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Zhu X, Wang H, Li Y, Rao D, Wang F, Gao Y, Zhong W, Zhao Y, Wu S, Chen X, Qiu H, Zhang W, Xia Z. A Novel 10-Base Pair Deletion in the First Exon of GmHY2a Promotes Hypocotyl Elongation, Induces Early Maturation, and Impairs Photosynthetic Performance in Soybean. Int J Mol Sci 2024; 25:6483. [PMID: 38928189 PMCID: PMC11203641 DOI: 10.3390/ijms25126483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/03/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Plants photoreceptors perceive changes in light quality and intensity and thereby regulate plant vegetative growth and reproductive development. By screening a γ irradiation-induced mutant library of the soybean (Glycine max) cultivar "Dongsheng 7", we identified Gmeny, a mutant with elongated nodes, yellowed leaves, decreased chlorophyll contents, altered photosynthetic performance, and early maturation. An analysis of bulked DNA and RNA data sampled from a population segregating for Gmeny, using the BVF-IGV pipeline established in our laboratory, identified a 10 bp deletion in the first exon of the candidate gene Glyma.02G304700. The causative mutation was verified by a variation analysis of over 500 genes in the candidate gene region and an association analysis, performed using two populations segregating for Gmeny. Glyma.02G304700 (GmHY2a) is a homolog of AtHY2a in Arabidopsis thaliana, which encodes a PΦB synthase involved in the biosynthesis of phytochrome. A transcriptome analysis of Gmeny using the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed changes in multiple functional pathways, including photosynthesis, gibberellic acid (GA) signaling, and flowering time, which may explain the observed mutant phenotypes. Further studies on the function of GmHY2a and its homologs will help us to understand its profound regulatory effects on photosynthesis, photomorphogenesis, and flowering time.
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Affiliation(s)
- Xiaobin Zhu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Wang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Yuzhuo Li
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Demin Rao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 132102, China; (D.R.); (H.Q.); (W.Z.)
| | - Feifei Wang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Yi Gao
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Weiyu Zhong
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Yujing Zhao
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
| | - Shihao Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.W.); (X.C.)
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (S.W.); (X.C.)
| | - Hongmei Qiu
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 132102, China; (D.R.); (H.Q.); (W.Z.)
| | - Wei Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun 132102, China; (D.R.); (H.Q.); (W.Z.)
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China; (X.Z.); (H.W.); (Y.L.); (F.W.); (Y.G.); (W.Z.); (Y.Z.)
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Yu H, Bhat JA, Li C, Zhao B, Bu M, Zhang Z, Guo T, Feng X. Identification of superior and rare haplotypes to optimize branch number in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:93. [PMID: 38570354 PMCID: PMC10991007 DOI: 10.1007/s00122-024-04596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
KEY MESSAGE Using the integrated approach in the present study, we identified eleven significant SNPs, seven stable QTLs and 20 candidate genes associated with branch number in soybean. Branch number is a key yield-related quantitative trait that directly affects the number of pods and seeds per soybean plant. In this study, an integrated approach with a genome-wide association study (GWAS) and haplotype and candidate gene analyses was used to determine the detailed genetic basis of branch number across a diverse set of soybean accessions. The GWAS revealed a total of eleven SNPs significantly associated with branch number across three environments using the five GWAS models. Based on the consistency of the SNP detection in multiple GWAS models and environments, seven genomic regions within the physical distance of ± 202.4 kb were delineated as stable QTLs. Of these QTLs, six QTLs were novel, viz., qBN7, qBN13, qBN16, qBN18, qBN19 and qBN20, whereas the remaining one, viz., qBN12, has been previously reported. Moreover, 11 haplotype blocks, viz., Hap4, Hap7, Hap12, Hap13A, Hap13B, Hap16, Hap17, Hap18, Hap19A, Hap19B and Hap20, were identified on nine different chromosomes. Haplotype allele number across the identified haplotype blocks varies from two to five, and different branch number phenotype is regulated by these alleles ranging from the lowest to highest through intermediate branching. Furthermore, 20 genes were identified underlying the genomic region of ± 202.4 kb of the identified SNPs as putative candidates; and six of them showed significant differential expression patterns among the soybean cultivars possessing contrasting branch number, which might be the potential candidates regulating branch number in soybean. The findings of this study can assist the soybean breeding programs for developing cultivars with desirable branch numbers.
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Affiliation(s)
- Hui Yu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- Zhejiang Lab, Hangzhou, 310012, China
| | | | - Candong Li
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, China
| | - Beifang Zhao
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Moran Bu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Zhirui Zhang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Tai Guo
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
- Zhejiang Lab, Hangzhou, 310012, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
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Shan Q, Zhou B, Wang Y, Hao F, Zhu L, Liu Y, Wang N, Wang F, Li X, Dong Y, Xu K, Zhou Y, Li H, Liu W, Gao H. Genome-Wide Identification and Comprehensive Analysis of the FtsH Gene Family in Soybean ( Glycine max). Int J Mol Sci 2023; 24:16996. [PMID: 38069319 PMCID: PMC10707429 DOI: 10.3390/ijms242316996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The filamentation temperature-sensitive H (FtsH) gene family is critical in regulating plant chloroplast development and photosynthesis. It plays a vital role in plant growth, development, and stress response. Although FtsH genes have been identified in a wide range of plants, there is no detailed study of the FtsH gene family in soybean (Glycine max). Here, we identified 34 GmFtsH genes, which could be categorized into eight groups, and GmFtsH genes in the same group had similar structures and conserved protein motifs. We also performed intraspecific and interspecific collinearity analysis and found that the GmFtsH family has large-scale gene duplication and is more closely related to Arabidopsis thaliana. Cis-acting elements analysis in the promoter region of the GmFtsH genes revealed that most genes contain developmental and stress response elements. Expression patterns based on transcriptome data and real-time reverse transcription quantitative PCR (qRT-PCR) showed that most of the GmFtsH genes were expressed at the highest levels in leaves. Then, GO enrichment analysis indicated that GmFtsH genes might function as a protein hydrolase. In addition, the GmFtsH13 protein was confirmed to be localized in chloroplasts by a transient expression experiment in tobacco. Taken together, the results of this study lay the foundation for the functional determination of GmFtsH genes and help researchers further understand the regulatory network in soybean leaf development.
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Affiliation(s)
- Qi Shan
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Baihui Zhou
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Yuanxin Wang
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Feiyu Hao
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Lin Zhu
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Yuhan Liu
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Nan Wang
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Fawei Wang
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Xiaowei Li
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Yuanyuan Dong
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Keheng Xu
- Sanya Institute of Breeding and Multiplication, School of Breeding and Multiplication, Hainan University, Sanya 572025, China; (K.X.); (Y.Z.); (H.L.)
| | - Yonggang Zhou
- Sanya Institute of Breeding and Multiplication, School of Breeding and Multiplication, Hainan University, Sanya 572025, China; (K.X.); (Y.Z.); (H.L.)
| | - Haiyan Li
- Sanya Institute of Breeding and Multiplication, School of Breeding and Multiplication, Hainan University, Sanya 572025, China; (K.X.); (Y.Z.); (H.L.)
| | - Weican Liu
- Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (Q.S.); (B.Z.); (Y.W.); (F.H.); (L.Z.); (Y.L.); (N.W.); (F.W.); (X.L.); (Y.D.)
| | - Hongtao Gao
- Sanya Institute of Breeding and Multiplication, School of Breeding and Multiplication, Hainan University, Sanya 572025, China; (K.X.); (Y.Z.); (H.L.)
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