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Dwivedi SL, Heslop‐Harrison P, Amas J, Ortiz R, Edwards D. Epistasis and pleiotropy-induced variation for plant breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2788-2807. [PMID: 38875130 PMCID: PMC11536456 DOI: 10.1111/pbi.14405] [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: 11/18/2023] [Revised: 05/07/2024] [Accepted: 05/24/2024] [Indexed: 06/16/2024]
Abstract
Epistasis refers to nonallelic interaction between genes that cause bias in estimates of genetic parameters for a phenotype with interactions of two or more genes affecting the same trait. Partitioning of epistatic effects allows true estimation of the genetic parameters affecting phenotypes. Multigenic variation plays a central role in the evolution of complex characteristics, among which pleiotropy, where a single gene affects several phenotypic characters, has a large influence. While pleiotropic interactions provide functional specificity, they increase the challenge of gene discovery and functional analysis. Overcoming pleiotropy-based phenotypic trade-offs offers potential for assisting breeding for complex traits. Modelling higher order nonallelic epistatic interaction, pleiotropy and non-pleiotropy-induced variation, and genotype × environment interaction in genomic selection may provide new paths to increase the productivity and stress tolerance for next generation of crop cultivars. Advances in statistical models, software and algorithm developments, and genomic research have facilitated dissecting the nature and extent of pleiotropy and epistasis. We overview emerging approaches to exploit positive (and avoid negative) epistatic and pleiotropic interactions in a plant breeding context, including developing avenues of artificial intelligence, novel exploitation of large-scale genomics and phenomics data, and involvement of genes with minor effects to analyse epistatic interactions and pleiotropic quantitative trait loci, including missing heritability.
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Affiliation(s)
| | - Pat Heslop‐Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Department of Genetics and Genome Biology, Institute for Environmental FuturesUniversity of LeicesterLeicesterUK
| | - Junrey Amas
- Centre for Applied Bioinformatics, School of Biological SciencesUniversity of Western AustraliaPerthWAAustralia
| | - Rodomiro Ortiz
- Department of Plant BreedingSwedish University of Agricultural SciencesAlnarpSweden
| | - David Edwards
- Centre for Applied Bioinformatics, School of Biological SciencesUniversity of Western AustraliaPerthWAAustralia
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2
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Zhang L, Chen Y, Leng Q, Lin X, Lu J, Xu Y, Li H, Xu S, Huang S, López Hernán A, Wang Y, Yin J, Niu J. A High-Resolution Linkage Map Construction and QTL Analysis for Morphological Traits in Anthurium ( Anthurium andraeanum Linden). PLANTS (BASEL, SWITZERLAND) 2023; 12:4185. [PMID: 38140512 PMCID: PMC10747322 DOI: 10.3390/plants12244185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Anthurium andraeanum Linden is a prominent ornamental plant belonging to the family Araceae and is cultivated worldwide. The morphology characteristics are crucial because they significantly impact ornamental values, commercial properties, and the efficiency of space utilization in production. However, only a few related investigations have been conducted in anthurium to date. In this study, an F1 genetic segregation population containing 160 progenies was generated through hybridization between potted and cut anthurium varieties. Fifteen morphological traits were assessed and revealed substantial levels of genetic variation and widespread positive correlation. Based on specific length amplified fragment (SLAF) sequencing technology, 8171 single nucleotide polymorphism (SNP) markers were developed, and the high-density linkage map of 2202.27 cM in length distributed on 15 linkage groups was constructed successfully, with an average distance of 0.30 cM. Using the inclusive composite interval mapping (ICIM) method, 59 QTLs related to 15 key morphological traits were successfully identified, which explained phenotypic variance (PVE) ranging from 6.21% to 17.74%. Thirty-three of those associated with 13 traits were designated as major QTLs with PVE > 10%. These findings offer valuable insights into the genetic basis of quantitative traits and are beneficial for molecular marker-assisted selection (MAS) in anthurium breeding.
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Affiliation(s)
- Linbi Zhang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
| | - Yanyan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- Institute of Crops Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qingyun Leng
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
| | - Xinge Lin
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
| | - Jinping Lu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
| | - Yueting Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
| | - Haiyan Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
| | - Shisong Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
| | - Shaohua Huang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
| | - Ariel López Hernán
- Multidisciplinary Workshop on Vascular Plants, Border Ecology Laboratory, University of Flores, Sede Comahue (UFLO), Rio Negro 8328, Argentina;
- Botanical Garden of Plottier City, Neuquen 8316, Argentina
| | - Yaru Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
| | - Junmei Yin
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
| | - Junhai Niu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China (Y.X.); (H.L.); (Y.W.)
