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Bu M, Fan W, Li R, He B, Cui P. Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies. Metabolites 2023; 13:1170. [PMID: 38132852 PMCID: PMC10744971 DOI: 10.3390/metabo13121170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.
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Affiliation(s)
- Mengjia Bu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Fan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruonan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bing He
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Cui
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Behera J, Rahman MM, Shockey J, Kilaru A. Acyl-CoA-dependent and acyl-CoA-independent avocado acyltransferases positively influence oleic acid content in nonseed triacylglycerols. FRONTIERS IN PLANT SCIENCE 2023; 13:1056582. [PMID: 36714784 PMCID: PMC9874167 DOI: 10.3389/fpls.2022.1056582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
In higher plants, acyl-CoA:diacylglycerol acyltransferase (DGAT) and phospholipid:diacylglycerol acyltransferase (PDAT) catalyze the terminal step of triacylglycerol (TAG) synthesis in acyl-CoA-dependent and -independent pathways, respectively. Avocado (Persea americana) mesocarp, a nonseed tissue, accumulates significant amounts of TAG (~70% by dry weight) that is rich in heart-healthy oleic acid (18:1). The oil accumulation stages of avocado mesocarp development coincide with high expression levels for type-1 DGAT (DGAT1) and PDAT1, although type-2 DGAT (DGAT2) expression remains low. The strong preference for oleic acid demonstrated by the avocado mesocarp TAG biosynthetic machinery represents lucrative biotechnological opportunities, yet functional characterization of these three acyltransferases has not been explored to date. We expressed avocado PaDGAT1, PaDGAT2, and PaPDAT1 in bakers' yeast and leaves of Nicotiana benthamiana. PaDGAT1 complemented the TAG biosynthesis deficiency in the quadruple mutant yeast strain H1246, and substantially elevated total cellular lipid content. In vitro enzyme assays showed that PaDGAT1 prefers oleic acid compared to palmitic acid (16:0). Both PaDGAT1 and PaPDAT1 increased the lipid content and elevated oleic acid levels when expressed independently or together, transiently in N. benthamiana leaves. These results indicate that PaDGAT1 and PaPDAT1 prefer oleate-containing substrates, and their coordinated expression likely contributes to sustained TAG synthesis that is enriched in oleic acid. This study establishes a knowledge base for future metabolic engineering studies focused on exploitation of the biochemical properties of PaDGAT1 and PaPDAT1.
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Affiliation(s)
- Jyoti Behera
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, United States
| | - Md Mahbubur Rahman
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, United States
- dNTP Laboratory, Teaneck, NJ, United States
| | - Jay Shockey
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, Commodity Utilization Research Unit, New Orleans, LA, United States
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, United States
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Zuo JF, Chen Y, Ge C, Liu JY, Zhang YM. Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM. FRONTIERS IN PLANT SCIENCE 2022; 13:1096457. [PMID: 36578334 PMCID: PMC9792120 DOI: 10.3389/fpls.2022.1096457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Although seed oil content and its fatty acid compositions in soybean were affected by environment, QTN-by-environment (QEIs) and gene-by-environment interactions (GEIs) were rarely reported in genome-wide association studies. METHODS The 3VmrMLM method was used to associate the trait phenotypes, measured in five to seven environments, of 286 soybean accessions with 106,013 SNPs for detecting QTNs and QEIs. RESULTS Seven oil metabolism genes (GmSACPD-A, GmSACPD-B, GmbZIP123, GmSWEET39, GmFATB1A, GmDGAT2D, and GmDGAT1B) around 598 QTNs and one oil metabolism gene GmFATB2B around 54 QEIs were verified in previous studies; 76 candidate genes and 66 candidate GEIs were predicted to be associated with these traits, in which 5 genes around QEIs were verified in other species to participate in oil metabolism, and had differential expression across environments. These genes were found to be related to soybean seed oil content in haplotype analysis. In addition, most candidate GEIs were co-expressed with drought response genes in co-expression network, and three KEGG pathways which respond to drought were enriched under drought stress rather than control condition; six candidate genes were hub genes in the co-expression networks under drought stress. DISCUSSION The above results indicated that GEIs, together with drought response genes in co-expression network, may respond to drought, and play important roles in regulating seed oil-related traits together with oil metabolism genes. These results provide important information for genetic basis, molecular mechanisms, and soybean breeding for seed oil-related traits.
