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Pod-shattering characteristics differences between two groups of soybeans are associated with specific changes in gene expression

Abstract

Soybean is an economically important leguminous crop, and pod dehiscence of soybean could cause huge yield loss. In this study, we measured fruit-cracking forces and percentages of dehisced pods for ten soybean accessions, then separated them into two groups as shattering-sensitive (SS) and shattering-resistant (SR) soybeans. Pod transcriptomes from these two groups were analyzed, and 225 differentially expressed genes (DEGs) were identified between SS and SR soybeans. Some of these DEGs have been previously reported to be associated with pod dehiscence in soybean. The expression patterns of selected DEGs were validated by real-time quantitative reverse transcription PCR, which confirmed the expression changes found in RNA-seq analysis. We also de novo identified 246 soybean pod-long intergenic ncRNAs (lincRNAs), 401 intronic lncRNAs, and 23 antisense lncRNAs from these transcriptomes. Furthermore, genes and lincRNAs co-expression network analysis showed that there are distinct expression patterns between SS and SR soybeans in some co-expression modules. In conclusion, we systematically investigated potential genes and molecular pathways as candidates for differences in soybean pod dehiscence and will provide a useful resource for molecular breeding of soybeans.

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Data availability

The RNA-seq datasets generated in this study have been deposited in the NCBI’s GEO database repository, and are accessible through GEO accession number GSE130010.

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Funding

This work was funded by the Natural Science Foundation of Jiangxi Province (20171ACB20001), National Science Foundation of China (Grants No. 31401077 and No. 31800224).

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Correspondence to Dong Wang or Youlin Zhu.

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Kang, X., Cai, J., Chen, Y. et al. Pod-shattering characteristics differences between two groups of soybeans are associated with specific changes in gene expression. Funct Integr Genomics 20, 201–210 (2020). https://doi.org/10.1007/s10142-019-00702-2

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Keywords

  • Pod dehiscence
  • RNA-seq
  • Long noncoding RNA
  • Soybean