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Qi Z, Guo C, Li H, Qiu H, Li H, Jong C, Yu G, Zhang Y, Hu L, Wu X, Xin D, Yang M, Liu C, Lv J, Wang X, Kong F, Chen Q. Natural variation in Fatty Acid 9 is a determinant of fatty acid and protein content. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:759-773. [PMID: 37937736 PMCID: PMC10893952 DOI: 10.1111/pbi.14222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Soybean is one of the most economically important crops worldwide and an important source of unsaturated fatty acids and protein for the human diet. Consumer demand for healthy fats and oils is increasing, and the global demand for vegetable oil is expected to double by 2050. Identification of key genes that regulate seed fatty acid content can facilitate molecular breeding of high-quality soybean varieties with enhanced fatty acid profiles. Here, we analysed the genetic architecture underlying variations in soybean seed fatty acid content using 547 accessions, including mainly landraces and cultivars from northeastern China. Through fatty acid profiling, genome re-sequencing, population genomics analyses, and GWAS, we identified a SEIPIN homologue at the FA9 locus as an important contributor to seed fatty acid content. Transgenic and multiomics analyses confirmed that FA9 was a key regulator of seed fatty acid content with pleiotropic effects on seed protein and seed size. We identified two major FA9 haplotypes in 1295 resequenced soybean accessions and assessed their phenotypic effects in a field planting of 424 accessions. Soybean accessions carrying FA9H2 had significantly higher total fatty acid contents and lower protein contents than those carrying FA9H1 . FA9H2 was absent in wild soybeans but present in 13% of landraces and 26% of cultivars, suggesting that it may have been selected during soybean post-domestication improvement. FA9 therefore represents a useful genetic resource for molecular breeding of high-quality soybean varieties with specific seed storage profiles.
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Affiliation(s)
- Zhaoming Qi
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Chaocheng Guo
- Shanghai Collaborative Innovation Center of Agri‐Seeds, Joint Center for Single Cell Biology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Hongmei Qiu
- Soybean Research InstituteJilin Academy of Agricultural Sciences/National Soybean Engineering CenterChangchunChina
| | - Hui Li
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - CholNam Jong
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Guolong Yu
- Shanghai Collaborative Innovation Center of Agri‐Seeds, Joint Center for Single Cell Biology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yu Zhang
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Limin Hu
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Xiaoxia Wu
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Dawei Xin
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Mingliang Yang
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Chunyan Liu
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
| | - Jian Lv
- Department of InnovationSyngenta Biotechnology ChinaBeijingChina
| | - Xu Wang
- Shanghai Collaborative Innovation Center of Agri‐Seeds, Joint Center for Single Cell Biology, School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Qingshan Chen
- College of AgricultureNortheast Agricultural UniversityHarbinHeilongjiangChina
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Wang N, Feng S, Ma X, Chen Q, Liu C, Qi Z. Meta-Analysis and Multiomics of a Chromosome Segment Substitution Line Reveal Candidate Genes Associated with Seed Hardness in Soybean. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16840-16854. [PMID: 37821458 DOI: 10.1021/acs.jafc.3c03950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Soybean seed hardness is a key trait that influences planting, nutritional quality, and postharvest processing, but its genetic and molecular mechanisms remain to be clarified. We used meta-analysis to detect 17 meta-quantitative trait locus (QTLs) for soybean seed hardness. We then identified a hard-seeded chromosome segment substitution line, R75, with fragments introduced from hard-seeded wild germplasm in four of the meta-QTL intervals. Observations of the seed coat ultrastructure revealed thicker palisade tissue in R75 than in its soft-seeded recurrent parent. Transcriptomics and proteomics of R75 and its recurrent parent revealed multiple candidate genes associated with seed hardness. Fifty-seven were located on homozygous introduced fragments, 26 in meta-QTL intervals, and one in both (Glyma.02G268600). Five initial candidates were selected for KASP marker development on the basis of their predicted functions and nonsynonymous SNPs. The selection efficiency of the markers was as high as 90% for nonhard lines and 43% for hard lines in the chromosome segment substitution line (CSSL) population.
