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Genome-wide identification and functional prediction of BYPASS1-related (BPS1) homologs in soybean

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Abstract

The BYPASS1-related gene (BPS1) encodes a protein with an unknown functional domain that regulates plant organ growth and development by inhibiting the continuous production of a root-derived long-distance signaling molecule called bypass (bps). We conducted a comprehensive study to investigate the BPS gene family in soybean and identified twenty-three BPS genes in Glycine max and twenty BPS genes in Glycine soja (wild soybean). Collinearity analysis revealied the existence of multiple orthologs of soybean BPS genes in wild soybean, indicating incomplete conservation between the BPS genes of soybean and wild soybean. Phylogenetic analysis successfully categorized all BPS genes into five distinct groups. We further scrutinized their chromosomal locations, gene structures, conserved motifs, cis-acting elements, and expression patterns. Leveraging publicly available data on genetic variation, phenotypic variation, and single-cell transcriptome sequencing of root nodules, we discovered a potential association between BPS genes and multiple soybean traits, particularly those related to the root nodule phenotype. This pioneering study provides a systematic and comprehensive examination of the BPS gene family in soybean. The findings establish a robust foundation for future investigations into the functional roles of BPS genes in plant growth and development.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grants 32090064 to F.K.) and the National Natural Science Foundation of China (32072086).

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Authors and Affiliations

  1. Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, China

    Xinxin Pei & Lin Zhao

  2. Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China

    Xinxin Pei, Fan Wang, Haiping Du, Milan He, Lanxin Li, Chuanjie Gou, Zheng Chen, Yanan Wang & Fanjiang Kong

Authors
  1. Xinxin Pei
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  2. Fan Wang
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  3. Haiping Du
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  4. Milan He
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  6. Chuanjie Gou
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  8. Yanan Wang
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  10. Lin Zhao
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Contributions

All authors contributed to the study’s conception and design. Fanjiang Kong and Lin Zhao designed the research; Xinxin Pei completed the bioinformatics analysis, wrote and revised the manuscript; Fan Wang, Haiping Du, and Milan He modified the manuscript; Lanxin Li, Chuanjie Gou, Zheng Chen, and Yanan Wang downloaded the data; and all authors read and approved the final version of the manuscript.

Corresponding authors

Correspondence to Fanjiang Kong or Lin Zhao.

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This article is part of the Topical Collection on Soybean Functional Genomics.

Supplementary information

Fig. s1

Haplotype analysis of GmBPS genes. (PNG 1084 kb)

High resolution image (EPS 6283 kb)

Fig. s2

UAMP visualization of GmBPS genes in single-cell gene maps of soybean nodules. (PNG 444 kb)

High resolution image (EPS 13505 kb)

Fig. s3

Barplot visualization of GmBPS genes in single-cell gene maps of soybean nodules. (PNG 3014 kb)

High resolution image (EPS 4809 kb)

Table s1

Results of Ka/Ks analysis between GmBPS. (XLSX 39 kb)

Table s2

Blast results of GmBPS14 and GmBPS21 in publicly available soybean genomes. (XLSX 19 kb)

Table s3

Details of cis-acting elements in the promoter regions in Glycine spp., Arabidopsis and P.vulgaris. (XLSX 463 kb)

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Pei, X., Wang, F., Du, H. et al. Genome-wide identification and functional prediction of BYPASS1-related (BPS1) homologs in soybean. Mol Breeding 43, 59 (2023). https://doi.org/10.1007/s11032-023-01403-2

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