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Li W, Wang D, Hong X, Shi J, Hong J, Su S, Loaiciga CR, Li J, Liang W, Shi J, Zhang D. Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome. PLANT CELL REPORTS 2023; 42:975-988. [PMID: 37016094 DOI: 10.1007/s00299-023-03006-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/17/2023] [Indexed: 05/12/2023]
Abstract
KEY MESSAGE Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. The functional genome is significant for rice breeding. MADS-box genes encode transcription factors that are indispensable for rice growth and development. The reported 15,362 novel genes in the rice pan-genome (RPAN) of Asian cultivated rice accessions provided a useful gene reservoir for the identification of more MADS-box candidates to overcome the limitation for the usage of only 75 MADS-box genes identified in Nipponbare for rice breeding. Here, we report the identification and validation of ten MADS-box homologous genes in RPAN. Origin and identity analysis indicated that they are originated from different wild rice accessions and structure of motif analysis revealed high variations in their amino acid sequences. Phylogenetic results with 277 MADS-box genes in 41 species showed that all these ten MADS-box homologous genes belong to type I (SRF-like, M-type). Gene expression analysis confirmed the existence of these ten MADS-box genes in IRIS_313-10,394, all of them were expressed in flower tissues, and six of them were highly expressed during seed development. Altogether, we identified and validated experimentally, for the first time, ten novel MADS-box genes in RPAN, which provides new genetic sources for rice improvement.
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Affiliation(s)
- Weihua Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Duoxiang Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaokun Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Hong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Su Su
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
| | - Cristopher Reyes Loaiciga
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, Adelaide, 5064, Australia
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Jadamba C, Vea RL, Ryu JH, Paek NC, Jang S, Chin JH, Yoo SC. GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea. Front Genet 2022; 13:1036747. [PMID: 36568369 PMCID: PMC9768348 DOI: 10.3389/fgene.2022.1036747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/13/2022] [Indexed: 12/12/2022] Open
Abstract
Heading date (Hd) is one of the main factors determining rice production and regional adaptation. To identify the genetic factors involved in the wide regional adaptability of rice, we conducted a genome-wide association study (GWAS) with 190 North Korean rice accessions selected for non-precocious flowering in the Philippines, a low-latitude region. Using both linear mixed models (LMM) and fixed and random model circulating probability unification (FarmCPU), we identified five significant loci for Hd in trials in 2018 and 2019. Among the five lead single nucleotide polymorphisms (SNPs), three were located adjacent to the known Hd genes, Heading date 3a (Hd3a), Heading date 5 (Hd5), and GF14-c. In contrast, three SNPs were located in novel loci with minor effects on heading. Further GWAS analysis for photoperiod insensitivity (PS) revealed no significant genes associated with PS, supporting that this North Korean (NK) population is largely photoperiod-insensitive. Haplotyping analysis showed that more than 80% of the NK varieties harbored nonfunctional alleles of major Hd genes investigated, of which a nonfunctional allele of Heading date 1 (Hd1) was observed in 66% of the varieties. Geographical distribution analysis of Hd allele combination types showed that nonfunctional alleles of floral repressor Hd genes enabled rice cultivation in high-latitude regions. In contrast, Hd1 alleles largely contributed to the wide regional adaptation of rice varieties. In conclusion, an allelic combination of Hd genes is critical for rice cultivation across wide areas.
