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学者姓名：关跃峰
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Abstract ：
Paralogous transcription factors (TFs) frequently recognize highly similar DNA motifs. Homodimerization can help distinguish them according to their different dimeric configurations. Here, by studying R2R3-MYB TFs, we show that homodimerization can also directly change the recognized DNA motifs to distinguish between similar TFs. By high-throughput SELEX, we profiled the specificity landscape for 40 R2R3-MYBs of subfamily VIII and curated 833 motif models. The dimeric models show that homodimeric binding has evoked specificity changes for AtMYBs. Focusing on AtMYB2 as an example, we show that homodimerization has modified its specificity and allowed it to recognize additional cis-regulatory sequences that are different from the closely related CCWAA-box AtMYBs and are unique among all AtMYBs. Genomic sites described by the modified dimeric specificities of AtMYB2 are conserved in evolution and involved in AtMYB2-specific transcriptional activation. Collectively, this study provides rich data on sequence preferences of VIII R2R3-MYBs and suggests an alternative mechanism that guides closely related TFs to respective cis-regulatory sites.
Keyword ：
cis-elements cis-elements DNA binding specificity DNA binding specificity homodimerization homodimerization MYB family transcription factors MYB family transcription factors paralogs paralogs regulatory noncoding genome regulatory noncoding genome transcriptional regulation transcriptional regulation
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| GB/T 7714 | Li, Tian , Chen, Hao , Ma, Nana et al. Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding [J]. | IMETA , 2025 , 4 (2) . |
| MLA | Li, Tian et al. "Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding" . | IMETA 4 . 2 (2025) . |
| APA | Li, Tian , Chen, Hao , Ma, Nana , Jiang, Dingkun , Wu, Jiacheng , Zhang, Xinfeng et al. Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding . | IMETA , 2025 , 4 (2) . |
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Abstract ：
Symbiotic nitrogen fixation in legume nodules requires substantial energy investment from host plants, and soybean (Glycine max (L.) supernodulation mutants show stunting and yield penalties due to overconsumption of carbon sources. We obtained soybean mutants differing in their nodulation ability, among which rhizobially induced cle1a/2a (ric1a/2a) has a moderate increase in nodule number, balanced carbon allocation, and enhanced carbon and nitrogen acquisition. In multi-year and multi-site field trials in China, two ric1a/2a lines had improved grain yield, protein content and sustained oil content, demonstrating that gene editing towards optimal nodulation improves soybean yield and quality. This study shows that optimizing soybean nodulation, rather than supernodulation, through editing improves N and C assimilation by balancing source-sink relationships. As a result, soybean yield and protein content are simultaneously increased in field conditions.
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| GB/T 7714 | Zhong, Xiangbin , Wang, Jie , Shi, Xiaolei et al. Genetically optimizing soybean nodulation improves yield and protein content [J]. | NATURE PLANTS , 2024 , 10 (5) . |
| MLA | Zhong, Xiangbin et al. "Genetically optimizing soybean nodulation improves yield and protein content" . | NATURE PLANTS 10 . 5 (2024) . |
| APA | Zhong, Xiangbin , Wang, Jie , Shi, Xiaolei , Bai, Mengyan , Yuan, Cuicui , Cai, Chenlin et al. Genetically optimizing soybean nodulation improves yield and protein content . | NATURE PLANTS , 2024 , 10 (5) . |
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Soybean is the primary source of plant protein for humans.Owing to the indigestibility of the raffinose family of oligosaccharides(RFO),raffinose and stachyose are considered anti-nutritive factors in soybean seeds.Low-RFO soybean cultivars are generated by mutagenesis of RFO biosynthesis genes,but the car-bohydrate profiles invite further modification to lower RFOs.This study employed a pooled multiplex genome editing approach to target four seed-specifically expressed genes mediating RFO biosynthesis,encoding three raffinose synthases(RS2,RS3,and RS4)and one stachyose synthase.In T1 progeny,rs2/rs3 and rs4/sts homozygous double mutants and a rs2/rs3/rs4/sts quadruple mutant(rfo-4m)were char-acterized.The rs2/rs3 mutant showed reduced raffinose and stachyose contents,but the rs4/sts mutant showed only reduced stachyose in seeds.The RFO contents in the rfo-4m mutant were almost eliminated.Metabolomic analysis showed that the mutation of four RFO biosynthesis genes led to a shift of metabolic profile in the seeds,including the accumulation of several oligosaccharides-related metabolites.These mutants could contribute to precision breeding of soybean cultivars for soy food production.