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Affiliation(s)
- Ning Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Shaowei Feng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Xuntong Ma
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China
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Sun M, Wei S, Liu J, Wang L, Zhang Y, Hu L, Piao J, Liang Z, Jiang H, Xin D, Zhao Y, Chen Q, Foyer CH, Liu C, Qi Z. The impact of GmTSA and GmALS on soybean salt tolerance: uncovering the molecular landscape of amino acid and secondary metabolism pathways. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:212. [PMID: 37740151 DOI: 10.1007/s00122-023-04461-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/08/2023] [Indexed: 09/24/2023]
Abstract
KEY MESSAGE GmTSA and GmALS were screened out for salt stress in soybean and explore the poteintial amino acid secondary metabolism pathways. Soybean (Glycine max L.) is an oil and protein crop of global importance, and salinity has significant effects on soybean growth. Here, a population of soybean chromosome segment substitution lines was screened to identify highly salt-tolerant lines. In total, 24 quantitative trait loci (QTLs) on seven chromosomes were associated with salt tolerance, and CSSL_R71 was selected for further analysis. Although numerous genes were differentially expressed in CSSL_R71 in response to salt statically no differently, transcript levels of classical salt-response genes, including those of the salt overly sensitive pathway. Rather, salt tolerance in CSSL_R71 was associated with changes in amino acid and lipid metabolism. In particular, changes in p-coumaric acid, shikimic acid, and pyrrole-2-carboxylic acid levels accompanied salt tolerance in CSSL_R71. Eleven differentially expressed genes (DEGs) related to amino acid and secondary metabolism were identified as candidate genes on the substituted chromosome fragment. Six of these showed differences in coding sequence between the parental genotypes. Crucially, overexpression of GmTSA (Glyma.03G158400, tryptophan synthase) significantly enhanced salt tolerance in soybean hairy roots, whereas overexpression of GmALS (Glyma.13G241000, acetolactate synthase) decreased salt tolerance. Two KASP markers were developed for GmALS and used to genotype salt-tolerant and salt-sensitive lines in the CSSL population. Non-synonymous mutations were directly associated with salt tolerance. Taken together, these data provide evidence that changes in amino acid and secondary metabolism have the potential to confer salt tolerance in soybean.
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Affiliation(s)
- Minghao Sun
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Siming Wei
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jiarui Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Luyao Wang
- Institute of Rural Revitalization Science and Technology, Heilongjiang Academy of Agricultural Sciences, Harbin, 150028, China
| | - Yu Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Limin Hu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Jingxi Piao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Zhao Liang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, 130033, China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Ying Zhao
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, UK.
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People's Republic of China.
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Rao PJM, Pallavi M, Bharathi Y, Priya PB, Sujatha P, Prabhavathi K. Insights into mechanisms of seed longevity in soybean: a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1206318. [PMID: 37546268 PMCID: PMC10400919 DOI: 10.3389/fpls.2023.1206318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/23/2023] [Indexed: 08/08/2023]
Abstract
Soybean, a crop of international importance, is challenged with the problem of seed longevity mainly due to its genetic composition and associated environmental cues. Soybean's fragile seed coat coupled with poor DNA integrity, ribosomal dysfunction, lipid peroxidation and poor antioxidant system constitute the rationale for fast deterioration. Variability among the genotypes for sensitivity to field weathering contributed to their differential seed longevity. Proportion and density of seed coat, glassy state of cells, calcium and lignin content, pore number, space between seed coat and cotyledon are some seed related traits that are strongly correlated to longevity. Further, efficient antioxidant system, surplus protective proteins, effective nucleotide and protein repair systems and free radical scavenging mechanisms also contributed to the storage potential of soybean seeds. Identification of molecular markers and QTLs associated with these mechanisms will pave way for enhanced selection efficiency for seed longevity in soybean breeding programs. This review reflects on the morphological, biochemical and molecular bases of seed longevity along with pointers on harvest, processing and storage strategies for extending vigour and viability in soybean.
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Jiang H, Zhou C, Ma J, Qu S, Liu F, Sun H, Zhao X, Han Y. Weighted gene co-expression network analysis identifies genes related to HG Type 0 resistance and verification of hub gene GmHg1. FRONTIERS IN PLANT SCIENCE 2023; 13:1118503. [PMID: 36777536 PMCID: PMC9911859 DOI: 10.3389/fpls.2022.1118503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION The soybean cyst nematode (SCN) is a major disease in soybean production thatseriously affects soybean yield. At present, there are no studies on weighted geneco-expression network analysis (WGCNA) related to SCN resistance. METHODS Here, transcriptome data from 36 soybean roots under SCN HG Type 0 (race 3) stresswere used in WGCNA to identify significant modules. RESULTS AND DISCUSSION A total of 10,000 differentially expressed genes and 21 modules were identified, of which the module most related to SCN was turquoise. In addition, the hub gene GmHg1 with high connectivity was selected, and its function was verified. GmHg1 encodes serine/threonine protein kinase (PK), and the expression of GmHg1 in SCN-resistant cultivars ('Dongnong L-204') and SCN-susceptible cultivars ('Heinong 37') increased significantly after HG Type 0 stress. Soybean plants transformed with GmHg1-OX had significantly increased SCN resistance. In contrast, the GmHg1-RNAi transgenic soybean plants significantly reduced SCN resistance. In transgenic materials, the expression patterns of 11 genes with the same expression trend as the GmHg1 gene in the 'turquoise module' were analyzed. Analysis showed that 11genes were co-expressed with GmHg1, which may be involved in the process of soybean resistance to SCN. Our work provides a new direction for studying the Molecular mechanism of soybean resistance to SCN.
