1
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Cho YB, Boyd RA, Ren Y, Lee MS, Jones SI, Ruiz-Vera UM, McGrath JM, Masters MD, Ort DR. Reducing chlorophyll levels in seed-filling stages results in higher seed nitrogen without impacting canopy carbon assimilation. PLANT, CELL & ENVIRONMENT 2024; 47:278-293. [PMID: 37828764 DOI: 10.1111/pce.14737] [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: 07/21/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
Chlorophyll is the major light-absorbing pigment for plant photosynthesis. While evolution has been selected for high chlorophyll content in leaves, previous work suggests that domesticated crops grown in modern high-density agricultural environments overinvest in chlorophyll production, thereby lowering light use and nitrogen use efficiency. To investigate the potential benefits of reducing chlorophyll levels, we created ethanol-inducible RNAi tobacco mutants that suppress Mg-chelatase subunit I (CHLI) with small RNA within 3 h of induction and reduce chlorophyll within 5 days in field conditions. We initiated chlorophyll reduction later in plant development to avoid the highly sensitive seedling stage and to allow young plants to have full green leaves to maximise light interception before canopy formation. This study demonstrated that leaf chlorophyll reduction >60% during seed-filling stages increased tobacco seed nitrogen concentration by as much as 17% while canopy photosynthesis, biomass and seed yields were maintained. These results indicate that time-specific reduction of chlorophyll could be a novel strategy that decouples the inverse relationship between yield and seed nitrogen by utilising saved nitrogen from the reduction of chlorophyll while maintaining full carbon assimilation capacity.
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Affiliation(s)
- Young B Cho
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ryan A Boyd
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yudong Ren
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Moon-Sub Lee
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sarah I Jones
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ursula M Ruiz-Vera
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Justin M McGrath
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Michael D Masters
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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2
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Cho YB, Stutz SS, Jones SI, Wang Y, Pelech EA, Ort DR. Impact of pod and seed photosynthesis on seed filling and canopy carbon gain in soybean. PLANT PHYSIOLOGY 2023; 193:966-979. [PMID: 37265110 DOI: 10.1093/plphys/kiad324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
There is a limited understanding of the carbon assimilation capacity of nonfoliar green tissues and its impact on yield and seed quality since most photosynthesis research focuses on leaf photosynthesis. In this study, we investigate the photosynthetic efficiency of soybean (Glycine max) pods and seeds in a field setting and evaluate its effect on mature seed weight and composition. We demonstrate that soybean pod and seed photosynthesis contributes 13% to 14% of the mature seed weight. Carbon assimilation by soybean pod and seed photosynthesis can compensate for 81% of carbon loss through the respiration of the same tissues, and our model predicts that soybean pod and seed photosynthesis contributes up to 9% of the total daily carbon gain of the canopy. Chlorophyll fluorescence (CF) shows that the operating efficiency of photosystem II in immature soybean seeds peaks at the 10 to 100 mg seed weight stage, while that of immature pods peaks at the 75 to 100 mg stage. This study provides quantitative information about the efficiency of soybean pod and seed photosynthesis during tissue development and its impact on yield.
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Affiliation(s)
- Young B Cho
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Samantha S Stutz
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sarah I Jones
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yu Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Elena A Pelech
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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3
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Shi J, Tian Z, Lai J, Huang X. Plant pan-genomics and its applications. MOLECULAR PLANT 2023; 16:168-186. [PMID: 36523157 DOI: 10.1016/j.molp.2022.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Plant genomes are so highly diverse that a substantial proportion of genomic sequences are not shared among individuals. The variable DNA sequences, along with the conserved core sequences, compose the more sophisticated pan-genome that represents the collection of all non-redundant DNA in a species. With rapid progress in genome sequencing technologies, pan-genome research in plants is now accelerating. Here we review recent advances in plant pan-genomics, including major driving forces of structural variations that constitute the variable sequences, methodological innovations for representing the pan-genome, and major successes in constructing plant pan-genomes. We also summarize recent efforts toward decoding the remaining dark matter in telomere-to-telomere or gapless plant genomes. These new genome resources, which have remarkable advantages over numerous previously assembled less-than-perfect genomes, are expected to become new references for genetic studies and plant breeding.
