 PMCID: PMC6474422 DOI: 10.1186/s12870-018-1493-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 10/19/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND 'Zhongshanshan' is the general designation for the superior interspecific hybrid clones of Taxodium species, which is widely grown for economic and ecological purposes in southern China. Growth is the priority objective in 'Zhongshanshan' tree improvement. A high-density linkage map is vital to efficiently identify key quantitative trait loci (QTLs) that affect growth. RESULTS In total, 403.16 Gb of data, containing 2016,336 paired-end reads, was obtained after preprocessing. The average sequencing depth was 28.49 in T. distichum var. distichum, 25.18 in T. mucronatum, and 11.12 in each progeny. In total, 524,662 high-quality SLAFs were detected, of which 249,619 were polymorphic, and 6166 of the polymorphic markers met the requirements for use in constructing a genetic map. The final map harbored 6156 SLAF markers on 11 linkage groups, and was 1137.86 cM in length, with an average distance of 0.18 cM between adjacent markers. Separate QTL analyses of traits in different years by CIM detected 7 QTLs. While combining multiple-year data, 13 QTLs were detected by ICIM. 5 QTLs were repeatedly detected by the two methods, and among them, 3 significant QTLs (q6-2, q4-2 and q2-1) were detected in at least two traits. Bioinformatic analysis discoveried a gene annotated as a leucine-rich repeat receptor-like kinase gene within q4-2. CONCLUSIONS This map is the most saturated one constructed in a Taxodiaceae species to date, and would provide useful information for future comparative mapping, genome assembly, and marker-assisted selection.
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Affiliation(s)
- Ying Yang
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Lei Xuan
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Chaoguang Yu
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ziyang Wang
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jianhua Xu
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Wencai Fan
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jinbo Guo
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yunlong Yin
- Plant Ecology Research Center, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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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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Cui C, Mei H, Liu Y, Zhang H, Zheng Y. Genetic Diversity, Population Structure, and Linkage Disequilibrium of an Association-Mapping Panel Revealed by Genome-Wide SNP Markers in Sesame. FRONTIERS IN PLANT SCIENCE 2017; 8:1189. [PMID: 28729877 PMCID: PMC5498554 DOI: 10.3389/fpls.2017.01189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 06/22/2017] [Indexed: 05/11/2023]
Abstract
The characterization of genetic diversity and population structure can be used in tandem to detect reliable phenotype-genotype associations. In the present study, we genotyped a set of 366 sesame germplasm accessions by using 89,924 single-nucleotide polymorphisms (SNPs). The number of SNPs on each chromosome was consistent with the physical length of the respective chromosome, and the average marker density was approximately 2.67 kb/SNP. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 1.1 × 10-3, with averages of 1.0 × 10-4, 2.7 × 10-4, and 3.6 × 10-4 obtained, respectively for three identified subgroups of the panel: Pop 1, Pop 2, and the Mixed. The genetic structure analysis revealed that these sesame germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in the panel. The genome-wide linkage disequilibrium (LD) analysis showed that an average LD extended up to ∼99 kb. The genetic diversity and population structure revealed in this study should provide guidance to the future design of association studies and the systematic utilization of the genetic variation characterizing the sesame panel.
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Affiliation(s)
- Chengqi Cui
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural UniversityNanjing, China
| | - Hongxian Mei
- Henan Sesame Research Center, Henan Academy of Agricultural SciencesZhengzhou, China
- Key Laboratory of Oil Crops in Huanghuaihai Plain, Ministry of AgricultureZhengzhou, China
- Henan Provincial Key Laboratory for Oil Crops ImprovementZhengzhou, China
| | - Yanyang Liu
- Henan Sesame Research Center, Henan Academy of Agricultural SciencesZhengzhou, China
- Key Laboratory of Oil Crops in Huanghuaihai Plain, Ministry of AgricultureZhengzhou, China
- Henan Provincial Key Laboratory for Oil Crops ImprovementZhengzhou, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural SciencesZhengzhou, China
- Key Laboratory of Oil Crops in Huanghuaihai Plain, Ministry of AgricultureZhengzhou, China
- Henan Provincial Key Laboratory for Oil Crops ImprovementZhengzhou, China
- *Correspondence: Haiyang Zhang, Yongzhan Zheng,
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural SciencesZhengzhou, China
- Key Laboratory of Oil Crops in Huanghuaihai Plain, Ministry of AgricultureZhengzhou, China
- Henan Provincial Key Laboratory for Oil Crops ImprovementZhengzhou, China
- *Correspondence: Haiyang Zhang, Yongzhan Zheng,
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