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| GB/T 7714 | Wenxin Lin , Huaqin Kuang , Mengyan Bai et al. Multiplex genome editing targeting soybean with ultra-low anti-nutritive oligosaccharides [J]. | 作物学报（英文版） , 2023 , 11 (3) : 825-831 . |
| MLA | Wenxin Lin et al. "Multiplex genome editing targeting soybean with ultra-low anti-nutritive oligosaccharides" . | 作物学报（英文版） 11 . 3 (2023) : 825-831 . |
| APA | Wenxin Lin , Huaqin Kuang , Mengyan Bai , Xiaomeng Jiang , Pengfei Zhou , Yinghua Li et al. Multiplex genome editing targeting soybean with ultra-low anti-nutritive oligosaccharides . | 作物学报（英文版） , 2023 , 11 (3) , 825-831 . |
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Abstract ：
Soybean is the primary source of plant protein for humans. Owing to the indigestibility of the raffinose family of oligosaccharides (RFO), raffinose and stachyose are considered anti-nutritive factors in soybean seeds. Low-RFO soybean cultivars are generated by mutagenesis of RFO biosynthesis genes, but the car-bohydrate profiles invite further modification to lower RFOs. This study employed a pooled multiplex genome editing approach to target four seed-specifically expressed genes mediating RFO biosynthesis, encoding three raffinose synthases (RS2, RS3, and RS4) and one stachyose synthase. In T1 progeny, rs2/ rs3 and rs4/sts homozygous double mutants and a rs2/rs3/rs4/sts quadruple mutant (rfo-4m) were char-acterized. The rs2/rs3 mutant showed reduced raffinose and stachyose contents, but the rs4/sts mutant showed only reduced stachyose in seeds. The RFO contents in the rfo-4m mutant were almost eliminated. Metabolomic analysis showed that the mutation of four RFO biosynthesis genes led to a shift of metabolic profile in the seeds, including the accumulation of several oligosaccharides-related metabolites. These mutants could contribute to precision breeding of soybean cultivars for soy food production.& COPY; 2022 Crop Science Society of China and Institute of Crop Science, CAAS. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Keyword ：
Genome editing Genome editing Precision breeding Precision breeding Raffinose Raffinose Raffinose family of oligosaccharides Raffinose family of oligosaccharides Soybean Soybean Stachyose Stachyose
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| GB/T 7714 | Lin, Wenxin , Kuang, Huaqin , Bai, Mengyan et al. Multiplex genome editing targeting soybean with ultra-low anti-nutritive oligosaccharides [J]. | CROP JOURNAL , 2023 , 11 (3) : 825-831 . |
| MLA | Lin, Wenxin et al. "Multiplex genome editing targeting soybean with ultra-low anti-nutritive oligosaccharides" . | CROP JOURNAL 11 . 3 (2023) : 825-831 . |
| APA | Lin, Wenxin , Kuang, Huaqin , Bai, Mengyan , Jiang, Xiaomeng , Zhou, Pengfei , Li, Yinghua et al. Multiplex genome editing targeting soybean with ultra-low anti-nutritive oligosaccharides . | CROP JOURNAL , 2023 , 11 (3) , 825-831 . |
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Fructose-1,6-bisphosphate aldolase (FBA) is an important catalytic enzyme in carbon metabolism and plays an important role in plant growth and development. Currently, the biological functions of FBA in soybean (Glycine max) remain unknown. In this study, we conducted research on FBA in soybean and identified 14 GmFBA genes. Among them, GmFBAc1 and GmFBAc2 are broadly expressed in different tissues. Double mutant lines of GmFBAc1 and GmFBAc2 were obtained by CRISPR-Cas9 gene editing technology. Compared with the wild type, the double-gene homozygous mutant gmfbac1gmfbac2 exhibited dwarf seedlings and narrow leaflets, indicating that GmFBAc1 and GmFBAc2 are critical for soybean growth and development. The gmfbac1gmfbac2 metabolomic analysis revealed that compared to the wild type, carbohydrate metabolism was reduced and amino acid metabolism was enhanced in gmfbac1gmfbac2 mutant leaves. Transcriptomic analysis showed that genes in IAA signaling and JA signaling were downregulated and upregulated, respectively. Our study demonstrates an important role of GmFBAc1 and GmFBAc2 in modulating carbon metabolism and phytohormone homeostasis.