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Affiliation(s)
- Junpeng Shi
- State Key Laboratory of Biocontrol, School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
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4
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Tabara M, Yamanashi R, Kuriyama K, Koiwa H, Fukuhara T. The dicing activity of DCL3 and DCL4 is negatively affected by flavonoids. PLANT MOLECULAR BIOLOGY 2023; 111:107-116. [PMID: 36219366 DOI: 10.1007/s11103-022-01314-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The dicing activities of DCL3 and DCL4 are inhibited by accumulated metabolites in soybean leaves. Epicatechin and 7,4'-dihydroxyflavone inhibited Arabidopsis DCL3 and DCL4 in vitro. Flavonoids are major secondary metabolites in plants, and soybean (Glycine max L.) is a representative plant that accumulates flavonoids, including isoflavonoids, to high levels. Naturally-occurring RNA interference (RNAi) against the chalcone synthase (CHS) gene represses flavonoid (anthocyanin) biosynthesis in an organ-specific manner, resulting in a colorless (yellow) seed coat in many soybean cultivars. To better understand seed coat-specific naturally-occurring RNAi in soybean, we characterized soybean Dicer-like (DCL) 3 and 4, which play critical roles in RNAi. Using a previously established dicing assay, two dicing activities producing 24- and 21-nt siRNAs, corresponding to DCL3 and DCL4, respectively, were detected in soybean. Dicing activity was detected in colorless seed coats where RNAi against CHS genes was found, but no dicing activity was detected in leaves where CHS expression was prevalent. Biochemical analysis revealed that soybean leaves contained two types of inhibitors effective for Arabidopsis Dicers (AtDCL3 and AtDCL4), one of which was a heat-labile high molecular weight compound of 50 to 100 kD while another was a low molecular weight substance. We found that some flavonoids, such as epicatechin and 7,4'-dihydroxyflavone, inhibited both AtDCL3 and AtDCL4, but AtDCL4 was more sensitive to these flavonoids than AtDCL3. These results suggest that flavonoids inhibit the dicing activity of DCL4 and thereby attenuate RNAi in soybean leaves.
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Affiliation(s)
- Midori Tabara
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, 1-1-1, Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan.
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
| | - Riho Yamanashi
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Kazunori Kuriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Hisashi Koiwa
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
- Vegetable and Fruit Improvement Center and Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Toshiyuki Fukuhara
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
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5
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Martínez-Fortún J, Phillips DW, Jones HD. Natural and artificial sources of genetic variation used in crop breeding: A baseline comparator for genome editing. Front Genome Ed 2022; 4:937853. [PMID: 36072906 PMCID: PMC9441798 DOI: 10.3389/fgeed.2022.937853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Traditional breeding has successfully selected beneficial traits for food, feed, and fibre crops over the last several thousand years. The last century has seen significant technological advancements particularly in marker assisted selection and the generation of induced genetic variation, including over the last few decades, through mutation breeding, genetic modification, and genome editing. While regulatory frameworks for traditional varietal development and for genetic modification with transgenes are broadly established, those for genome editing are lacking or are still evolving in many regions. In particular, the lack of “foreign” recombinant DNA in genome edited plants and that the resulting SNPs or INDELs are indistinguishable from those seen in traditional breeding has challenged development of new legislation. Where products of genome editing and other novel breeding technologies possess no transgenes and could have been generated via traditional methods, we argue that it is logical and proportionate to apply equivalent legislative oversight that already exists for traditional breeding and novel foods. This review analyses the types and the scale of spontaneous and induced genetic variation that can be selected during traditional plant breeding activities. It provides a base line from which to judge whether genetic changes brought about by techniques of genome editing or other reverse genetic methods are indeed comparable to those routinely found using traditional methods of plant breeding.
