PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes

Chao Qin; Ying hui Li; Delin Li; Xueru Zhang; Lingping Kong; Yonggang Zhou; Xiangguang Lyu; Ronghuan Ji; Xiuzhi Wei; Qican Cheng; Zhiwei Jia; Xiaojiao Li; Qiang Wang; Yueqiang Wang; Wen Huang; Chunyan Yang; Like Liu; Xing Wang; Guangnan Xing; Guoyu Hu; Zhihui Shan; Ruizhen Wang; Haiyan Li; Hongyu Li; Tao Zhao; Jun Liu; Yuping Lu; Xiping Hu; Fanjiang Kong; Li juan Qiu; Bin Liu

doi:10.1038/s41467-023-42608-5

PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes

Chao Qin, Ying hui Li, Delin Li, Xueru Zhang, Lingping Kong, Yonggang Zhou, Xiangguang Lyu, Ronghuan Ji, Xiuzhi Wei, Qican Cheng, Zhiwei Jia, Xiaojiao Li, Qiang Wang, Yueqiang Wang, Wen Huang, Chunyan Yang, Like Liu, Xing Wang, Guangnan Xing, Guoyu HuZhihui Shan, Ruizhen Wang, Haiyan Li, Hongyu Li, Tao Zhao, Jun Liu, Yuping Lu, Xiping Hu, Fanjiang Kong, Li juan Qiu, Bin Liu

Research output: Contribution to journal › Article › peer-review

Abstract

Shading in combination with extended photoperiods can cause exaggerated stem elongation (ESE) in soybean, leading to lodging and reduced yields when planted at high-density in high-latitude regions. However, the genetic basis of plant height in adaptation to these regions remains unclear. Here, through a genome-wide association study, we identify a plant height regulating gene on chromosome 13 (PH13) encoding a WD40 protein with three main haplotypes in natural populations. We find that an insertion of a Ty1/Copia-like retrotransposon in the haplotype 3 leads to a truncated PH13^H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13 ^H3 allele has been strongly selected for genetic improvement at high latitudes. Deletion of both PH13 and its paralogue PHP can prevent shade-induced ESE and allow high-density planting. This study provides insights into the mechanism of shade-resistance and offers potential solutions for breeding high-yielding soybean cultivar for high-latitude regions.

Original language	English
Article number	6813
Journal	Nature Communications
Volume	14
Issue number	1
DOIs	https://doi.org/10.1038/s41467-023-42608-5
State	Published - 26 Oct 2023
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2023, The Author(s).

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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10.1038/s41467-023-42608-5

Cite this

Qin, C., Li, Y. H., Li, D., Zhang, X., Kong, L., Zhou, Y., Lyu, X., Ji, R., Wei, X., Cheng, Q., Jia, Z., Li, X., Wang, Q., Wang, Y., Huang, W., Yang, C., Liu, L., Wang, X., Xing, G., ... Liu, B. (2023). PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes. Nature Communications, 14(1), Article 6813. https://doi.org/10.1038/s41467-023-42608-5

@article{fa97dc80c747433690a428c1478d1828,

title = "PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes",

abstract = "Shading in combination with extended photoperiods can cause exaggerated stem elongation (ESE) in soybean, leading to lodging and reduced yields when planted at high-density in high-latitude regions. However, the genetic basis of plant height in adaptation to these regions remains unclear. Here, through a genome-wide association study, we identify a plant height regulating gene on chromosome 13 (PH13) encoding a WD40 protein with three main haplotypes in natural populations. We find that an insertion of a Ty1/Copia-like retrotransposon in the haplotype 3 leads to a truncated PH13H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13 H3 allele has been strongly selected for genetic improvement at high latitudes. Deletion of both PH13 and its paralogue PHP can prevent shade-induced ESE and allow high-density planting. This study provides insights into the mechanism of shade-resistance and offers potential solutions for breeding high-yielding soybean cultivar for high-latitude regions.",

author = "Chao Qin and Li, {Ying hui} and Delin Li and Xueru Zhang and Lingping Kong and Yonggang Zhou and Xiangguang Lyu and Ronghuan Ji and Xiuzhi Wei and Qican Cheng and Zhiwei Jia and Xiaojiao Li and Qiang Wang and Yueqiang Wang and Wen Huang and Chunyan Yang and Like Liu and Xing Wang and Guangnan Xing and Guoyu Hu and Zhihui Shan and Ruizhen Wang and Haiyan Li and Hongyu Li and Tao Zhao and Jun Liu and Yuping Lu and Xiping Hu and Fanjiang Kong and Qiu, {Li juan} and Bin Liu",