Keyword ：
Glycine max Glycine max GmFBA GmFBA narrow leaflet narrow leaflet phytohormone phytohormone
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| GB/T 7714 | Qiu, Zhimin , Bai, Mengyan , Kuang, Huaqin et al. Cytosolic Fructose-1,6-bisphosphate Aldolases Modulate Primary Metabolism and Phytohormone Homeostasis in Soybean [J]. | AGRONOMY-BASEL , 2023 , 13 (5) . |
| MLA | Qiu, Zhimin et al. "Cytosolic Fructose-1,6-bisphosphate Aldolases Modulate Primary Metabolism and Phytohormone Homeostasis in Soybean" . | AGRONOMY-BASEL 13 . 5 (2023) . |
| APA | Qiu, Zhimin , Bai, Mengyan , Kuang, Huaqin , Wang, Xin , Yu, Xiaomin , Zhong, Xiangbin et al. Cytosolic Fructose-1,6-bisphosphate Aldolases Modulate Primary Metabolism and Phytohormone Homeostasis in Soybean . | AGRONOMY-BASEL , 2023 , 13 (5) . |
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The gene networks surrounding Nod factor receptors that govern the symbiotic process between legumes and rhizobia remain largely unexplored. Here, we identify 13 novel GmNFR1a-associated proteins by yeast two-hybrid screening, and describe a potential interacting protein, GmBI-1a. GmBI-1a had the highest positive correlation with GmNFR1a in a co-expression network analysis, and its expression at the mRNA level in roots was enhanced by rhizobial infection. Moreover, GmBI-1a-GmNFR1a interaction was shown to occur in vitro and in vivo. The GmBI-1a protein was localized to multiple subcellular locations, including the endoplasmic reticulum and plasma membrane. Overexpression of GmBI-1a increased the nodule number in transgenic hairy roots or transgenic soybean, whereas down-regulation of GmBI-1a transcripts by RNA interference reduced the nodule number. In addition, the nodules in GmBI-1a-overexpressing plants became smaller in size and infected area with reduced nitrogenase activity. In GmBI-1a-overexpressing transgenic soybean, the elevated GmBI-1a also promoted plant growth and suppressed the expression of defense signaling-related genes. Infection thread analysis of GmBI-1a-overexpressing plants showed that GmBI-1a promoted rhizobial infection. Collectively, our findings support a GmNFR1a-associated protein in the Nod factor signaling pathway and shed new light on the regulatory mechanism of GmNFR1a in rhizobial symbiosis.