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Affiliation(s)
- Jian-Fang Zuo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ying Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chao Ge
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jin-Yang Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yuan-Ming Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Kuczynski C, McCorkle S, Keereetaweep J, Shanklin J, Schwender J. An expanded role for the transcription factor WRINKLED1 in the biosynthesis of triacylglycerols during seed development. FRONTIERS IN PLANT SCIENCE 2022; 13:955589. [PMID: 35991420 PMCID: PMC9389262 DOI: 10.3389/fpls.2022.955589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/28/2022] [Indexed: 06/12/2023]
Abstract
The transcription factor WRINKLED1 (WRI1) is known as a master regulator of fatty acid synthesis in developing oilseeds of Arabidopsis thaliana and other species. WRI1 is known to directly stimulate the expression of many fatty acid biosynthetic enzymes and a few targets in the lower part of the glycolytic pathway. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors is controlled by WRI1. To shortlist possible gene targets for future in-planta experimental validation, here we present a strategy that combines phylogenetic foot printing of cis-regulatory elements with additional layers of evidence. Upstream regions of protein-encoding genes in A. thaliana were searched for the previously described DNA-binding consensus for WRI1, the ASML1/WRI1 (AW)-box. For about 900 genes, AW-box sites were found to be conserved across orthologous upstream regions in 11 related species of the crucifer family. For 145 select potential target genes identified this way, affinity of upstream AW-box sequences to WRI1 was assayed by Microscale Thermophoresis. This allowed definition of a refined WRI1 DNA-binding consensus. We find that known WRI1 gene targets are predictable with good confidence when upstream AW-sites are phylogenetically conserved, specifically binding WRI1 in the in vitro assay, positioned in proximity to the transcriptional start site, and if the gene is co-expressed with WRI1 during seed development. When targets predicted in this way are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in glycolysis and fatty acid biosynthesis by WRI1. Several of the newly predicted targets are in the upper glycolysis pathway and the pentose phosphate pathway. Of these, plastidic isoforms of fructokinase (FRK3) and of phosphoglucose isomerase (PGI1) are particularly corroborated by previously reported seed phenotypes of respective null mutations.
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Liu N, Liu J, Fan S, Liu H, Zhou XR, Hua W, Zheng M. An integrated omics analysis reveals the gene expression profiles of maize, castor bean, and rapeseed for seed oil biosynthesis. BMC PLANT BIOLOGY 2022; 22:153. [PMID: 35350998 PMCID: PMC8966334 DOI: 10.1186/s12870-022-03495-y] [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: 12/20/2021] [Accepted: 02/25/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Seed storage lipids are valuable for human diet and for the sustainable development of mankind. In recent decades, many lipid metabolism genes and pathways have been identified, but the molecular mechanisms that underlie differences in seed oil biosynthesis in species with developed embryo and endosperm are not fully understood. RESULTS We performed comparative genome and transcriptome analyses of castor bean and rapeseed, which have high seed oil contents, and maize, which has a low seed oil content. These results revealed the molecular underpinnings of the low seed oil content in maize. First of all, transcriptome analyses showed that more than 61% of the lipid- and carbohydrate-related genes were regulated in castor bean and rapeseed, but only 20.1% of the lipid-related genes and 22.5% of the carbohydrate-related genes were regulated in maize. Then, compared to castor bean and rapeseed, fewer lipid biosynthesis genes but more lipid metabolism genes were regulated in the maize embryo. More importantly, most maize genes encoding lipid-related transcription factors, triacylglycerol (TAG) biosynthetic enzymes, pentose phosphate pathway (PPP) and Calvin Cycle proteins were not regulated during seed oil synthesis, despite the presence of many homologs in the maize genome. Additionally, we observed differential regulation of vital oil biosynthetic enzymes and extremely high expression levels of oil biosynthetic genes in castor bean, which were consistent with the rapid accumulation of oil in castor bean developing seeds. CONCLUSIONS Compared to high-oil seeds (castor bean and rapeseed), less oil biosynthetic genes were regulated during the seed development in low-oil seed (maize). These results shed light on molecular mechanisms of lipid biosynthesis in maize, castor bean, and rapeseed. They can provide information on key target genes that may be useful for future experimental manipulation of oil production in oil plants.
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Affiliation(s)
- Nian Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Shihang Fan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hongfang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | | | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China.
| | - Ming Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China.