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6
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Yuan B, Yuan C, Wang Y, Liu X, Qi G, Wang Y, Dong L, Zhao H, Li Y, Dong Y. Identification of genetic loci conferring seed coat color based on a high-density map in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:968618. [PMID: 35979081 PMCID: PMC9376438 DOI: 10.3389/fpls.2022.968618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/11/2022] [Indexed: 05/26/2023]
Abstract
Seed coat color is a typical evolutionary trait. Identification of the genetic loci that control seed coat color during the domestication of wild soybean could clarify the genetic variations between cultivated and wild soybean. We used 276 F10 recombinant inbred lines (RILs) from the cross between a cultivated soybean (JY47) and a wild soybean (ZYD00321) as the materials to identify the quantitative trait loci (QTLs) for seed coat color. We constructed a high-density genetic map using re-sequencing technology. The average distance between adjacent markers was 0.31 cM on this map, comprising 9,083 bin markers. We identified two stable QTLs (qSC08 and qSC11) for seed coat color using this map, which, respectively, explained 21.933 and 26.934% of the phenotypic variation. Two candidate genes (CHS3C and CHS4A) in qSC08 were identified according to the parental re-sequencing data and gene function annotations. Five genes (LOC100786658, LOC100801691, LOC100806824, LOC100795475, and LOC100787559) were predicted in the novel QTL qSC11, which, according to gene function annotations, might control seed coat color. This result could facilitate the identification of beneficial genes from wild soybean and provide useful information to clarify the genetic variations for seed coat color in cultivated and wild soybean.
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Affiliation(s)
- Baoqi Yuan
- College of Agronomy, Jilin Agricultural University, Changchun, China
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Cuiping Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Yumin Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Xiaodong Liu
- Crop Germplasm Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Guangxun Qi
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Yingnan Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Lingchao Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Hongkun Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Yuqiu Li
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
| | - Yingshan Dong
- College of Agronomy, Jilin Agricultural University, Changchun, China
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, China
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7
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Lu N, Rao X, Li Y, Jun JH, Dixon RA. Dissecting the transcriptional regulation of proanthocyanidin and anthocyanin biosynthesis in soybean (Glycine max). PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1429-1442. [PMID: 33539645 PMCID: PMC8313137 DOI: 10.1111/pbi.13562] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 01/12/2021] [Accepted: 01/29/2021] [Indexed: 05/20/2023]
Abstract
Proanthocyanidins (PAs), also known as condensed tannins, are plant natural products that are beneficial for human and livestock health. As one of the largest grown crops in the world, soybean (Glycine max) is widely used as human food and animal feed. Many cultivated soybeans with yellow seed coats lack PAs or anthocyanins, although some soybean cultivars have coloured seed coats that contain these compounds. Here, we analyse the transcriptional control of PA and anthocyanin biosynthesis in soybean. Ectopic expression of the transcription factors (TFs) GmTT2A, GmTT2B, GmMYB5A or R in soybean hairy roots induced the accumulation of PAs (primarily in phloem tissues) or anthocyanins and led to up-regulation of 1775, 856, 1411 and 1766 genes, respectively, several of which encode enzymes involved in PA biosynthesis. The genes regulated by GmTT2A and GmTT2B partially overlapped, suggesting conserved but potentially divergent roles for these two TFs in regulating PA accumulation in soybean. The two key enzymes anthocyanidin reductase and leucoanthocyanidin reductase were differentially upregulated, by GmTT2A/GmTT2B and GmMYB5A, respectively. Transgenic soybean plants overexpressing GmTT2B or MtLAP1 (a proven up-regulator of the upstream reactions for production of precursors for PA biosynthesis in legumes) showed increased accumulation of PAs and anthocyanins, respectively, associated with transcriptional reprogramming paralleling the RNA-seq data collected in soybean hairy roots. Collectively, our results show that engineered PA biosynthesis in soybean exhibits qualitative and spatial differences from the better-studied model systems Arabidopsis thaliana and Medicago truncatula, and suggest targets for engineering PAs in soybean plants.