Keyword ：
GmBI-1 & alpha GmBI-1 & alpha GmNFR1 & alpha GmNFR1 & alpha ;nodulation ;nodulation protein-protein interaction protein-protein interaction root nodule symbiosis root nodule symbiosis soybean soybean yeast two-hybrid screening yeast two-hybrid screening
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| GB/T 7714 | Yuan, Songli , Ke, Danxia , Liu, Bo et al. The Bax inhibitor GmBI-1α interacts with a Nod factor receptor and plays a dual role in the legume-rhizobia symbiosis [J]. | JOURNAL OF EXPERIMENTAL BOTANY , 2023 , 74 (18) : 5820-5839 . |
| MLA | Yuan, Songli et al. "The Bax inhibitor GmBI-1α interacts with a Nod factor receptor and plays a dual role in the legume-rhizobia symbiosis" . | JOURNAL OF EXPERIMENTAL BOTANY 74 . 18 (2023) : 5820-5839 . |
| APA | Yuan, Songli , Ke, Danxia , Liu, Bo , Zhang, Mengke , Li, Xiangyong , Chen, Haifeng et al. The Bax inhibitor GmBI-1α interacts with a Nod factor receptor and plays a dual role in the legume-rhizobia symbiosis . | JOURNAL OF EXPERIMENTAL BOTANY , 2023 , 74 (18) , 5820-5839 . |
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Symbiotic nitrogen fixation (SNF) in legumes is suppressed by the presence of soil inorganic. nitrogen (N). Here the authors characterize a transcriptional regulatory network underlying the N-inhibition of SNF in soybean nodules. Legumes can utilize atmospheric nitrogen via symbiotic nitrogen fixation, but this process is inhibited by high soil inorganic nitrogen. So far, how high nitrogen inhibits N-2 fixation in mature nodules is still poorly understood. Here we construct a co-expression network in soybean nodule and find that a dynamic and reversible transcriptional network underlies the high N inhibition of N-2 fixation. Intriguingly, several NAC transcription factors (TFs), designated as Soybean Nitrogen Associated NAPs (SNAPs), are amongst the most connected hub TFs. The nodules of snap1/2/3/4 quadruple mutants show less sensitivity to the high nitrogen inhibition of nitrogenase activity and acceleration of senescence. Integrative analysis shows that these SNAP TFs largely influence the high nitrogen transcriptional response through direct regulation of a subnetwork of senescence-associated genes and transcriptional regulators. We propose that the SNAP-mediated transcriptional network may trigger nodule senescence in response to high nitrogen.
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| GB/T 7714 | Wang, Xin , Qiu, Zhimin , Zhu, Wenjun et al. The NAC transcription factors SNAP1/2/3/4 are central regulators mediating high nitrogen responses in mature nodules of soybean [J]. | NATURE COMMUNICATIONS , 2023 , 14 (1) . |
| MLA | Wang, Xin et al. "The NAC transcription factors SNAP1/2/3/4 are central regulators mediating high nitrogen responses in mature nodules of soybean" . | NATURE COMMUNICATIONS 14 . 1 (2023) . |
| APA | Wang, Xin , Qiu, Zhimin , Zhu, Wenjun , Wang, Nan , Bai, Mengyan , Kuang, Huaqin et al. The NAC transcription factors SNAP1/2/3/4 are central regulators mediating high nitrogen responses in mature nodules of soybean . | NATURE COMMUNICATIONS , 2023 , 14 (1) . |
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Soybean is one of the most versatile crops for oil production, human diets, and feedstocks. The vegetative biomass of soybean is an important determinant of seed yield and is crucial for the forage usages. However, the genetic control of soybean biomass is not well explained. In this work, we used a soybean germplasm population, including 231 improved cultivars, 207 landraces, and 121 wild soybeans, to investigate the genetic basis of biomass accumulation of soybean plants at the V6 stage. We found that biomass-related traits, including NDW (nodule dry weight), RDW (root dry weight), SDW (shoot dry weight), and TDW (total dry weight), were domesticated during soybean evolution. In total, 10 loci, encompassing 47 putative candidate genes, were detected for all biomass-related traits by a genome-wide association study. Among these loci, seven domestication sweeps and six improvement sweeps were identified. Glyma.05G047900, a purple acid phosphatase, was a strong candidate gene to improve biomass for future soybean breeding. This study provided new insights into the genetic basis of biomass accumulation during soybean evolution.
Keyword ：
Biomass Biomass Genetic basis Genetic basis GWAS GWAS Soybean evolution Soybean evolution Symbiotic nitrogen fixation Symbiotic nitrogen fixation
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| GB/T 7714 | Wang, Xin , Zhou, Shaodong , Wang, Jie et al. Genome-wide association study for biomass accumulation traits in soybean [J]. | MOLECULAR BREEDING , 2023 , 43 (5) . |
| MLA | Wang, Xin et al. "Genome-wide association study for biomass accumulation traits in soybean" . | MOLECULAR BREEDING 43 . 5 (2023) . |
| APA | Wang, Xin , Zhou, Shaodong , Wang, Jie , Lin, Wenxin , Yao, Xiaolei , Su, Jiaqing et al. Genome-wide association study for biomass accumulation traits in soybean . | MOLECULAR BREEDING , 2023 , 43 (5) . |
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Pod shattering can lead to devastating yield loss of soybean and has been a negatively selected trait in soybean domestication and breeding. Nevertheless, a significant portion of soybean cultivars are still pod shattering-susceptible, limiting their regional and climatic adaptabilities. Here we performed genetic diagnosis on the shattering-susceptible trait of a national registered cultivar, Huachun6 (HC6), and found that HC6 carries the susceptible genotype of a candidate Pod dehiscence 1 (PDH1) gene, which exists in a significant portion of soybean cultivars. We next performed genome editing on PDH1 gene by clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9). In T2 progenies, several transgene-free lines with pdh1 mutations were characterized without affecting major agronomic traits. The pdh1 mutation significantly improved the pod shattering resistance which is associated with aberrant lignin distribution in inner sclerenchyma. Our work demonstrated that precision breeding by genome editing on PDH1 holds great potential for precisely improving pod shattering resistance and adaptability of soybean cultivars. © 2022, The Author(s).