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Zhang Z, Gong J, Zhang Z, Gong W, Li J, Shi Y, Liu A, Ge Q, Pan J, Fan S, Deng X, Li S, Chen Q, Yuan Y, Shang H. Identification and analysis of oil candidate genes reveals the molecular basis of cottonseed oil accumulation in Gossypium hirsutum L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:449-460. [PMID: 34714356 DOI: 10.1007/s00122-021-03975-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/15/2021] [Indexed: 05/14/2023]
Abstract
Based on the integration of QTL-mapping and regulatory network analyses, five high-confidence stable QTL regions, six candidate genes and two microRNAs that potentially affect the cottonseed oil content were discovered. Cottonseed oil is increasingly becoming a promising target for edible oil with its high content of unsaturated fatty acids. In this study, a recombinant inbred line (RIL) cotton population was constructed to detect quantitative trait loci (QTLs) for the cottonseed oil content. A total of 39 QTLs were detected across eight different environments, of which five QTLs were stable. Forty-three candidate genes potentially involved in carbon metabolism, fatty acid synthesis and triacylglycerol biosynthesis processes were further obtained in the stable QTL regions. Transcriptome analysis showed that nineteen of these candidate genes expressed during the developing cottonseed ovules and may affect the cottonseed oil content. Besides, transcription factor (TF) and microRNA (miRNA) co-regulatory network analyses based on the nineteen candidate genes suggested that six genes, two core miRNAs (ghr-miR2949b and ghr-miR2949c), and one TF GhHSL1 were considered to be closely associated with the cottonseed oil content. Moreover, four vital genes were validated by quantitative real-time PCR (qRT-PCR). These results provide insights into the oil accumulation mechanism in developing cottonseed ovules through the construction of a detailed oil accumulation model.
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Affiliation(s)
- Zhibin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Ürümqi, 830001, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Shaoqi Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Quanjia Chen
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Ürümqi, 830001, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China.
- Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Ürümqi, 830001, China.
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China.
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Turquetti-Moraes DK, Moharana KC, Almeida-Silva F, Pedrosa-Silva F, Venancio TM. Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean. Gene 2022; 808:145976. [PMID: 34592351 DOI: 10.1016/j.gene.2021.145976] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022]
Abstract
Soybean is a major source of edible protein and oil. Oil content is a quantitative trait that is significantly determined by genetic and environmental factors. Over the past 30 years, a large volume of soybean genetic, genomic, and transcriptomic data have been accumulated. Nevertheless, integrative analyses of such data remain scarce, in spite of their importance for crop improvement. We hypothesized that the co-occurrence of genomic regions for oil-related traits in different studies may reveal more stable regions encompassing important genetic determinants of oil content and quality in soybean. We integrated publicly available data, obtained with distinct techniques, to discover and prioritize candidate genes involved in oil biosynthesis and regulation in soybean. We detected key fatty acid biosynthesis genes (e.g., BCCP2 and ACCase, FADs, KAS family proteins) and several transcription factors, which are likely regulators of oil biosynthesis. In addition, we identified new candidates for seed oil accumulation and quality, such as Glyma.03G213300 and Glyma.19G160700, which encode a translocator protein homolog and a histone acetyltransferase, respectively. Further, oil and protein genomic hotspots are strongly associated with breeding and not with domestication, suggesting that soybean domestication prioritized other traits. The genes identified here are promising targets for breeding programs and for the development of soybean lines with increased oil content and quality.
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Affiliation(s)
- Dayana K Turquetti-Moraes
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Kanhu C Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Fabricio Almeida-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.
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Zuo JF, Ikram M, Liu JY, Han CY, Niu Y, Dunwell JM, Zhang YM. Domestication and improvement genes reveal the differences of seed size- and oil-related traits in soybean domestication and improvement. Comput Struct Biotechnol J 2022; 20:2951-2964. [PMID: 35782726 PMCID: PMC9213226 DOI: 10.1016/j.csbj.2022.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 12/01/2022] Open
Abstract
Due to reduced diversity, it is essential to map domesticated and improved genes. 13 known and 442 candidate genes were mined for seed size- and oil-related traits. All the genes were used to explain trait changes in domestication and improvement. 56 domesticated and 15 improved genes may be valuable for future soybean breeding. This study provides useful gene resources for future breeding and biology research.