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Affiliation(s)
- Haipeng Jiang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Changjun Zhou
- Soybean Molecular Breeding Faculty Daqing Branch, Heilongjiang Academy of Agricultrual Science, Daqing, China
| | - Jinglin Ma
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Shuo Qu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Fang Liu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Haowen Sun
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
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Jia Y, Yao M, He X, Xiong X, Guan M, Liu Z, Guan C, Qian L. Transcriptome and Regional Association Analyses Reveal the Effects of Oleosin Genes on the Accumulation of Oil Content in Brassica napus. PLANTS (BASEL, SWITZERLAND) 2022; 11:3140. [PMID: 36432869 PMCID: PMC9698637 DOI: 10.3390/plants11223140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/03/2022] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
Rapeseed stores lipids in the form of oil bodies. Oil bodies in the seeds of higher plants are surrounded by oleosins. Adjusting oleosin protein levels can prevent the fusion of oil bodies and maintain oil body size during seed development. However, oil contents are affected by many factors, and studies on the complex molecular regulatory mechanisms underlying the variations in seed oil contents of B. napus are limited. In this study, a total of 53 BnOLEO (B. napus oleosin) genes were identified in the genome of B. napus through a genome-wide analysis. The promoter sequences of oleosin genes consisted of various light-, hormone-, and stress-related cis-acting elements, along with transcription factor (TF) binding sites, for 25 TF families in 53 BnOLEO genes. The differentially expressed oleosin genes between two high- and two low-oil-content accessions were explored. BnOLEO3-C09, BnOLEO4-A02, BnOLEO4-A09, BnOLEO2-C04, BnOLEO1-C01, and BnOLEO7-A03 showed higher expressions in the high-oil-content accessions than in low-oil-content accessions, at 25, 35, and 45 days after pollination (DAP) in two different environments. A regional association analysis of 50 re-sequenced rapeseed accessions was used to further analyze these six BnOLEO genes, and it revealed that the nucleotide variations in the BnOLEO1-C01 and BnOLEO7-A03 gene regions were related to the phenotypic variations in seed oil content. Moreover, a co-expression network analysis revealed that the BnOLEO genes were directly linked to lipid/fatty acid metabolism, TF, lipid transport, and carbohydrate genes, thus forming a molecular network involved in seed oil accumulation. These favorable haplotypes can be utilized in molecular marker-assisted selection in order to further improve seed oil contents in rapeseed.
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Povilus RA, Friedman WE. Transcriptomes across fertilization and seed development in the water lily Nymphaea thermarum (Nymphaeales): evidence for epigenetic patterning during reproduction. PLANT REPRODUCTION 2022; 35:161-178. [PMID: 35184212 DOI: 10.1007/s00497-022-00438-3] [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: 05/19/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
The first record of gene expression during seed development within the Nymphaeales provides evidence for a variety of biological processes, including dynamic epigenetic patterning during sexual reproduction in the water lily Nymphaea thermarum. Studies of gene expression during seed development have been performed for a growing collection of species from a phylogenetically broad sampling of flowering plants (angiosperms). However, angiosperm lineages whose origins predate the divergence of monocots and eudicots have been largely overlooked. In order to provide a new resource for understanding the early evolution of seed development in flowering plants, we sequenced transcriptomes of whole ovules and seeds from three key stages of reproductive development in the waterlily Nymphaea thermarum, an experimentally tractable member of the Nymphaeales. We first explore patterns of gene expression, beginning with mature ovules and continuing through fertilization into early- and mid-stages of seed development. We find patterns of gene expression that corroborate histological/morphological observations of seed development in this species, such as expression of genes involved in starch synthesis and transcription factors that have been associated with embryo and endosperm development in other species. We also find evidence for processes that were previously not known to be occurring during seed development in this species, such as epigenetic modification. We then examine the expression of genes associated with patterning DNA and histone methylation-processes that are essential for seed development in distantly related and structurally diverse monocots and eudicots. Around 89% of transcripts putatively homologous to DNA and histone methylation modifiers are expressed during seed development in N. thermarum, including homologs of genes known to pattern imprinting-related epigenetic modifications. Our results suggest that dynamic epigenetic patterning is a deeply conserved aspect of angiosperm seed development.
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Affiliation(s)
- Rebecca A Povilus
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - William E Friedman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
- Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA, 02131, USA.
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Song J, Mavraganis I, Shen W, Yang H, Cram D, Xiang D, Patterson N, Zou J. Transcriptome dissection of candidate genes associated with lentil seed quality traits. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:815-826. [PMID: 35395134 DOI: 10.1111/plb.13426] [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: 01/11/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Lentils provide a rich plant-based protein source and staple food in many parts of the world. Despite numerous nutritional benefits, lentil seeds also possess undesirable elements, such as anti-nutritional factors. Understanding the genetic networks of seed metabolism is of great importance for improving the seed nutritional profile. We applied RNA sequencing analysis to survey the transcriptome of developing lentil seeds and compared this with that of the pod shells and leaves. In total, we identified 2622 genes differentially expressed among the tissues examined. Genes preferentially expressed in seeds were enriched in the Gene Ontology (GO) terms associated with development, nitrogen and carbon (N/C) metabolism and lipid synthesis. We further categorized seed preferentially expressed genes based on their involvement in storage protein production, starch accumulation, lipid and suberin metabolism, phytate, saponin and phenylpropanoid biosynthesis. The availability of transcript profile datasets on lentil seed metabolism and a roadmap of candidate genes presented here will be of great value for breeding strategies towards further improvement of lentil seed quality traits.