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| GB/T 7714 | Guan, Yuefeng , Yan, Long , Song, Shikui et al. Elimination of an unfavorable allele conferring pod shattering in an elite soybean cultivar by CRISPR/Cas9 [J]. | aBIOTECH , 2022 , 3 (2) : 110-114 . |
| MLA | Guan, Yuefeng et al. "Elimination of an unfavorable allele conferring pod shattering in an elite soybean cultivar by CRISPR/Cas9" . | aBIOTECH 3 . 2 (2022) : 110-114 . |
| APA | Guan, Yuefeng , Yan, Long , Song, Shikui , Yao, Xiaolei , Zhou, Shaodong , Bai, Mengyan et al. Elimination of an unfavorable allele conferring pod shattering in an elite soybean cultivar by CRISPR/Cas9 . | aBIOTECH , 2022 , 3 (2) , 110-114 . |
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Crop breeding during the Green Revolution resulted in high yields largely due to the creation of plants with semi-dwarf architectures that could tolerate high-density planting. Although semi-dwarf varieties have been developed in rice, wheat and maize, none was reported in soybean (Glycine max), and few genes controlling plant architecture have been characterized in soybean. Here, we demonstrate that the auxin efflux transporter PINFORMED1 (GmPIN1), which determines polar auxin transport, regulates the leaf petiole angle in soybean. CRISPR-Cas9-induced Gmpin1abc and Gmpin1bc multiple mutants displayed a compact architecture with a smaller petiole angle than wild-type plants. GmPIN1 transcripts and auxin were distributed asymmetrically in the petiole base, with high levels of GmPIN1a/c transcript and auxin in the lower cells, which resulted in asymmetric cell expansion. By contrast, the (iso)flavonoid content was greater in the upper petiole cells than in the lower cells. Our results suggest that (iso)flavonoids inhibit GmPIN1a/c expression to regulate the petiole angle. Overall, our study demonstrates that a signal cascade that integrates (iso)flavonoid biosynthesis, GmPIN1a/c expression, auxin accumulation, and cell expansion in an asymmetric manner creates a desirable petiole curvature in soybean. This study provides a genetic resource for improving soybean plant architecture.
Keyword ：
auxin auxin flavonoid flavonoid GmPIN1 GmPIN1 petiole angle petiole angle soybean soybean
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| GB/T 7714 | Zhang, Zhongqin , Gao, Le , Ke, Meiyu et al. GmPIN1-mediated auxin asymmetry regulates leaf petiole angle and plant architecture in soybean [J]. | JOURNAL OF INTEGRATIVE PLANT BIOLOGY , 2022 , 64 (7) : 1325-1338 . |
| MLA | Zhang, Zhongqin et al. "GmPIN1-mediated auxin asymmetry regulates leaf petiole angle and plant architecture in soybean" . | JOURNAL OF INTEGRATIVE PLANT BIOLOGY 64 . 7 (2022) : 1325-1338 . |
| APA | Zhang, Zhongqin , Gao, Le , Ke, Meiyu , Gao, Zhen , Tu, Tianli , Huang, Laimei et al. GmPIN1-mediated auxin asymmetry regulates leaf petiole angle and plant architecture in soybean . | JOURNAL OF INTEGRATIVE PLANT BIOLOGY , 2022 , 64 (7) , 1325-1338 . |
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