To address domestication and improvement studies of soybean seed size- and oil-related traits, a series of domesticated and improved regions, loci, and candidate genes were identified in 286 soybean accessions using domestication and improvement analyses, genome-wide association studies, quantitative trait locus (QTL) mapping and bulked segregant analyses in this study. As a result, 534 candidate domestication regions (CDRs) and 458 candidate improvement regions (CIRs) were identified in this study and integrated with those in five and three previous studies, respectively, to obtain 952 CDRs and 538 CIRs; 1469 loci for soybean seed size- and oil-related traits were identified in this study and integrated with those in Soybase to obtain 433 QTL clusters. The two results were intersected to obtain 245 domestication and 221 improvement loci for the above traits. Around these trait-related domestication and improvement loci, 7 domestication and 7 improvement genes were found to be truly associated with these traits, and 372 candidate domestication and 87 candidate improvement genes were identified using gene expression, SNP variants in genome, miRNA binding, KEGG pathway, DNA methylation, and haplotype analysis. These genes were used to explain the trait changes in domestication and improvement. As a result, the trait changes can be explained by their frequencies of elite haplotypes, base mutations in coding region, and three factors affecting their expression levels. In addition, 56 domestication and 15 improvement genes may be valuable for future soybean breeding. This study can provide useful gene resources for future soybean breeding and molecular biology research.
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Affiliation(s)
- Jian-Fang Zuo
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Ikram
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jin-Yang Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chun-Yu Han
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuan Niu
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Corresponding author.
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Ji H, Liu D, Yang Z. High oil accumulation in tuber of yellow nutsedge compared to purple nutsedge is associated with more abundant expression of genes involved in fatty acid synthesis and triacylglycerol storage. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:54. [PMID: 33653389 PMCID: PMC7923336 DOI: 10.1186/s13068-021-01909-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/18/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Yellow nutsedge is a unique plant species that can accumulate up to 35% oil of tuber dry weight, perhaps the highest level observed in the tuber tissues of plant kingdom. To gain insight into the molecular mechanism that leads to high oil accumulation in yellow nutsedge, gene expression profiles of oil production pathways involved carbon metabolism, fatty acid synthesis, triacylglycerol synthesis, and triacylglycerol storage during tuber development were compared with purple nutsedge, the closest relative of yellow nutsedge that is poor in oil accumulation. RESULTS Compared with purple nutsedge, high oil accumulation in yellow nutsedge was associated with significant up-regulation of specific key enzymes of plastidial RubisCO bypass as well as malate and pyruvate metabolism, almost all fatty acid synthesis enzymes, and seed-like oil-body proteins. However, overall transcripts for carbon metabolism toward carbon precursor for fatty acid synthesis were comparable and for triacylglycerol synthesis were similar in both species. Two seed-like master transcription factors ABI3 and WRI1 were found to display similar transcript patterns but were expressed at 6.5- and 14.3-fold higher levels in yellow nutsedge than in purple nutsedge, respectively. A weighted gene co-expression network analysis revealed that ABI3 was in strong transcriptional coordination with WRI1 and other key oil-related genes. CONCLUSIONS These results implied that pyruvate availability and fatty acid synthesis in plastid, along with triacylglycerol storage in oil bodies, rather than triacylglycerol synthesis in endoplasmic reticulum, are the major factors responsible for high oil production in tuber of yellow nutsedge, and ABI3 most likely plays a critical role in regulating oil accumulation. This study is of significance with regard to understanding the molecular mechanism controlling carbon partitioning toward oil production in oil-rich tuber and provides a valuable reference for enhancing oil accumulation in non-seed tissues of crops through genetic breeding or metabolic engineering.
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Affiliation(s)
- Hongying Ji
- Key Lab of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Dantong Liu
- Key Lab of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhenle Yang
- Key Lab of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
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Liu JY, Zhang YW, Han X, Zuo JF, Zhang Z, Shang H, Song Q, Zhang YM. An evolutionary population structure model reveals pleiotropic effects of GmPDAT for traits related to seed size and oil content in soybean. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6988-7002. [PMID: 32926130 DOI: 10.1093/jxb/eraa426] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 05/20/2023]
Abstract
Seed oil traits in soybean that are of benefit to human nutrition and health have been selected for during crop domestication. However, these domesticated traits have significant differences across various evolutionary types. In this study, we found that the integration of evolutionary population structure (evolutionary types) with genome-wide association studies increased the power of gene detection, and it identified one locus for traits related to seed size and oil content on chromosome 13. This domestication locus, together with another one in a 200-kb region, was confirmed by the GEMMA and EMMAX software. The candidate gene, GmPDAT, had higher expressional levels in high-oil and large-seed accessions than in low-oil and small-seed accessions. Overexpression lines had increased seed size and oil content, whereas RNAi lines had decreased seed size and oil content. The molecular mechanism of GmPDAT was deduced based on results from linkage analysis for triacylglycerols and on histocytological comparisons of transgenic soybean seeds. Our results illustrate a new approach for identifying domestication genes with pleiotropic effects.