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Affiliation(s)
- J Song
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - I Mavraganis
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - W Shen
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - H Yang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - D Cram
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - D Xiang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - N Patterson
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - J Zou
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
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Liu J, Dong L, Duan R, Hu L, Zhao Y, Zhang L, Wang X. Transcriptomic Analysis Reveals the Regulatory Networks and Hub Genes Controlling the Unsaturated Fatty Acid Contents of Developing Seed in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:876371. [PMID: 35646018 PMCID: PMC9134122 DOI: 10.3389/fpls.2022.876371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
Soybean [Glycine max (L.) Merr.] is one of the most important crops, which produces about 25% of the world's edible oil. The nutritional value of soybean oil depends mostly on the relative contents of three unsaturated fatty acids (UFAs), i.e., oleic acid, linoleic acid (LA), and linolenic acid. However, the biosynthetic mechanism of UFAs remains largely unknown, and there are few studies on RNA-seq analysis of developing seeds. To identify the candidate genes and related pathways involved in the regulation of UFA contents during seed development in soybean, two soybean lines with different UFA profiles were selected from 314 cultivars and landraces originated from Southern China, and RNA-seq analysis was performed in soybean seeds at three developmental stages. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a series of genes and pathways related to fatty acid metabolism were identified, and 40 days after flowering (DAF) was found to be the crucial period in the formation of UFA profiles. Further, weighted gene co-expression network analysis identified three modules with six genes whose functions were highly associated with the contents of oleic and LA. The detailed functional investigation of the networks and hub genes could further improve the understanding of the underlying molecular mechanism of UFA contents and might provide some ideas for the improvement in fatty acids profiles in soybean.
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Affiliation(s)
- Junqi Liu
- School of Agriculture, Yunnan University, Kunming, China
| | - Liang Dong
- School of Agriculture, Yunnan University, Kunming, China
| | - Runqing Duan
- School of Agriculture, Yunnan University, Kunming, China
| | - Li Hu
- School of Agriculture, Yunnan University, Kunming, China
| | - Yinyue Zhao
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Liang Zhang
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xianzhi Wang
- School of Agriculture, Yunnan University, Kunming, China
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Cao P, Zhao Y, Wu F, Xin D, Liu C, Wu X, Lv J, Chen Q, Qi Z. Multi-Omics Techniques for Soybean Molecular Breeding. Int J Mol Sci 2022; 23:4994. [PMID: 35563386 PMCID: PMC9099442 DOI: 10.3390/ijms23094994] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite soybean varieties with specific oil compositions to meet various end-use targets. The assembly of soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in soybean research. It facilitated advances in soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate soybean breeding in the future. This review will be of interest not only to soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement.
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Affiliation(s)
- Pan Cao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Ying Zhao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Fengjiao Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Jian Lv
- Department of Innovation, Syngenta Biotechnology China, Beijing 102206, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
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Li J, Ding H, Wang Z, El-Ansary D, Adams R, Han J, Meng S. Translation, Cultural Adaptation, Reliability, and Validity Testing of a Chinese Version of the Self-Administered Mediterranean Diet Scale. Front Nutr 2022; 9:831109. [PMID: 35419397 PMCID: PMC8996054 DOI: 10.3389/fnut.2022.831109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Mediterranean Diet management for people with cardiovascular disease (CVD) or CVD risk is supported by evidence. However, there is no valid Chinese language instrument for the measurement of adherence to this diet. The objective of this study was to generate a Chinese version of the Mediterranean Diet Scale (MDS-Chinese) and to validate a self-administered version with Chinese participants with CVD or CVD risk. The MDS-Chinese was created by translation and cultural adaptation and tested for psychometric properties. A panel of 10 experts in the field, who evaluated the MDS-Chinese content, showed that the content validity index ranged from 0.88 to 1.00. Sixteen native Chinese speakers with CVD or CVD risk evaluated the clarity of the MDS-Chinese, and the resulting instruction and items clarity scores ranged from 9.2 to 10.0. A total of 326 participants completed the MDS-Chinese and a Chinese version of the Coronary Artery Disease Education Questionnaire–Short Version (CADE-Q SV). Analysis indicated that the MDS-Chinese has 4 factors, and the Pearson's correlation between the MDS-Chinese and CADE-Q SV was 0.73. Fifty randomly selected participants completed the MDS-Chinese again with a 1-week interval to assess reliability. Internal consistency was acceptable (Cronbach's α was 0.62) and the inter-class correlation reliability coefficients (ICC) for each item ranged from 0.73 to 0.88. This study showed that the MDS-Chinese has acceptable reliability and validity for use among those in the Chinese population with CVD or CVD risk. Given that diet is one of the key secondary prevention strategies for management in cardiac rehabilitation, the MDS-Chinese instrument may be a useful and convenient tool for use with those in the Chinese population with CVD or with high risk of CVD, to monitor the level of Mediterranean diet (MD) adherence, information which is important for clinical practice. In addition, the establishment of the MDS-Chinese gives a fundamental tool for diet-related CVD research in the Chinese population. Moreover, employment of the MDS-Chinese in the Chinese community may improve awareness of the importance of a healthy diet in CVD prevention and management.Clinical Trial Registration:http://www.chictr.org.cn/enIndex.aspx, identifier: ChiCTR2000032810.