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Affiliation(s)
- Nan Lu
- Department of Biological SciencesBioDiscovery InstituteUniversity of North TexasDentonTXUSA
| | - Xiaolan Rao
- Department of Biological SciencesBioDiscovery InstituteUniversity of North TexasDentonTXUSA
| | - Ying Li
- Department of Biological SciencesBioDiscovery InstituteUniversity of North TexasDentonTXUSA
| | - Ji Hyung Jun
- Department of Biological SciencesBioDiscovery InstituteUniversity of North TexasDentonTXUSA
| | - Richard A. Dixon
- Department of Biological SciencesBioDiscovery InstituteUniversity of North TexasDentonTXUSA
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8
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Jia J, Ji R, Li Z, Yu Y, Nakano M, Long Y, Feng L, Qin C, Lu D, Zhan J, Xia R, Meyers BC, Liu B, Zhai J. Soybean DICER-LIKE2 Regulates Seed Coat Color via Production of Primary 22-Nucleotide Small Interfering RNAs from Long Inverted Repeats. THE PLANT CELL 2020; 32:3662-3673. [PMID: 33077493 PMCID: PMC7721327 DOI: 10.1105/tpc.20.00562] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/16/2020] [Accepted: 10/15/2020] [Indexed: 05/02/2023]
Abstract
In plants, 22-nucleotide small RNAs trigger the production of secondary small interfering RNAs (siRNAs) and enhance silencing. DICER-LIKE2 (DCL2)-dependent 22-nucleotide siRNAs are rare in Arabidopsis (Arabidopsis thaliana) and are thought to function mainly during viral infection; by contrast, these siRNAs are abundant in many crops such as soybean (Glycine max) and maize (Zea mays). Here, we studied soybean 22-nucleotide siRNAs by applying CRISPR-Cas9 to simultaneously knock out the two copies of soybean DCL2, GmDCL2a and GmDCL2b, in the Tianlong1 cultivar. Small RNA sequencing revealed that most 22-nucleotide siRNAs are derived from long inverted repeats (LIRs) and disappeared in the Gmdcl2a/2b double mutant. De novo assembly of a Tianlong1 reference genome and transcriptome profiling identified an intronic LIR formed by the chalcone synthase (CHS) genes CHS1 and CHS3 This LIR is the source of primary 22-nucleotide siRNAs that target other CHS genes and trigger the production of secondary 21-nucleotide siRNAs. Disruption of this process in Gmdcl2a/2b mutants substantially increased CHS mRNA levels in the seed coat, thus changing the coat color from yellow to brown. Our results demonstrated that endogenous LIR-derived transcripts in soybean are predominantly processed by GmDCL2 into 22-nucleotide siRNAs and uncovered a role for DCL2 in regulating natural traits.
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Affiliation(s)
- Jinbu Jia
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ronghuan Ji
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhuowen Li
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yiming Yu
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
| | - Mayumi Nakano
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Yanping Long
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
| | - Li Feng
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chao Qin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dongdong Lu
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
| | - Junpeng Zhan
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Rui Xia
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - Bin Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jixian Zhai
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen 518055, China
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9
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Kim JH, Park JS, Lee CY, Jeong MG, Xu JL, Choi Y, Jung HW, Choi HK. Dissecting seed pigmentation-associated genomic loci and genes by employing dual approaches of reference-based and k-mer-based GWAS with 438 Glycine accessions. PLoS One 2020; 15:e0243085. [PMID: 33259564 PMCID: PMC7707508 DOI: 10.1371/journal.pone.0243085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/15/2020] [Indexed: 11/19/2022] Open
Abstract
The soybean is agro-economically the most important among all cultivated legume crops, and its seed color is considered one of the most attractive factors in the selection-by-breeders. Thus, genome-wide identification of genes and loci associated with seed colors is critical for the precision breeding of crop soybeans. To dissect seed pigmentation-associated genomic loci and genes, we employed dual approaches by combining reference-based genome-wide association study (rbGWAS) and k-mer-based reference-free GWAS (rfGWAS) with 438 Glycine accessions. The dual analytical strategy allowed us to identify four major genomic loci (designated as SP1-SP4 in this study) associated with the seed colors of soybeans. The k-mer analysis enabled us to find an important recombination event that occurred between subtilisin and I-cluster B in the soybean genome, which could describe a special structural feature of ii allele within the I locus (SP3). Importantly, mapping analyses of both mRNAs and small RNAs allowed us to reveal that the subtilisin-CHS1/CHS3 chimeric transcripts generate and act as an initiator towards 'mirtron (i.e., intron-harboring miRNA precursor)'-triggered silencing of chalcone synthase (CHS) genes. Consequently, the results led us to propose a working model of 'mirtron-triggered gene silencing (MTGS)' to elucidate a long-standing puzzle in the genome-wide CHS gene silencing mechanism. In summary, our study reports four major genomic loci, lists of key genes and genome-wide variations that are associated with seed pigmentation in soybeans. In addition, we propose that the MTGS mechanism plays a crucial role in the genome-wide silencing of CHS genes, thereby suggesting a clue to currently predominant soybean cultivars with the yellow seed coat. Finally, this study will provide a broad insight into the interactions and correlations among seed color-associated genes and loci within the context of anthocyanin biosynthetic pathways.