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Affiliation(s)
- Jin-Yang Liu
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Ya-Wen Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xu Han
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jian-Fang Zuo
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhibin Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Haihong Shang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, USA
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Liu JY, Li P, Zhang YW, Zuo JF, Li G, Han X, Dunwell JM, Zhang YM. Three-dimensional genetic networks among seed oil-related traits, metabolites and genes reveal the genetic foundations of oil synthesis in soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1103-1124. [PMID: 32344462 DOI: 10.1111/tpj.14788] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/21/2020] [Indexed: 05/11/2023]
Abstract
Although the biochemical and genetic basis of lipid metabolism is clear in Arabidopsis, there is limited information concerning the relevant genes in Glycine max (soybean). To address this issue, we constructed three-dimensional genetic networks using six seed oil-related traits, 52 lipid metabolism-related metabolites and 54 294 SNPs in 286 soybean accessions in total. As a result, 284 and 279 candidate genes were found to be significantly associated with seed oil-related traits and metabolites by phenotypic and metabolic genome-wide association studies and multi-omics analyses, respectively. Using minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) analyses, six seed oil-related traits were found to be significantly related to 31 metabolites. Among the above candidate genes, 36 genes were found to be associated with oil synthesis (27 genes), amino acid synthesis (four genes) and the tricarboxylic acid (TCA) cycle (five genes), and four genes (GmFATB1a, GmPDAT, GmPLDα1 and GmDAGAT1) are already known to be related to oil synthesis. Using this information, 133 three-dimensional genetic networks were constructed, 24 of which are known, e.g. pyruvate-GmPDAT-GmFATA2-oil content. Using these networks, GmPDAT, GmAGT and GmACP4 reveal the genetic relationships between pyruvate and the three major nutrients, and GmPDAT, GmZF351 and GmPgs1 reveal the genetic relationships between amino acids and seed oil content. In addition, GmCds1, along with average temperature in July and the rainfall from June to September, influence seed oil content across years. This study provides a new approach for the construction of three-dimensional genetic networks and reveals new information for soybean seed oil improvement and the identification of gene function.
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Affiliation(s)
- Jin-Yang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pei Li
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ya-Wen Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian-Fang Zuo
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guo Li
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Han
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, UK
| | - Yuan-Ming Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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12
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Zuo JF, Niu Y, Cheng P, Feng JY, Han SF, Zhang YH, Shu G, Wang Y, Zhang YM. Effect of marker segregation distortion on high density linkage map construction and QTL mapping in Soybean (Glycine max L.). Heredity (Edinb) 2019; 123:579-592. [PMID: 31152165 PMCID: PMC6972858 DOI: 10.1038/s41437-019-0238-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 02/01/2023] Open
Abstract
Marker segregation distortion is a natural phenomenon. Severely distorted markers are usually excluded in the construction of linkage maps. We investigated the effect of marker segregation distortion on linkage map construction and quantitative trait locus (QTL) mapping. A total of 519 recombinant inbred lines of soybean from orthogonal and reciprocal crosses between LSZZH and NN493-1 were genotyped by specific length amplified fragment markers and seed linoleic acid content was measured in three environments. As a result, twenty linkage groups were constructed with 11,846 markers, including 1513 (12.77%) significantly distorted markers, on 20 chromosomes, and the map length was 2475.86 cM with an average marker-interval of 0.21 cM. The inclusion of distorted markers in the analysis was shown to not only improve the grouping of the markers from the same chromosomes, and the consistency of linkage maps with genome, but also increase genome coverage by markers. Combining genotypic data from both orthogonal and reciprocal crosses decreased the proportion of distorted markers and then improved the quality of linkage maps. Validation of the linkage maps was confirmed by the high collinearity between positions of markers in the soybean reference genome and in linkage maps and by the high consistency of 24 QTL regions in this study compared with the previously reported QTLs and lipid metabolism related genes. Additionally, linkage maps that include distorted markers could add more information to the outputs from QTL mapping. These results provide important information for linkage mapping, gene cloning and marker-assisted selection in soybean.