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Affiliation(s)
- Jiajia Li
- School of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Huirong Ding
- Department of Nursing, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zheng Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Doa El-Ansary
- School of Kinesiology, Shanghai University of Sport, Shanghai, China
- Department of Health Professions, Faculty of Art, Health and Design, Swinburne University of Technology, Melbourne, VIC, Australia
- Department of Surgery, School of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Roger Adams
- Research Institute for Sport and Exercise, University of Canberra, Canberra, ACT, Australia
| | - Jia Han
- College of Rehabilitation Sciences, Shanghai University of Medicine and Health Sciences, Shanghai, China
- *Correspondence: Jia Han
| | - Shu Meng
- Department of Cardiology, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shu Meng
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12
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Han X, Li J, Zhao Y, Zhang Z, Jiang H, Wang J, Feng X, Zhang Y, Du Z, Wu X, Chen Q, Qi Z. Integrated transcriptomic and proteomic characterization of a chromosome segment substitution line reveals a new regulatory network controlling the seed storage profile of soybean. Food Energy Secur 2022. [DOI: 10.1002/fes3.381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Xue Han
- College of Agriculture Northeast Agricultural University Harbin China
- Heilongjiang Academy of Land Reclamation Sciences Harbin China
| | - Jiapeng Li
- College of Agriculture Northeast Agricultural University Harbin China
| | - Yabin Zhao
- College of Agriculture Northeast Agricultural University Harbin China
| | - Zhanguo Zhang
- College of Agriculture Northeast Agricultural University Harbin China
| | - Hongwei Jiang
- Soybean Research Institute Jilin Academy of Agricultural Sciences Changchun China
| | - Jinxing Wang
- Suihua Branch Institute, HeiLongJiang Academy of Agricultural Sciences Suihua China
| | - Xuezhen Feng
- College of Agriculture Northeast Agricultural University Harbin China
| | - Yu Zhang
- College of Agriculture Northeast Agricultural University Harbin China
| | - Ziyue Du
- College of Agriculture Northeast Agricultural University Harbin China
| | - Xiaoxia Wu
- College of Agriculture Northeast Agricultural University Harbin China
| | - Qingshan Chen
- College of Agriculture Northeast Agricultural University Harbin China
| | - Zhaoming Qi
- College of Agriculture Northeast Agricultural University Harbin China
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13
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Su L, Xu C, Zeng S, Su L, Joshi T, Stacey G, Xu D. Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model. FRONTIERS IN PLANT SCIENCE 2022; 13:831204. [PMID: 35310659 PMCID: PMC8927983 DOI: 10.3389/fpls.2022.831204] [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: 12/08/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Plant tissues are distinguished by their gene expression patterns, which can help identify tissue-specific highly expressed genes and their differential functional modules. For this purpose, large-scale soybean transcriptome samples were collected and processed starting from raw sequencing reads in a uniform analysis pipeline. To address the gene expression heterogeneity in different tissues, we utilized an adversarial deconfounding autoencoder (AD-AE) model to map gene expressions into a latent space and adapted a standard unsupervised autoencoder (AE) model to help effectively extract meaningful biological signals from the noisy data. As a result, four groups of 1,743, 914, 2,107, and 1,451 genes were found highly expressed specifically in leaf, root, seed and nodule tissues, respectively. To obtain key transcription factors (TFs), hub genes and their functional modules in each tissue, we constructed tissue-specific gene regulatory networks (GRNs), and differential correlation networks by using corrected and compressed gene expression data. We validated our results from the literature and gene enrichment analysis, which confirmed many identified tissue-specific genes. Our study represents the largest gene expression analysis in soybean tissues to date. It provides valuable targets for tissue-specific research and helps uncover broader biological patterns. Code is publicly available with open source at https://github.com/LingtaoSu/SoyMeta.
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Affiliation(s)
- Lingtao Su
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Chunhui Xu
- Institute for Data Science and Informatics, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Shuai Zeng
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Li Su
- Institute for Data Science and Informatics, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Trupti Joshi
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Institute for Data Science and Informatics, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Health Management and Informatics and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Gary Stacey
- Division of Plant Sciences and Technology and Biochemistry Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Dong Xu
- Department of Electrical Engineering and Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Institute for Data Science and Informatics, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
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14
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Tian T, Chen L, Ai Y, He H. Selection of Candidate Genes Conferring Blast Resistance and Heat Tolerance in Rice through Integration of Meta-QTLs and RNA-Seq. Genes (Basel) 2022; 13:genes13020224. [PMID: 35205268 PMCID: PMC8871662 DOI: 10.3390/genes13020224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 02/04/2023] Open
Abstract
Due to global warming, high temperature is a significant environmental stress for rice production. Rice (Oryza sativa L.), one of the most crucial cereal crops, is also seriously devastated by Magnaporthe oryzae. Therefore, it is essential to breed new rice cultivars with blast and heat tolerance. Although progress had been made in QTL mapping and RNA-seq analysis in rice in response to blast and heat stresses, there are few reports on simultaneously mining blast-resistant and heat-tolerant genes. In this study, we separately conducted meta-analysis of 839 blast-resistant and 308 heat-tolerant QTLs in rice. Consequently, 7054 genes were identified in 67 blast-resistant meta-QTLs with an average interval of 1.00 Mb. Likewise, 6425 genes were obtained in 40 heat-tolerant meta-QTLs with an average interval of 1.49 Mb. Additionally, using differentially expressed genes (DEGs) in the previous research and GO enrichment analysis, 55 DEGs were co-located on the common regions of 16 blast-resistant and 14 heat-tolerant meta-QTLs. Among, OsChib3H-c, OsJAMyb, Pi-k, OsWAK1, OsMT2b, OsTPS3, OsHI-LOX, OsACLA-2 and OsGS2 were the significant candidate genes to be further investigated. These results could provide the gene resources for rice breeding with excellent resistance to these 2 stresses, and help to understand how plants response to the combination stresses of blast fungus and high temperature.