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Affiliation(s)
- Jin-Hyun Kim
- Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Joo-Seok Park
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Chae-Young Lee
- Department of Medical Bioscience, Dong-A University, Busan, Republic of Korea
| | - Min-Gyun Jeong
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Jiu Liang Xu
- Systems Biotechnology Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Yongsoo Choi
- Systems Biotechnology Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Ho-Won Jung
- Department of Molecular Genetics, Dong-A University, Busan, Republic of Korea
| | - Hong-Kyu Choi
- Department of Molecular Genetics, Dong-A University, Busan, Republic of Korea
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10
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Zabala G, Kour A, Vodkin LO. Overexpression of an ethylene-forming ACC oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max. BMC Genomics 2020; 21:716. [PMID: 33066734 PMCID: PMC7566151 DOI: 10.1186/s12864-020-07130-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/08/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a smaller hilum region where the seed attaches to the pod and also results in seed coat cracking surrounding the hilum region. RESULTS RNAs were extracted from immature seed from an extended hilum region (i.e., the hilum and a small ring of tissue surrounding the hilum in which the cracks form) at three different developmental stages:10-25, 25-50 and 50-100 mg seed fresh weight in two independent replicates for each stage. The transcriptomes of these samples from both the Clark isoline containing the mi allele (PI 547628, UC413, ii R t mi G), and its recurrent Clark 63 parent isoline (PI 548532, UC7, ii R T Mi g), which was used for six generations of backcrossing, were compared for differential expression of 88,648 Glyma models of the soybean genome Wm82.a2. The RNA sequence data obtained from the 12 cDNA libraries were subjected to padj value < 0.05 and at least two-fold expression differences to select with confidence genes differentially expressed in the hilum-containing tissue of the seed coat between the two lines. Glyma.09G008400 annotated as encoding an ethylene forming enzyme, ACC oxidase (ACO), was found to be highly overexpressed in the mi hilum region at 165 RPKMs (reads per kilobase per million mapped reads) compared to the standard line at just 0.03 RPKMs. Evidence of changes in expression of genes downstream of the ethylene pathway included those involved in auxin and gibberellin hormone action and extensive differences in expression of cell wall protein genes. These changes are postulated to determine the restricted hilum size and cracking phenotypes. CONCLUSIONS We present transcriptome and phenotypic evidence that substantially higher expression of an ethylene-forming ACO gene likely shifts hormone balance and sets in motion downstream changes resulting in a smaller hilum phenotype and the cracks observed in the minute hilum (mi) isoline as compared to its recurrent parent.
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Affiliation(s)
- Gracia Zabala
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61981, USA
| | - Anupreet Kour
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61981, USA
- Present address: Robert M. Berne Cardiovascular Research Institute, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, USA
| | - Lila O Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61981, USA.