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Affiliation(s)
- Jian-Fang Zuo
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuan Niu
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Peng Cheng
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian-Ying Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shi-Feng Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying-Hao Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guoping Shu
- Center of Molecular Breeding and Biotechnology, Beijing Lantron Seed Corp., Beijing, 100081, China
| | - Yibo Wang
- Center of Molecular Breeding and Biotechnology, Beijing Lantron Seed Corp., Beijing, 100081, China
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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13
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Du W, Xiong CW, Ding J, Nybom H, Ruan CJ, Guo H. Tandem Mass Tag Based Quantitative Proteomics of Developing Sea Buckthorn Berries Reveals Candidate Proteins Related to Lipid Metabolism. J Proteome Res 2019; 18:1958-1969. [PMID: 30990047 DOI: 10.1021/acs.jproteome.8b00764] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sea buckthorn ( Hippophae L.) is an economically important shrub or small tree distributed in Eurasia. Most of its well-recognized medicinal and nutraceutical products are derived from its berry oil, which is rich in monounsaturated omega-7 (C16:1) fatty acid and polyunsaturated omega-6 (C18:2) and omega-3 (C18:3) fatty acids. In this study, tandem mass tags (TMT)-based quantitative analysis was used to investigate protein profiles of lipid metabolism in sea buckthorn berries harvested 30, 50, and 70 days after flowering. In total, 8626 proteins were identified, 6170 of which were quantified. Deep analysis results for the proteins identified and related pathways revealed initial fatty acid accumulation during whole-berry development. The abundance of most key enzymes involved in fatty acid and triacylglycerol (TAG) biosynthesis peaked at 50 days after flowering, but TAG synthesis through the PDAT (phospholipid: diacylglycerol acyltransferase) pathway mostly occurred early in berry development. In addition, the patterns of proteins involved in lipid metabolism were confirmed by combined quantitative real-time polymerase chain reaction, enzyme-linked immunosorbent assay, and parallel reaction monitoring analyses. Our data on the proteomic spectrum of sea buckthorn berries provide a scientific basic for understanding lipid metabolism and related pathways in the developing berries.
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Affiliation(s)
- Wei Du
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education , Dalian Nationalities University , Dalian 116600 , China
| | - Chao-Wei Xiong
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education , Dalian Nationalities University , Dalian 116600 , China
| | - Jian Ding
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education , Dalian Nationalities University , Dalian 116600 , China
| | - Hilde Nybom
- Department of Plant Breeding-Balsgård , Swedish University of Agricultural Sciences , Fjälkestadsvägen 459 , SE-29194 Kristianstad , Sweden
| | - Cheng-Jiang Ruan
- Institute of Plant Resources, Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education , Dalian Nationalities University , Dalian 116600 , China
| | - Hai Guo
- Conseco Sea Buckthorn Co. Ltd. , Beijing 100038 , China.,Inner Mongolia Hijing Environment Protection Science and Technology Co. Ltd , Inner Mongolia 017000 , China
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14
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Xiao Y, Xia W, Mason AS, Cao Z, Fan H, Zhang B, Zhang J, Ma Z, Peng M, Huang D. Genetic control of fatty acid composition in coconut (Cocos nucifera), African oil palm (Elaeis guineensis), and date palm (Phoenix dactylifera). PLANTA 2019; 249:333-350. [PMID: 30194535 DOI: 10.1007/s00425-018-3003-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/03/2018] [Indexed: 05/26/2023]
Abstract
Predominant gene isoforms and expression bias in lipid metabolism pathways are highly conserved between oil-producing Arecaceae crop species coconut and oil palm, but diverge in non-oil-producing species date palm. Coconut (Cocos nucifera), African oil palm (Elaeis guineensis) and date palm (Phoenix dactylifera) are three major crop species in the Arecaceae family for which genome sequences have recently become available. Coconut and African oil palm both store oil in their endosperms, while date palm fruits contain very little oil. We analyzed fatty acid composition in three coconut tissues (leaf, endosperm and embryo) and in two African oil palm tissues (leaf and mesocarp), and identified 806, 840 and 848 lipid-related genes in 22 lipid metabolism pathways from the coconut, African oil palm and date palm genomes, respectively. The majority of lipid-related genes were highly homologous and retained in homologous segments between the three species. Genes involved in the conversion of pyruvate to fatty acid had a five-to-sixfold higher expression in the coconut endosperm and oil palm mesocarp than in the leaf or embryo tissues based on Fragments Per Kilobase of transcript per Million mapped reads values. A close evolutionary relationship between predominant gene isoforms and high conservation of gene expression bias in the lipid and carbohydrate gene metabolism pathways was observed for the two oil-producing species coconut and oil palm, differing from that of date palm, a non-oil-producing species. Our results elucidate the similarities and differences in lipid metabolism between the three major Arecaceae crop species, providing important information for physiology studies as well as breeding for fatty acid composition and oil content in these crops.
