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Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome

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Abstract

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Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding.

Abstract

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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All data generated or analyzed during this study are included in this published article and its supplementary information files.

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Acknowledgements

The authors would like to thank Mr. Zibo Chen and Ms. Mingjiao Chen for planting the rice, and suggestions by Dr. Geng Tian and Dr. Hongzhang Xue.

Funding

This work was funded by Yazhou Bay Seed Laboratory Project (B21HJ8104) and the Program of Introducing Talents of Discipline to Universities (111 Project, B14016).

Author information

Author notes

  1. Weihua Li and Duoxiang Wang contributed equally to this work.

Authors and Affiliations

  1. 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

    Weihua Li, Duoxiang Wang, Jin Shi, Jun Hong, Su Su, Wanqi Liang, Jianxin Shi & Dabing Zhang

  2. Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China

    Weihua Li, Cristopher Reyes Loaiciga & Jing Li

  3. Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China

    Su Su, Wanqi Liang, Jianxin Shi & Dabing Zhang

  4. 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

    Xiaokun Hong

  5. School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, Adelaide, 5064, Australia

    Dabing Zhang

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  1. Weihua Li
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Contributions

DBZ, JXS, JL, WQL conceived and designed the project. WHL drafted the manuscript. WHL, XKH, JS performed bioinformatic analysis. DXW, WHL, SXB, SS performed experiments. JXS, Cristopher Reyes Loaiciga revised the manuscript. All authors had read and approved the manuscript.

Corresponding author

Correspondence to Jianxin Shi.

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Communicated by Zheng-Yi Xu.

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Supplementary Information

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Supplementary file1 (PDF 10 KB)

Supplementary file2 (PDF 42 KB)

Table S1. Domains of identified MADS-box homologous genes

Supplementary file3 (XLSX 20 KB)

Table S2. The distribution of identified MADS-box homologous genes in 3010 rice accessions

Supplementary file4 (XLSX 1461 KB)

Table S3. The identities of identified MADS-box homologous genes with 7 wild rice

Supplementary file5 (XLSX 56 KB)

299_2023_3006_MOESM6_ESM.xlsx

Table S4 The Chromosome number of the homologous of the ten MADS-box in 32 rice accessions (Third generation sequencing)

Supplementary file6 (XLSX 17 KB)

Table S5. The expression of identified MADS-box homologous genes in IRIS_313_10394

Supplementary file7 (XLSX 77 KB)

Table S6. The primers used in this study

Supplementary file8 (XLSX 12 KB)

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Li, W., Wang, D., Hong, X. et al. Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome. Plant Cell Rep 42, 975–988 (2023). https://doi.org/10.1007/s00299-023-03006-9

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