- The Engineering Technology Research Center of Tropical Ornamental Plant Germplasm Innovation and Utilization, Danzhou 571737, China
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3
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Kim S, Lee E, Lee J, An YJ, Oh E, Kim JI, Kim SW, Kim MY, Lee MH, Cho KS. Identification of QTLs and allelic effect controlling lignan content in sesame ( Sesamum indicum L.) using QTL-seq approach. Front Genet 2023; 14:1289793. [PMID: 38148976 PMCID: PMC10750367 DOI: 10.3389/fgene.2023.1289793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Sesame (Sesamum indicum L.), an oilseed crop, is gaining worldwide recognition for its healthy functional ingredients as consumption increases. The content of lignans, known for their antioxidant and anti-inflammatory effects, is a key agronomic trait that determines the industrialization of sesame. However, the study of the genetics and physiology of lignans in sesame is challenging, as they are influenced by multiple genes and environmental factors, therefore, the understanding of gene function and synthetic pathways related to lignan in sesame is still limited. To address these knowledge gaps, we conducted genetic analyses using F7 recombinant inbred line (RIL) populations derived from Goenbaek and Gomazou as low and high lignin content variants, respectively. Using the QTL-seq approach, we identified three loci, qLignan1-1, qLignan6-1, and qLignan11-1, that control lignan content, specifically sesamin and sesamolin. The allelic effect between loci was evaluated using the RIL population. qLignan6-1 had an additive effect that increased lignan content when combined with the other two loci, suggesting that it could be an important factor in gene pyramiding for the development of high-lignan varieties. This study not only highlights the value of sesame lignan, but also provides valuable insights for the development of high-lignan varieties through the use of DNA markers in breeding strategies. Overall, this research contributes to our understanding of the importance of sesame oil and facilitates progress in sesame breeding for improved lignan content.
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Affiliation(s)
- Sungup Kim
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Eunsoo Lee
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Jeongeun Lee
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Yeon Ju An
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Eunyoung Oh
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Jung In Kim
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Sang Woo Kim
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Min Young Kim
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Myoung Hee Lee
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Kwang-Soo Cho
- Central Crop Breeding Research Division, Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
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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, 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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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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Dossou SSK, Song S, Liu A, Li D, Zhou R, Berhe M, Zhang Y, Sheng C, Wang Z, You J, Wang L. Resequencing of 410 Sesame Accessions Identifies SINST1 as the Major Underlying Gene for Lignans Variation. Int J Mol Sci 2023; 24:1055. [PMID: 36674569 PMCID: PMC9860558 DOI: 10.3390/ijms24021055] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Sesame is a promising oilseed crop that produces specific lignans of clinical importance. Hence, a molecular description of the regulatory mechanisms of lignan biosynthesis is essential for crop improvement. Here, we resequence 410 sesame accessions and identify 5.38 and 1.16 million SNPs (single nucleotide polymorphisms) and InDels, respectively. Population genomic analyses reveal that sesame has evolved a geographic pattern categorized into northern (NC), middle (MC), and southern (SC) groups, with potential origin in the southern region and subsequent introduction to the other regions. Selective sweeps analysis uncovers 120 and 75 significant selected genomic regions in MC and NC groups, respectively. By screening these genomic regions, we unveiled 184 common genes positively selected in these subpopulations for exploitation in sesame improvement. Genome-wide association study identifies 17 and 72 SNP loci for sesamin and sesamolin variation, respectively, and 11 candidate causative genes. The major pleiotropic SNPC/A locus for lignans variation is located in the exon of the gene SiNST1. Further analyses revealed that this locus was positively selected in higher lignan content sesame accessions, and the "C" allele is favorable for a higher accumulation of lignans. Overexpression of SiNST1C in sesame hairy roots significantly up-regulated the expression of SiMYB58, SiMYB209, SiMYB134, SiMYB276, and most of the monolignol biosynthetic genes. Consequently, the lignans content was significantly increased, and the lignin content was slightly increased. Our findings provide insights into lignans and lignin regulation in sesame and will facilitate molecular breeding of elite varieties and marker-traits association studies.
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Affiliation(s)
- Senouwa Segla Koffi Dossou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Laboratory of Plant Physiology and Biotechnologies, Faculty of Sciences, University of Lomé, Lomé 01BP 1515, Togo
| | - Shengnan Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Muez Berhe
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chen Sheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Zhijian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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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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9
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Wei P, Zhao F, Wang Z, Wang Q, Chai X, Hou G, Meng Q. Sesame ( Sesamum indicum L.): A Comprehensive Review of Nutritional Value, Phytochemical Composition, Health Benefits, Development of Food, and Industrial Applications. Nutrients 2022; 14:nu14194079. [PMID: 36235731 PMCID: PMC9573514 DOI: 10.3390/nu14194079] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Sesame (Sesamum indicum L.), of the Pedaliaceae family, is one of the first oil crops used in humans. It is widely grown and has a mellow flavor and high nutritional value, making it very popular in the diet. Sesame seeds are rich in protein and lipids and have many health benefits. A number of in vitro and in vivo studies and clinical trials have found sesame seeds to be rich in lignan-like active ingredients. They have antioxidant, cholesterol reduction, blood lipid regulation, liver and kidney protection, cardiovascular system protection, anti-inflammatory, anti-tumor, and other effects, which have great benefits to human health. In addition, the aqueous extract of sesame has been shown to be safe for animals. As an important medicinal and edible homologous food, sesame is used in various aspects of daily life such as food, feed, and cosmetics. The health food applications of sesame are increasing. This paper reviews the progress of research on the nutritional value, chemical composition, pharmacological effects, and processing uses of sesame to support the further development of more functionalities of sesame.