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11
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Saruta M, Ashina H, Matsumoto T, Okubo H, Hiraoka M, Kasai A, Ohnishi S, Funatsuki H, Kawasaki M, Sano T, Senda M. A major gene for tolerance to cold-induced seed coat discoloration relieves viral seed mottling in soybean. BREEDING SCIENCE 2020; 70:449-455. [PMID: 32968347 PMCID: PMC7495198 DOI: 10.1270/jsbbs.19162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
In yellow soybeans, inhibition of seed coat pigmentation by RNA silencing of CHS genes is suppressed by low temperature and a viral suppressor, resulting in 'cold-induced seed coat discoloration' and 'seed mottling', respectively. Differences exist in the degree of cold-induced seed coat discoloration among Japanese yellow soybean cultivars; for example, Toyomusume is sensitive, Toyohomare has some tolerance, and Toyoharuka is highly tolerant. In this study, we compared the degree of seed mottling severity due to soybean mosaic virus (SMV) among these three soybean cultivars. Obvious differences were found, with the order of severity as follows: Toyohomare > Toyomusume > Toyoharuka. RNA gel blot analysis indicated that CHS transcript abundance in the seed coat, which was increased by SMV infection, was responsible for the severity of seed mottling. Quantitative reverse transcription PCR analysis revealed why mottling was most severe in SMV-infected Toyohomare: the SMV titer in its seed coat was higher than in the other two infected cultivars. We further suggest that a major gene (Ic) for tolerance to cold-induced seed coat discoloration can relieve the severity of seed mottling in SMV-infected Toyoharuka.
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Affiliation(s)
- Masayasu Saruta
- National Agricultural Research Organization Western Region Agricultural Research Center, 1-3-1 Senyu, Zentsuji, Kagawa 765-8508, Japan
| | - Hirotaka Ashina
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Takuro Matsumoto
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Harumitsu Okubo
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Miho Hiraoka
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Atsushi Kasai
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Shizen Ohnishi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, 2, Minami 9 sen, Shinsei, Memuro-cho, Kasai-gun, Hokkaido 082-0081, Japan
| | - Hideyuki Funatsuki
- National Agricultural Research Organization Hokkaido Region Agricultural Research Center, Hitsujigaoka, Sapporo, Hokkaido 062-8555, Japan
| | - Michio Kawasaki
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Teruo Sano
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Mineo Senda
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
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12
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Li Z, Han Y, Niu H, Wang Y, Jiang B, Weng Y. Gynoecy instability in cucumber ( Cucumis sativus L.) is due to unequal crossover at the copy number variation-dependent Femaleness ( F) locus. HORTICULTURE RESEARCH 2020; 7:32. [PMID: 32194968 PMCID: PMC7072070 DOI: 10.1038/s41438-020-0251-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 05/06/2023]
Abstract
Cucumber, Cucumis sativus is an important vegetable crop, and gynoecy has played a critical role in yield increase of hybrid cucumber production. Cucumber has a unique genetic system for gynoecious sex expression, which is determined by the copy number variation (CNV)-based, dominant, and dosage-dependent femaleness (F) locus. However, this gynoecy expression system seems unstable since monecious plants could often be found in F-dependent gynoecious cucumber inbreds. We hypothesized that gynoecy instability (gynoecy loss) may be due to unequal crossing over (UCO) during meiosis among repeat units of the CNV. In this study, using high throughput genome resequencing, fiber-FISH and genomic qPCR analyses, we first confirmed and refined the structure of the F locus, which was a CNV of a 30.2-kb tandem repeat. Gynoecious plants contained three genes: CsACS1, CsACS1G, and CsMYB, of which CsACS1G is a duplication of CsACS1 but with a recombinant distal promoter that may contribute to gynoecy sex expression. In two large populations from self-pollinated gynoecious inbred lines, 'gynoecy loss' mutants were identified with similar mutation rates (~0.12%). We show that these monecious mutants have lost CsACS1G. In addition, we identified gynoecious lines in natural populations that carry two copies of CSACS1G. We proposed a model to explain gynoecy instability in F-dependent cucumbers, which is caused by UCO among CSACS1/G units during meiosis. The findings present a convincing case that the phenotypic variation of an economically important trait is associated with the dynamic changes of copy numbers at the F locus. This work also has important implications in cucumber breeding.
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Affiliation(s)
- Zheng Li
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100 China
| | - Yonghua Han
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 China
| | - Huanhuan Niu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100 China
| | - Yuhui Wang
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
| | - Biao Jiang
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, Guangdong 510640 China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- USDA-ARS, Vegetable Crops Research Unit, Madison, WI 53706 USA
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