Genome-wide analysis of the soybean GmGRP gene family identifies putative cold-responsive genes.
5 affiliations
- 1Heihe Branch Institute, Heilongjiang Academy of Agricultural Sciences, No. 345 Huancheng West Road, Heihe City, Heilongjiang Province, 164399, China.
- 2Hulunbuir Academy of Agricultural and Animal Husbandry Sciences, Ulanhot, 137400, China.
- 3Hulunbuir Agriculture and Animal Husbandry Bureau Comprehensive Support Center, Ulanhot, 137400, China.
- 4Heihe Branch Institute, Heilongjiang Academy of Agricultural Sciences, No. 345 Huancheng West Road, Heihe City, Heilongjiang Province, 164399, China. [email protected].
- 5Soybean Research Institute of Heilongjiang Academy of Agriculture Sciences, Harbin, 150086, China. [email protected].
Abstract
Glycine-rich proteins (GRPs) play essential roles in plant growth, development, and stress responses, but systematic studies in soybean remain limited. In this study, using the soybean reference genome, 11 GmGRP gene members were identified with tools such as Pfam, SMART, CDD, and HMMER, and their physicochemical properties, phylogenetic relationships, gene structure, conserved motifs, and promoter cis-acting elements were systematically analyzed. Phylogenetic analysis showed that GmGRPs can be divided into multiple subgroups and share conserved biological functions with GRPs in Arabidopsis, rice, and maize. Gene structure and motif analysis revealed significant structural differences across subgroups, whereas members within the same group are highly conserved. Promoter element analysis showed that GmGRPs are extensively enriched for ABA-, JA-, SA-, GA-, and cold-responsive regulatory elements, suggesting that these genes may participate in regulating multiple hormonal and stress signals.Collinearity results showed that two pairs of homologous genes may have arisen from gene duplication. Tissue expression analysis indicated that GmGRPs exhibit significant tissue specificity, with different members potentially performing different biological functions.Promoter analysis identified low-temperature response (LTR) cis-elements in the promoters of GmGRP7 and GmGRP8, suggesting these two members are candidates for cold-responsive regulation, pending experimental validation. Expression patterns varied substantially among family members and across time points. GmGRP8, GmGRP9, and GmGRP10 displayed pronounced induction, reaching peak fold-changes of approximately 11-, 13-, and 14-fold relative to the 0 h control at 6-12 h, respectively. In contrast, GmGRP3, GmGRP11, and several other members showed a progressive decline in transcript abundance under sustained cold. These findings are consistent with the promoter-based prediction that GmGRP7 and GmGRP8 are cold-responsive candidates, and suggest that additional GmGRP members may also participate in low-temperature responses through distinct expression dynamics.
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BibTeX
@article{wei2026genomewide,
title = {{Genome-wide analysis of the soybean GmGRP gene family identifies putative cold-responsive genes.}},
author = {Xinyu Wei and Wencheng Lu and Hongchang Jia and Xiaoguang Yu and Xiaofei Yan and Henan Diao and Ying Liu and Zhibin Gao and Dezhi Han and Honglei Ren},
journal = {BMC plant biology},
year = {2026},
month = jul,
doi = {10.1186/s12870-026-09623-2},
url = {https://europepmc.org/article/MED/42902146},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Genome-wide analysis of the soybean GmGRP gene family identifies putative cold-responsive genes.
AU - Xinyu Wei
AU - Wencheng Lu
AU - Hongchang Jia
AU - Xiaoguang Yu
AU - Xiaofei Yan
AU - Henan Diao
AU - Ying Liu
AU - Zhibin Gao
AU - Dezhi Han
AU - Honglei Ren
PY - 2026
DA - 2026/07/01
JO - BMC plant biology
DO - 10.1186/s12870-026-09623-2
UR - https://europepmc.org/article/MED/42902146
AB - Glycine-rich proteins (GRPs) play essential roles in plant growth, development, and stress responses, but systematic studies in soybean remain limited. In this study, using the soybean reference genome, 11 GmGRP gene members were identified with tools such as Pfam, SMART, CDD, and HMMER, and their physicochemical properties, phylogenetic relationships, gene structure, conserved motifs, and promoter cis-acting elements were systematically analyzed. Phylogenetic analysis showed that GmGRPs can be divided into multiple subgroups and share conserved biological functions with GRPs in Arabidopsis, rice, and maize. Gene structure and motif analysis revealed significant structural differences across subgroups, whereas members within the same group are highly conserved. Promoter element analysis showed that GmGRPs are extensively enriched for ABA-, JA-, SA-, GA-, and cold-responsive regulatory elements, suggesting that these genes may participate in regulating multiple hormonal and stress signals.Collinearity results showed that two pairs of homologous genes may have arisen from gene duplication. Tissue expression analysis indicated that GmGRPs exhibit significant tissue specificity, with different members potentially performing different biological functions.Promoter analysis identified low-temperature response (LTR) cis-elements in the promoters of GmGRP7 and GmGRP8, suggesting these two members are candidates for cold-responsive regulation, pending experimental validation. Expression patterns varied substantially among family members and across time points. GmGRP8, GmGRP9, and GmGRP10 displayed pronounced induction, reaching peak fold-changes of approximately 11-, 13-, and 14-fold relative to the 0 h control at 6-12 h, respectively. In contrast, GmGRP3, GmGRP11, and several other members showed a progressive decline in transcript abundance under sustained cold. These findings are consistent with the promoter-based prediction that GmGRP7 and GmGRP8 are cold-responsive candidates, and suggest that additional GmGRP members may also participate in low-temperature responses through distinct expression dynamics.
SN - 1471-2229
ER -