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Affiliation(s)
| | | | - Yufang Ai
- Correspondence: (Y.A.); (H.H.); Tel.: +86-0591-8378-9367 (H.H.)
| | - Huaqin He
- Correspondence: (Y.A.); (H.H.); Tel.: +86-0591-8378-9367 (H.H.)
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15
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Verma SK, Mittal S, Gayacharan, Wankhede DP, Parida SK, Chattopadhyay D, Prasad G, Mishra DC, Joshi DC, Singh M, Singh K, Singh AK. Transcriptome Analysis Reveals Key Pathways and Candidate Genes Controlling Seed Development and Size in Ricebean (Vigna umbellata). Front Genet 2022; 12:791355. [PMID: 35126460 PMCID: PMC8815620 DOI: 10.3389/fgene.2021.791355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/23/2021] [Indexed: 11/27/2022] Open
Abstract
Ricebean (Vigna umbellata) is a lesser known pulse with well-recognized potential. Recently, it has emerged as a legume with endowed nutritional potential because of high concentration of quality protein and other vital nutrients in its seeds. However, the genes and pathways involved in regulating seed development and size are not understood in this crop. In our study, we analyzed the transcriptome of two genotypes with contrasting grain size (IC426787: large seeded and IC552985: small seeded) at two different time points, namely, 5 and 10 days post-anthesis (DPA). The bold seeded genotype across the time points (B5_B10) revealed 6,928 differentially expressed genes (DEGs), whereas the small seeded genotype across the time point (S5_S10) contributed to 14,544 DEGs. We have also identified several candidate genes for seed development–related traits like seed size and 100-seed weight. On the basis of similarity search and domain analysis, some candidate genes (PHO1, cytokinin dehydrogenase, A-type cytokinin, and ARR response negative regulator) related to 100-seed weight and seed size showed downregulation in the small seeded genotype. The MapMan and KEGG analysis confirmed that auxin and cytokinin pathways varied in both the contrasting genotypes and can therefore be the regulators of the seed size and other seed development–related traits in ricebeans. A total of 51 genes encoding SCFTIR1/AFB, Aux/IAA, ARFs, E3 ubiquitin transferase enzyme, and 26S proteasome showing distinct expression dynamics in bold and small genotypes were also identified. We have also validated randomly selected SSR markers in eight accessions of the Vigna species (V. umbellata: 6; Vigna radiata: 1; and Vigna mungo: 1). Cross-species transferability pattern of ricebean–derived SSR markers was higher in V. radiata (73.08%) than V. mungo (50%). To the best of our knowledge, this is the first transcriptomic study conducted in this crop to understand the molecular basis of any trait. It would provide us a comprehensive understanding of the complex transcriptome dynamics during the seed development and gene regulatory mechanism of the seed size determination in ricebeans.
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16
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Zhang H, Hu Z, Yang Y, Liu X, Lv H, Song BH, An YQC, Li Z, Zhang D. Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development. BMC Genomics 2021; 22:453. [PMID: 34134624 PMCID: PMC8207594 DOI: 10.1186/s12864-021-07783-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealing the underlying regulatory activities is critical for seed improvement. RESULTS In this study, we profiled the transcriptomes of developing seeds at 20, 25, 30, and 40 days after flowering (DAF), as these stages represent critical time points of seed development from early to full development. We identified a set of highly abundant genes and highlighted the importance of these genes in supporting nutrient accumulation and transcriptional regulation for seed development. We identified 8925 differentially expressed genes (DEGs) that exhibited temporal expression patterns over the course and expression specificities in distinct tissues, including seeds and nonseed tissues (roots, stems, and leaves). Genes specific to nonseed tissues might have tissue-associated roles, with relatively low transcript abundance in developing seeds, suggesting their spatially supportive roles in seed development. Coexpression network analysis identified several underexplored genes in soybeans that bridge tissue-specific gene modules. CONCLUSIONS Our study provides a global view of gene activities and biological processes critical for seed formation in soybeans and prioritizes a set of genes for further study. The results of this study help to elucidate the mechanism controlling seed development and storage reserves.
