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Natural variation of the Dt2 promoter controls plant height and node number in semi-determinant soybean

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Abstract

Soybean (Glycine max (L.) Merrill) is an important legume crop worldwide. Plant height (PH) is a quantitative trait that is closely related to node number (NN) and internode length (IL) on the main stem, which together affect soybean yield. To identify candidate genes controlling these three traits in soybean, we examined a recombinant inbred line (RIL) population derived from a cross between two soybean varieties with semi-determinate stems (Dt1Dt1Dt2Dt2), JKK378 and HXW. A quantitative trait locus (QTL) named qPH18 was identified that simultaneously controls PH, NN, and IL; this region harbors the semi-determinant gene Dt2. Sequencing of the Dt2 promoter from JKK378 identified three polymorphisms relative to HXW, including two single nucleotide polymorphism (SNPs) and an 18-bp insertion/deletion polymorphism (Indel). Dt2 expression was lower in the qPH18JKK378 group than in the qPH18HXW group, whereas the expression level of the downstream gene Dt1 showed the opposite tendency. A transient transfection assay confirmed that Dt2 promoter activity is lower in JKK378 compared to HXW. We propose that the polymorphisms in the dominant Dt2 promoter underlie the differences in Dt2 expression and its downstream gene Dt1 in the two parents, thereby affecting PH, NN, IL, and grain weight per plant without altering stem growth habit. Compared to the PH18HXW allele, the qPH18JKK378 allele suppresses Dt2 expression, which releases the inhibition of Dt1 expression, thus enhancing NN and grain yield. Our findings shed light on the mechanism underlying NN and PH in soybean and provide a molecular marker to facilitate breeding.

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Acknowledgements

We would like to acknowledge Mrs. Yafeng Liu for phenotyping and managing the field.

Funding

This work was supported by National Natural Science Foundation of China (31930083) and EUCLEG Horizon 2020 of European Union (No.727312). This work was also funded by the National Key Research and Development Program (Nos. 2017YFE0111000), National Natural Science Foundation of China (31701445, 31930083, 31725021, 31801384), the Major Program of Guangdong Basic and Applied Research (2019B030302006), and Open Project Foundation of National Key Laboratory for Crop Genetics and Germplasm Enhancement (ZKW201901).

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CF, FK, and BL designed the experiments. KK, TS, YW, HY, HD, MH, TL, LM, CL, CY, WS, LC, YL, and BY carried out the experiments. KK, LK, SL, LW, XZ, SL, BL, FK, and CF analyzed the data. KK, FK, BL, and CF wrote the paper.

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Correspondence to Baohui Liu, Fanjiang Kong or Chao Fang.

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The authors declare no competing interests.

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Kou, K., Su, T., Wang, Y. et al. Natural variation of the Dt2 promoter controls plant height and node number in semi-determinant soybean. Mol Breeding 41, 40 (2021). https://doi.org/10.1007/s11032-021-01235-y

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  • DOI: https://doi.org/10.1007/s11032-021-01235-y

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