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Affiliation(s)
- Yong Xiao
- Coconut Research Institute, CATAS, Wenchang, 571339, Hainan, People's Republic of China
| | - Wei Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China.
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Zengying Cao
- MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, 571101, Hainan, People's Republic of China
| | - Haikuo Fan
- Coconut Research Institute, CATAS, Wenchang, 571339, Hainan, People's Republic of China
| | - Bo Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Jinlan Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Zilong Ma
- MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, 571101, Hainan, People's Republic of China
| | - Ming Peng
- MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, 571101, Hainan, People's Republic of China
| | - Dongyi Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China
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15
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Zhang Z, Dunwell JM, Zhang YM. An integrated omics analysis reveals molecular mechanisms that are associated with differences in seed oil content between Glycine max and Brassica napus. BMC PLANT BIOLOGY 2018; 18:328. [PMID: 30514240 PMCID: PMC6280547 DOI: 10.1186/s12870-018-1542-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 11/20/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Rapeseed (Brassica napus L.) and soybean (Glycine max L.) seeds are rich in both protein and oil, which are major sources of biofuels and nutrition. Although the difference in seed oil content between soybean (~ 20%) and rapeseed (~ 40%) exists, little is known about its underlying molecular mechanism. RESULTS An integrated omics analysis was performed in soybean, rapeseed, Arabidopsis (Arabidopsis thaliana L. Heynh), and sesame (Sesamum indicum L.), based on Arabidopsis acyl-lipid metabolism- and carbon metabolism-related genes. As a result, candidate genes and their transcription factors and microRNAs, along with phylogenetic analysis and co-expression network analysis of the PEPC gene family, were found to be largely associated with the difference between the two species. First, three soybean genes (Glyma.13G148600, Glyma.13G207900 and Glyma.12G122900) co-expressed with GmPEPC1 are specifically enriched during seed storage protein accumulation stages, while the expression of BnPEPC1 is putatively inhibited by bna-miR169, and two genes BnSTKA and BnCKII are co-expressed with BnPEPC1 and are specifically associated with plant circadian rhythm, which are related to seed oil biosynthesis. Then, in de novo fatty acid synthesis there are rapeseed-specific genes encoding subunits β-CT (BnaC05g37990D) and BCCP1 (BnaA03g06000D) of heterogeneous ACCase, which could interfere with synthesis rate, and β-CT is positively regulated by four transcription factors (BnaA01g37250D, BnaA02g26190D, BnaC01g01040D and BnaC07g21470D). In triglyceride synthesis, GmLPAAT2 is putatively inhibited by three miRNAs (gma-miR171, gma-miR1516 and gma-miR5775). Finally, in rapeseed there was evidence for the expansion of gene families, CALO, OBO and STERO, related to lipid storage, and the contraction of gene families, LOX, LAH and HSI2, related to oil degradation. CONCLUSIONS The molecular mechanisms associated with differences in seed oil content provide the basis for future breeding efforts to improve seed oil content.