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Affiliation(s)
- Panpan Wei
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Ministry of Education, Yantai University, Yantai 264005, China
| | - Fenglan Zhao
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Ministry of Education, Yantai University, Yantai 264005, China
| | - Zhen Wang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Ministry of Education, Yantai University, Yantai 264005, China
| | - Qibao Wang
- School of Biological Science, Jining Medical University, Rizhao 276800, China
| | - Xiaoyun Chai
- Department of Organic Chemistry, School of Pharmacy, Naval Medical University, Shanghai 200433, China
- Correspondence: (X.C.); (G.H.); (Q.M.)
| | - Guige Hou
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
- Correspondence: (X.C.); (G.H.); (Q.M.)
| | - Qingguo Meng
- Key Laboratory of Molecular Pharmacology and Drug Evaluation, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, School of Pharmacy, Ministry of Education, Yantai University, Yantai 264005, China
- Correspondence: (X.C.); (G.H.); (Q.M.)
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Zhou W, Song S, Segla Koffi Dossou S, Zhou R, Wei X, Wang Z, Sheng C, Zhang Y, You J, Wang L. Genome-wide association analysis and transcriptome reveal novel loci and a candidate regulatory gene of fatty acid biosynthesis in sesame (Sesamum indicum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 186:220-231. [PMID: 35921726 DOI: 10.1016/j.plaphy.2022.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
The regulatory mechanisms of fatty acid (FA) biosynthesis and triacylglycerols (TAGs) assembly remain largely misunderstood in sesame. Gas chromatography was used to analyze the natural variation in FA compositions and oil content (OC) in 400 sesame accessions grown in three different environments. The phenotypic data was associated with the newly released SNP data from whole-genome resequencing, and 43 significant loci for FA and OC were identified. Comparative transcriptomics analysis of high-OC and low-OC materials was performed, and 515 differentially expressed genes (DEGs) were identified across three seed developmental stages. By integrating the genome-wide association study (GWAS) and DEGs analysis, twenty candidate genes were identified, of which SiTPS1 (trehalose-6-phosphate synthase 1) has emerged as a key regulatory gene of FAs and TAGs metabolism in sesame. Overexpression of SiTPS1 in transgenic Arabidopsis influenced FA composition and significantly increased OC. Our study provides resources for the markers-based improvement of OC and quality in sesame and other crops.
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Affiliation(s)
- Wangyi Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Shengnan Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Senouwa Segla Koffi Dossou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhijian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Chen Sheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops 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 and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
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You J, Li D, Yang L, Dossou SSK, Zhou R, Zhang Y, Wang L. CRISPR/Cas9-Mediated Efficient Targeted Mutagenesis in Sesame ( Sesamum indicum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:935825. [PMID: 35898225 PMCID: PMC9309882 DOI: 10.3389/fpls.2022.935825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has been widely utilized for targeted genome modification in a wide range of species. It is a powerful genome editing technology, providing significant benefits for gene functional research and molecular breeding. However, to date, no study has applied this genome editing tool to sesame (Sesamum indicum L.), one of the most ancient and important oil crops used widely in diverse industries such as food and medicine. Herein, the CRISPR/Cas9 system along with hairy root transformation was used to induce targeted mutagenesis in sesame. Two single guide RNAs (sgRNAs) were designed to target two sesame cytochrome P450 genes (CYP81Q1 and CYP92B14), which are the key biosynthetic gene of sesamin and sesamolin, respectively. Sequencing data illustrated the expected InDel mutations at the target sites, with 90.63 and 93.33% mutation frequency in CYP81Q1 and CYP92B14, respectively. The most common editing event was single nucleotide deletion and insertion. Sequencing of potential off-target sites of CYP92B14-sgRNA showed no off-target events in cases of three mismatches. High-performance liquid chromatography analysis showed that sesamin and sesamolin biosynthesis was effectively disrupted in the mutated hairy roots, confirming the crucial role of CYP81Q1 and CYP92B14 in sesame lignan biosynthesis. These results demonstrated that targeted mutagenesis was efficiently created by the CRISPR/Cas9 system, and CRISPR/Cas9 coupled with hairy root transformation is an effective tool for assessing gene functions in sesame.
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