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Affiliation(s)
- Hengyou Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhenbin Hu
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haiyan Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit at Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Zhimin Li
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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17
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Sun S, Yi C, Ma J, Wang S, Peirats-Llobet M, Lewsey MG, Whelan J, Shou H. Analysis of Spatio-Temporal Transcriptome Profiles of Soybean ( Glycine max) Tissues during Early Seed Development. Int J Mol Sci 2020; 21:E7603. [PMID: 33066688 PMCID: PMC7589660 DOI: 10.3390/ijms21207603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 01/17/2023] Open
Abstract
Soybean (Glycine max) is an important crop providing oil and protein for both human and animal consumption. Knowing which biological processes take place in specific tissues in a temporal manner will enable directed breeding or synthetic approaches to improve seed quantity and quality. We analyzed a genome-wide transcriptome dataset from embryo, endosperm, endothelium, epidermis, hilum, outer and inner integument and suspensor at the global, heart and cotyledon stages of soybean seed development. The tissue specificity of gene expression was greater than stage specificity, and only three genes were differentially expressed in all seed tissues. Tissues had both unique and shared enriched functional categories of tissue-specifically expressed genes associated with them. Strong spatio-temporal correlation in gene expression was identified using weighted gene co-expression network analysis, with the most co-expression occurring in one seed tissue. Transcription factors with distinct spatiotemporal gene expression programs in each seed tissue were identified as candidate regulators of expression within those tissues. Gene ontology (GO) enrichment of orthogroup clusters revealed the conserved functions and unique roles of orthogroups with similar and contrasting expression patterns in transcript abundance between soybean and Arabidopsis during embryo proper and endosperm development. Key regulators in each seed tissue and hub genes connecting those networks were characterized by constructing gene regulatory networks. Our findings provide an important resource for describing the structure and function of individual soybean seed compartments during early seed development.
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Affiliation(s)
- Shuo Sun
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
| | - Changyu Yi
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
| | - Jing Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
| | - Shoudong Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Changchun 130102, China;
| | - Marta Peirats-Llobet
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
| | - Mathew G. Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia;
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia
| | - James Whelan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
- Australian Research Council Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Victoria 3086, Australia; (C.Y.); (M.P.-L.)
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Huixia Shou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; (S.S.); (J.M.)
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18
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Lu B, An F, Cao L, Gao Q, Wang X, Yang Y, Liu P, Yang B, Chen T, Li XC, Chen Q, Liu J. Comparative transcriptomics characterized the distinct biosynthetic abilities of terpenoid and paeoniflorin biosynthesis in herbaceous peony strains. PeerJ 2020; 8:e8895. [PMID: 32341893 PMCID: PMC7179566 DOI: 10.7717/peerj.8895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 03/11/2020] [Indexed: 12/27/2022] Open
Abstract
The herbaceous peony (Paeonia lactiflora Pall.) is a perennial flowering plant of the Paeoniaceae species that is widely cultivated for medical and ornamental uses. The monoterpene glucoside paeoniflorin and its derivatives are the active compounds of the P. lactiflora roots. However, the gene regulation pathways associated with monoterpene and paeoniflorin biosynthesis in P. lactiflora are still unclear. Here, we selected three genotypes of P. lactiflora with distinct morphologic features and chemical compositions that were a result of long-term reproductive isolation. We performed an RNA-sequencing experiment to profile the transcriptome changes of the shoots and roots. Using de novo assembly analysis, we identified 36,264 unigenes, including 521 genes responsible for encoding transcription factors. We also identified 28,925 unigenes that were differentially expressed in different organs and/or genotypes. Pathway enrichment analysis showed that the P. lactiflora unigenes were significantly overrepresented in several secondary metabolite biosynthesis pathways. We identified and profiled 33 genes responsible for encoding the enzymescontrolling the major catalytic reactions in the terpenoid backbone and in monoterpenoid biosynthesis. Our study identified the candidate genes in the terpenoid biosynthesis pathways, providing useful information for metabolic engineering of P. lactiflora intended for pharmaceutical uses and facilitating the development of strategies to improve marker-assist P. lactiflora in the future.
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Affiliation(s)
- Baowei Lu
- Bozhou University, Bozhou, Anhui, China
| | | | - Liangjing Cao
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Gao
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuan Wang
- Department of Biological Sciences, Xian Jiaotong-Liverpool University, Suzhou, China
| | | | | | | | - Tong Chen
- National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, China
| | - Xin-Chang Li
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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19
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Chang Y, Wang M, Li J, Lu S. Transcriptomic analysis reveals potential genes involved in tanshinone biosynthesis in Salvia miltiorrhiza. Sci Rep 2019; 9:14929. [PMID: 31624328 PMCID: PMC6797793 DOI: 10.1038/s41598-019-51535-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/28/2019] [Indexed: 12/17/2022] Open
Abstract
Tanshinones are important bioactive components in Salvia miltiorrhiza and mainly accumulate in the periderms of mature roots. Tanshinone biosynthesis is a complicated process, and little is known about the third stage of the pathway. To investigate potential genes that are responsible for tanshinone biosynthesis, we conducted transcriptome profiling analysis of two S. miltiorrhiza cultivars. Differential expression analysis provided 2,149 differentially expressed genes (DEGs) for further analysis. GO and KEGG analysis showed that the DEGs were mainly associated with the biosynthesis of secondary metabolites. Weighted gene coexpression network analysis (WGCNA) was further performed to identify a “cyan” module associated with tanshinone biosynthesis. In this module, 25 cytochromes P450 (CYPs), three 2-oxoglutarate-dependent dioxygenases (2OGDs), one short-chain alcohol dehydrogenases (SDRs) and eight transcription factors were found to be likely involved in tanshinone biosynthesis. Among these CYPs, 14 CYPs have been reported previously, and 11 CYPs were identified in this study. Expression analysis showed that four newly identified CYPs were upregulated upon application of MeJA, suggesting their possible roles in tanshinone biosynthesis. Overall, this study not only identified candidate genes involved in tanshinone biosynthesis but also provided a basis for characterization of genes involved in important active ingredients of other traditional Chinese medicinal plants.