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Affiliation(s)
- Zhibin Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000 China
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AS UK
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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16
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Li QT, Lu X, Song QX, Chen HW, Wei W, Tao JJ, Bian XH, Shen M, Ma B, Zhang WK, Bi YD, Li W, Lai YC, Lam SM, Shui GH, Chen SY, Zhang JS. Selection for a Zinc-Finger Protein Contributes to Seed Oil Increase during Soybean Domestication. PLANT PHYSIOLOGY 2017; 173:2208-2224. [PMID: 28184009 PMCID: PMC5373050 DOI: 10.1104/pp.16.01610] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/06/2017] [Indexed: 05/18/2023]
Abstract
Seed oil is a momentous agronomical trait of soybean (Glycine max) targeted by domestication in breeding. Although multiple oil-related genes have been uncovered, knowledge of the regulatory mechanism of seed oil biosynthesis is currently limited. We demonstrate that the seed-preferred gene GmZF351, encoding a tandem CCCH zinc finger protein, is selected during domestication. Further analysis shows that GmZF351 facilitates oil accumulation by directly activating WRINKLED1, BIOTIN CARBOXYL CARRIER PROTEIN2, 3-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III, DIACYLGLYCEROL O-ACYLTRANSFERASE1, and OLEOSIN2 in transgenic Arabidopsis (Arabidopsis thaliana) seeds. Overexpression of GmZF351 in transgenic soybean also activates lipid biosynthesis genes, thereby accelerating seed oil accumulation. The ZF351 haplotype from the cultivated soybean group and the wild soybean (Glycine soja) subgroup III correlates well with high gene expression level, seed oil contents and promoter activity, suggesting that selection of GmZF351 expression leads to increased seed oil content in cultivated soybean. Our study provides novel insights into the regulatory mechanism for seed oil accumulation, and the manipulation of GmZF351 may have great potential in the improvement of oil production in soybean and other related crops.
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Affiliation(s)
- Qing-Tian Li
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Xiang Lu
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Qing-Xin Song
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Hao-Wei Chen
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Wei Wei
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Jian-Jun Tao
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Xiao-Hua Bian
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Ming Shen
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Biao Ma
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Wan-Ke Zhang
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Ying-Dong Bi
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Wei Li
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Yong-Cai Lai
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Sin-Man Lam
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Guang-Hou Shui
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Shou-Yi Chen
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
| | - Jin-Song Zhang
- State Key Laboratory of Plant Genomics (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.) and State Key Laboratory of Molecular Developmental Biology (S.L., G.S.), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- University of the Chinese Academy of Sciences, Beijing 100049, China (Q.L., X.L., Q.S., H.C., W.W., J.T., X.B., M.S., B.M., W.Z., S.C., J.Z.); and
- Institute of Farming and Cultivation, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin 150086, China (Y.B., W.L., Y.L.)
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Sanyal A, Decocq G. Adaptive evolution of seed oil content in angiosperms: accounting for the global patterns of seed oils. BMC Evol Biol 2016; 16:187. [PMID: 27613109 PMCID: PMC5017040 DOI: 10.1186/s12862-016-0752-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 08/23/2016] [Indexed: 11/22/2022] Open
Abstract
Background Studies of the biogeographic distribution of seed oil content in plants are fundamental to understanding the mechanisms of adaptive evolution in plants as seed oil is the primary energy source needed for germination and establishment of plants. However, seed oil content as an adaptive trait in plants is poorly understood. Here, we examine the adaptive nature of seed oil content in 168 angiosperm families occurring in different biomes across the world. We also explore the role of multiple seed traits like seed oil content and composition in plant adaptation in a phylogenetic and nonphylogenetic context. Result It was observed that the seed oil content in tropical plants (28.4 %) was significantly higher than the temperate plants (24.6 %). A significant relationship between oil content and latitude was observed in three families Papaveraceae, Sapindaceae and Sapotaceae indicating that selective forces correlated with latitude influence seed oil content. Evaluation of the response of seed oil content and composition to latitude and the correlation between seed oil content and composition showed that multiple seed traits, seed oil content and composition contribute towards plant adaptation. Investigation of the presence or absence of phylogenetic signals across 168 angiosperm families in 62 clades revealed that members of seven clades evolved to have high or low seed oil content independently as they did not share a common evolutionary path. Conclusion The study provides us an insight into the biogeographical distribution and the adaptive role of seed oil content in plants. The study indicates that multiple seed traits like seed oil content and the fatty acid composition of the seed oils determine the fitness of the plants and validate the adaptive hypothesis that seed oil quantity and quality are crucial to plant adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0752-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anushree Sanyal
- Unité "Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, FRE 3498 CNRS), Université de Picardie Jules Verne, 1 rue des Louvels, Amiens Cedex, FR-80037, France. .,Institute for Organismal Biology, Systematic Biology, Uppsala University, Uppsala, 75236, Sweden.
| | - Guillaume Decocq
- Unité "Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, FRE 3498 CNRS), Université de Picardie Jules Verne, 1 rue des Louvels, Amiens Cedex, FR-80037, France
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