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Affiliation(s)
- Chuluuntsetseg Jadamba
- Crop Molecular Breeding Laboratory, Department of Plant Life and Environmental Science, Hankyong National University, Anseong, South Korea
| | - Richie L. Vea
- Bureau of Plant Industry, National Seed Quality Control Services, San Mateo, Isabela Philippines
| | - Jung-Hoon Ryu
- Crop Molecular Breeding Laboratory, Department of Plant Life and Environmental Science, Hankyong National University, Anseong, South Korea
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Su Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, South Korea,*Correspondence: Joong Hyoun Chin, ; Soo-Cheul Yoo,
| | - Soo-Cheul Yoo
- Crop Molecular Breeding Laboratory, Department of Plant Life and Environmental Science, Hankyong National University, Anseong, South Korea,Carbon-Neutral Resources Research Center, Hankyong National University, Seoul, South Korea,*Correspondence: Joong Hyoun Chin, ; Soo-Cheul Yoo,
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Chen L, Yan Y, Ke H, Zhang Z, Meng C, Ma L, Sun Z, Chen B, Liu Z, Wang G, Yang J, Wu J, Li Z, Wu L, Zhang G, Zhang Y, Wang X, Ma Z. SEP-like genes of Gossypium hirsutum promote flowering via targeting different loci in a concentration-dependent manner. FRONTIERS IN PLANT SCIENCE 2022; 13:990221. [PMID: 36531379 PMCID: PMC9752867 DOI: 10.3389/fpls.2022.990221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
SEP genes are famous for their function in the morphological novelty of bisexual flowers. Although the diverse functions of SEP genes were reported, only the regulatory mechanisms underlying floral organ development have been addressed. In this study, we identified SEP-like genes in Gossypium and found that SEP3 genes were duplicated in diploid cotton varieties. GhSEP4.1 and GhSEP4.2 were abundantly transcribed in the shoot apical meristem (SAM), but only GhSEP4.2 was expressed in the leaf vasculature. The expression pattern of GhSEPs in floral organs was conserved with that of homologs in Arabidopsis, except for GhSEP2 that was preponderantly expressed in ovules and fibers. The overexpression and silencing of each single GhSEP gene suggested their distinct role in promoting flowering via direct binding to GhAP1 and GhLFY genomic regions. The curly leaf and floral defects in overexpression lines with a higher expression of GhSEP genes revealed the concentration-dependent target gene regulation of GhSEP proteins. Moreover, GhSEP proteins were able to dimerize and interact with flowering time regulators. Together, our results suggest the dominant role of GhSEP4.2 in leaves to promote flowering via GhAP1-A04, and differently accumulated GhSEP proteins in the SAM alternately participate in forming the dynamic tetramer complexes to target at the different loci of GhAP1 and GhLFY to maintain reproductive growth. The regulatory roles of cotton SEP genes reveal their conserved and diversified functions.
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Yang S, Li L, Zhang J, Geng Y, Guo F, Wang J, Meng J, Sui N, Wan S, Li X. Transcriptome and Differential Expression Profiling Analysis of the Mechanism of Ca 2+ Regulation in Peanut ( Arachis hypogaea) Pod Development. FRONTIERS IN PLANT SCIENCE 2017; 8:1609. [PMID: 29033956 PMCID: PMC5625282 DOI: 10.3389/fpls.2017.01609] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/04/2017] [Indexed: 05/23/2023]
Abstract
Calcium not only serves as a necessary nutrient for plant growth but also acts as a ubiquitous central hub in a large number of signaling pathways. Free Ca2+ deficiency in the soil may cause early embryo abortion, which eventually led to abnormal development of peanut pod during the harvest season. To understand the mechanisms of Ca2+ regulation in pod development, transcriptome analysis of peanut gynophores and pods was performed by comparing the treatments between free Ca2+ sufficiency and free Ca2+ deficiency using Illumina HiSeq™ 2000. 9,903,082,800 nt bases are generated totally. After assembly, the average length of 102,819 unigenes is 999 nt, N50 is 1,782 nt. RNA-seq based gene expression profilings showed a large number of genes at the transcriptional level changed significantly between the aerial pegs and underground swelling pods under free Ca2+ sufficienct or deficiency treatments, respectively. Genes encoding key members of Ca2+ signaling transduction pathway, enzymes for hormone metabolism, cell division and growth, transcriptional factor as well as embryo development were highlighted. This information provides useful information for our further study. The results of digital gene expression (DGE) indicated that exogenous calcium might contribute to the development of peanut pod through its signal transduction pathway, meanwhile, promote the normal transition of the gynophores to the reproductive development.