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Affiliation(s)
- Yujie Chang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.,Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jiang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
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20
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Yu JY, Zhang ZG, Huang SY, Han X, Wang XY, Pan WJ, Qin HT, Qi HD, Yin ZG, Qu KX, Zhang ZX, Liu SS, Jiang HW, Liu CY, Hu ZB, Wu XX, Chen QS, Xin DW, Qi ZM. Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing. Genes (Basel) 2019; 10:E408. [PMID: 31142023 PMCID: PMC6628032 DOI: 10.3390/genes10060408] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 01/05/2023] Open
Abstract
Soybeans are an important cash crop and are widely used as a source of vegetable protein and edible oil. MicroRNAs (miRNA) are endogenous small RNA that play an important regulatory role in the evolutionarily conserved system of gene expression. In this study, we selected four lines with extreme phenotypes, as well as high or low protein and oil content, from the chromosome segment substitution line (CSSL) constructed from suinong (SN14) and ZYD00006, and planted and sampled at three stages of grain development for small RNA sequencing and expression analysis. The sequencing results revealed the expression pattern of miRNA in the materials, and predicted miRNA-targeted regulatory genes, including 1967 pairs of corresponding relationships between known-miRNA and their target genes, as well as 597 pairs of corresponding relationships between novel-miRNA and their target genes. After screening and annotating genes that were targeted for regulation, five specific genes were identified to be differentially expressed during seed development and subsequently analyzed for their regulatory relationship with miRNAs. The expression pattern of the targeted gene was verified by Real-time Quantitative PCR (RT-qPCR). Our research provides more information about the miRNA regulatory network in soybeans and further identifies useful genes that regulate storage during soy grain development, providing a theoretical basis for the regulation of soybean quality traits.
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Affiliation(s)
- Jing-Yao Yu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhan-Guo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Shi-Yu Huang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Xue Han
- Department of Horticulture, Michigan State University, East Lansing 48824, MI, USA.
| | - Xin-Yu Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Wen-Jing Pan
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Hong-Tao Qin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Hui-Dong Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhen-Gong Yin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Ke-Xin Qu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Ze-Xin Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Shan-Shan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Hong-Wei Jiang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Chun-Yan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhen-Bang Hu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Xiao-Xia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
- Green Food Research Institute in Heilongjiang Province, Harbin 150030, Heilongjiang, China.
| | - Qing-Shan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Da-Wei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Zhao-Ming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
- Department of Plant Soil and Microbe Science, Michigan State University, East Lansing, MI 48824, USA.
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Warsame AO, O'Sullivan DM, Tosi P. Seed Storage Proteins of Faba Bean ( Vicia faba L): Current Status and Prospects for Genetic Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12617-12626. [PMID: 30403850 DOI: 10.1021/acs.jafc.8b04992] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Faba bean ( Vicia faba L.) is one of the foremost candidate crops for simultaneously increasing both sustainability and global supply of plant protein. On a dry matter basis, its seeds contain about 29% protein of which more than 80% consists of globulin storage proteins (vicilin and legumin). However, to achieve optimum utilization of this crop for human and animal nutrition, both protein content and quality have to be improved. Though initial investigations on the heritability of these traits indicated the possibility for genetic improvement, little has been achieved so far, partly due to the lack of genetic information coupled with the complex relationship between protein content and grain yield. This review reports on the current knowledge on Vicia faba seed storage proteins, their structure, composition, and genetic control, and highlights key areas for further improvement of the content and composition of Vicia faba seed storage proteins on the basis of recent advances in Vicia faba genome knowledge and genetic tools.
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Affiliation(s)
- Ahmed O Warsame
- School of Agriculture, Policy and Development, University of Reading , Reading RG6 6AR , United Kingdom
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading , Reading RG6 6AR , United Kingdom
| | - Paola Tosi
- School of Agriculture, Policy and Development, University of Reading , Reading RG6 6AR , United Kingdom
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Di Silvestre D, Bergamaschi A, Bellini E, Mauri P. Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World. Proteomes 2018; 6:proteomes6020027. [PMID: 29865292 PMCID: PMC6027444 DOI: 10.3390/proteomes6020027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/26/2022] Open
Abstract
The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.
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Affiliation(s)
- Dario Di Silvestre
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Andrea Bergamaschi
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Edoardo Bellini
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - PierLuigi Mauri
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
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