note = "Publisher Copyright: {\textcopyright} 2023, The Author(s).",

year = "2023",

month = oct,

day = "26",

doi = "10.1038/s41467-023-42608-5",

language = "English",

volume = "14",

journal = "Nature Communications",

issn = "2041-1723",

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Qin, C, Li, YH, Li, D, Zhang, X, Kong, L, Zhou, Y, Lyu, X, Ji, R, Wei, X, Cheng, Q, Jia, Z, Li, X, Wang, Q, Wang, Y, Huang, W, Yang, C, Liu, L, Wang, X, Xing, G, Hu, G, Shan, Z, Wang, R, Li, H, Li, H, Zhao, T, Liu, J, Lu, Y, Hu, X, Kong, F, Qiu, LJ & Liu, B 2023, 'PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes', Nature Communications, vol. 14, no. 1, 6813. https://doi.org/10.1038/s41467-023-42608-5

TY - JOUR

T1 - PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes

AU - Qin, Chao

AU - Li, Ying hui

AU - Li, Delin

AU - Zhang, Xueru

AU - Kong, Lingping

AU - Zhou, Yonggang

AU - Lyu, Xiangguang

AU - Ji, Ronghuan

AU - Wei, Xiuzhi

AU - Cheng, Qican

AU - Jia, Zhiwei

AU - Li, Xiaojiao

AU - Wang, Qiang

AU - Wang, Yueqiang

AU - Huang, Wen

AU - Yang, Chunyan

AU - Liu, Like

AU - Wang, Xing

AU - Xing, Guangnan

AU - Hu, Guoyu

AU - Shan, Zhihui

AU - Wang, Ruizhen

AU - Li, Haiyan

AU - Li, Hongyu

AU - Zhao, Tao

AU - Liu, Jun

AU - Lu, Yuping

AU - Hu, Xiping

AU - Kong, Fanjiang

AU - Qiu, Li juan

AU - Liu, Bin

PY - 2023/10/26

Y1 - 2023/10/26

N2 - Shading in combination with extended photoperiods can cause exaggerated stem elongation (ESE) in soybean, leading to lodging and reduced yields when planted at high-density in high-latitude regions. However, the genetic basis of plant height in adaptation to these regions remains unclear. Here, through a genome-wide association study, we identify a plant height regulating gene on chromosome 13 (PH13) encoding a WD40 protein with three main haplotypes in natural populations. We find that an insertion of a Ty1/Copia-like retrotransposon in the haplotype 3 leads to a truncated PH13H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13 H3 allele has been strongly selected for genetic improvement at high latitudes. Deletion of both PH13 and its paralogue PHP can prevent shade-induced ESE and allow high-density planting. This study provides insights into the mechanism of shade-resistance and offers potential solutions for breeding high-yielding soybean cultivar for high-latitude regions.

AB - Shading in combination with extended photoperiods can cause exaggerated stem elongation (ESE) in soybean, leading to lodging and reduced yields when planted at high-density in high-latitude regions. However, the genetic basis of plant height in adaptation to these regions remains unclear. Here, through a genome-wide association study, we identify a plant height regulating gene on chromosome 13 (PH13) encoding a WD40 protein with three main haplotypes in natural populations. We find that an insertion of a Ty1/Copia-like retrotransposon in the haplotype 3 leads to a truncated PH13H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13 H3 allele has been strongly selected for genetic improvement at high latitudes. Deletion of both PH13 and its paralogue PHP can prevent shade-induced ESE and allow high-density planting. This study provides insights into the mechanism of shade-resistance and offers potential solutions for breeding high-yielding soybean cultivar for high-latitude regions.

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U2 - 10.1038/s41467-023-42608-5

DO - 10.1038/s41467-023-42608-5

M3 - Article

C2 - 37884530

AN - SCOPUS:85175002951

SN - 2041-1723

VL - 14

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 6813

ER -

PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes

Abstract

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ASJC Scopus subject areas

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