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Affiliation(s)
- Sha Yang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lin Li
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jialei Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yun Geng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Feng Guo
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jianguo Wang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jingjing Meng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Na Sui
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Shubo Wan
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xinguo Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
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Jang S, Li HY, Kuo ML. Ectopic expression of Arabidopsis FD and FD PARALOGUE in rice results in dwarfism with size reduction of spikelets. Sci Rep 2017; 7:44477. [PMID: 28290557 PMCID: PMC5349553 DOI: 10.1038/srep44477] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/09/2017] [Indexed: 11/14/2022] Open
Abstract
Key flowering genes, FD and FD PARALOGUE (FDP) encoding bZIP transcription factors that interact with a FLOWERING LOCUS T (FT) in Arabidopsis were ectopically expressed in rice since we found AtFD and AtFDP also interact with HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1). Transgenic rice plants overexpressing AtFD and AtFDP caused reduction in plant height and spikelet size with decreased expression of genes involved in cell elongation without significant flowering time alteration in spite of increased expression of OsMADS14 and OsMADS15, rice homologues of APETALA1 (AP1) in the leaves. Simultaneous overexpression of AtFD and AtFDP enhanced phenotypes seen with overexpression of either single gene while transgenic rice plants expressing AtFD or AtFDP under the control of phloem-specific Hd3a promoter were indistinguishable from wild-type rice. Candidate genes responsible for the phenotypes were identified by comparison of microarray hybridization and their expression pattern was also examined in WT and transgenic rice plants. It has so far not been reported that AtFD and AtFDP affect cell elongation in plants, and our findings provide novel insight into the possible roles of AtFD and AtFDP in the mesophyll cells of plants, and potential genetic tools for manipulation of crop architecture.
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Affiliation(s)
- Seonghoe Jang
- Biotechnology Center in Southern Taiwan (BCST), No. 59 Siraya Blvd., Xinshi Dist., Tainan 74145/Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
- Institute of Tropical Plant Science, National Cheng Kung University, No. 1 University Road, East Dist., Tainan 70101, Taiwan
| | - Hsing-Yi Li
- Biotechnology Center in Southern Taiwan (BCST), No. 59 Siraya Blvd., Xinshi Dist., Tainan 74145/Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Mei-Lin Kuo
- Biotechnology Center in Southern Taiwan (BCST), No. 59 Siraya Blvd., Xinshi Dist., Tainan 74145/Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
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Jang S. Functional Characterization of PhapLEAFY, a FLORICAULA/LEAFY Ortholog in Phalaenopsis aphrodite. PLANT & CELL PHYSIOLOGY 2015; 56:2234-47. [PMID: 26493518 DOI: 10.1093/pcp/pcv130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 08/31/2015] [Indexed: 05/05/2023]
Abstract
The plant-specific transcription factor LEAFY (LFY) is considered to be a master regulator of flower development in the model plant, Arabidopsis. This protein plays a dual role in plant growth, integrating signals from the floral inductive pathways and acting as a floral meristem identity gene by activating genes for floral organ development. Although LFY occupies an important position in flower development, the functional divergence of LFY homologs has been demonstrated in several plants including monocots and gymnosperms. In particular, the functional roles of LFY genes from orchid species such as Phalaenopsis that contain unique floral morphologies with distinct expression patterns of floral organ identity genes remain elusive. Here, PhapLFY, an ortholog of Arabidopsis LFY from Phalaenopsis aphrodite subsp. formosana, a Taiwanese native monopodial orchid, was isolated and characterized through analyses of expression and protein activity. PhapLFY transcripts accumulated in the floral primordia of developing inflorescences, and the PhapLFY protein had transcriptional autoactivation activity forming as a homodimer. Furthermore, PhapLFY rescues the aberrant floral phenotypes of Arabidopsis lfy mutants. Overexpression of PhapLFY alone or together with PhapFT1, a P. aphrodite subsp. formosana homolog of Arabidopsis FLOWERING LOCUS T (FT) in rice, caused precocious heading. Consistently, a higher Chl content in the sepals and morphological changes in epidermal cells were observed in the floral organs of PhapLFY knock-down orchids generated by virus-induced gene silencing. Taken together, these results suggest that PhapLFY is functionally distinct from RICE FLORICAULA/LEAFY (RFL) but similar to Arabidopsis LFY based on phenotypes of our transgenic Arabidopsis and rice plants.
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Affiliation(s)
- Seonghoe Jang
- Biotechnology Center in Southern Taiwan (BCST), No. 59, Siraya Blvd, Xinshi Dist., Tainan 74145/Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Institute of Tropical Plant Science, National Cheng Kung University, No. 1 University Road, East Dist., Tainan 70101, Taiwan
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