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Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize.
BMC Evol Biol. 2020 07 29; 20(1):91.BE

Abstract

BACKGROUND

The SIAMESE (SIM) locus is a cell-cycle kinase inhibitor (CKI) gene that has to date been identified only in plants; it encodes a protein that promotes transformation from mitosis to endoreplication. Members of the SIAMESE-RELATED (SMR) family have similar functions, and some are related to cell-cycle responses and abiotic stresses. However, the functions of SMRs are poorly understood in maize (Zea mays L.).

RESULTS

In the present study, 12 putative SMRs were identified throughout the entire genome of maize, and these were clustered into six groups together with the SMRs from seven other plant species. Members of the ZmSMR family were divided into four groups according to their protein sequences. Various cis-acting elements in the upstream sequences of ZmSMRs responded to abiotic stresses. Expression analyses revealed that all ZmSMRs were upregulated at 5, 20, 25, and 35 days after pollination. In addition, we found that ZmSMR9/11/12 may have regulated the initiation of endoreplication in endosperm central cells. Additionally, ZmSMR2/10 may have been primarily responsible for the endoreplication regulation of outer endosperm or aleurone cells. The relatively high expression levels of almost all ZmSMRs in the ears and tassels also implied that these genes may function in seed development. The effects of treatments with ABA, heat, cold, salt, and drought on maize seedlings and expression of ZmSMR genes suggested that ZmSMRs were strongly associated with response to abiotic stresses.

CONCLUSION

The present study is the first to conduct a genome-wide analysis of members of the ZmSMR family by investigating their locations in chromosomes, identifying regulatory elements in their promoter regions, and examining motifs in their protein sequences. Expression analysis of different endosperm developmental periods, tissues, abiotic stresses, and hormonal treatments suggests that ZmSMR genes may function in endoreplication and regulate the development of reproductive organs. These results may provide valuable information for future studies of the functions of the SMR family in maize.

Authors+Show Affiliations

Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. Maize engineering technology research center of shaanxi province, Yangling, 712100, Shaanxi, China.Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. Maize engineering technology research center of shaanxi province, Yangling, 712100, Shaanxi, China.Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. Maize engineering technology research center of shaanxi province, Yangling, 712100, Shaanxi, China.Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. Maize engineering technology research center of shaanxi province, Yangling, 712100, Shaanxi, China.Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. Maize engineering technology research center of shaanxi province, Yangling, 712100, Shaanxi, China.Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. Maize engineering technology research center of shaanxi province, Yangling, 712100, Shaanxi, China.Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. Maize engineering technology research center of shaanxi province, Yangling, 712100, Shaanxi, China.Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China. gdwei@nwsuaf.edu.cn. Maize engineering technology research center of shaanxi province, Yangling, 712100, Shaanxi, China. gdwei@nwsuaf.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32727363

Citation

Zhang, Zhengquan, et al. "Genome-wide Evolutionary Characterization and Expression Analysis of SIAMESE-RELATED Family Genes in Maize." BMC Evolutionary Biology, vol. 20, no. 1, 2020, p. 91.
Zhang Z, Qu J, Li F, et al. Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize. BMC Evol Biol. 2020;20(1):91.
Zhang, Z., Qu, J., Li, F., Li, S., Xu, S., Zhang, R., Xue, J., & Guo, D. (2020). Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize. BMC Evolutionary Biology, 20(1), 91. https://doi.org/10.1186/s12862-020-01619-2
Zhang Z, et al. Genome-wide Evolutionary Characterization and Expression Analysis of SIAMESE-RELATED Family Genes in Maize. BMC Evol Biol. 2020 07 29;20(1):91. PubMed PMID: 32727363.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide evolutionary characterization and expression analysis of SIAMESE-RELATED family genes in maize. AU - Zhang,Zhengquan, AU - Qu,Jianzhou, AU - Li,Feifei, AU - Li,Silu, AU - Xu,Shutu, AU - Zhang,Renhe, AU - Xue,Jiquan, AU - Guo,Dongwei, Y1 - 2020/07/29/ PY - 2019/07/07/received PY - 2020/04/29/accepted PY - 2020/7/31/entrez PY - 2020/7/31/pubmed PY - 2020/9/17/medline KW - Endoreduplication KW - Endosperm KW - Gene expression KW - Genome-wide analysis KW - Maize KW - Stress tolerance KW - ZmSMR gene family SP - 91 EP - 91 JF - BMC evolutionary biology JO - BMC Evol Biol VL - 20 IS - 1 N2 - BACKGROUND: The SIAMESE (SIM) locus is a cell-cycle kinase inhibitor (CKI) gene that has to date been identified only in plants; it encodes a protein that promotes transformation from mitosis to endoreplication. Members of the SIAMESE-RELATED (SMR) family have similar functions, and some are related to cell-cycle responses and abiotic stresses. However, the functions of SMRs are poorly understood in maize (Zea mays L.). RESULTS: In the present study, 12 putative SMRs were identified throughout the entire genome of maize, and these were clustered into six groups together with the SMRs from seven other plant species. Members of the ZmSMR family were divided into four groups according to their protein sequences. Various cis-acting elements in the upstream sequences of ZmSMRs responded to abiotic stresses. Expression analyses revealed that all ZmSMRs were upregulated at 5, 20, 25, and 35 days after pollination. In addition, we found that ZmSMR9/11/12 may have regulated the initiation of endoreplication in endosperm central cells. Additionally, ZmSMR2/10 may have been primarily responsible for the endoreplication regulation of outer endosperm or aleurone cells. The relatively high expression levels of almost all ZmSMRs in the ears and tassels also implied that these genes may function in seed development. The effects of treatments with ABA, heat, cold, salt, and drought on maize seedlings and expression of ZmSMR genes suggested that ZmSMRs were strongly associated with response to abiotic stresses. CONCLUSION: The present study is the first to conduct a genome-wide analysis of members of the ZmSMR family by investigating their locations in chromosomes, identifying regulatory elements in their promoter regions, and examining motifs in their protein sequences. Expression analysis of different endosperm developmental periods, tissues, abiotic stresses, and hormonal treatments suggests that ZmSMR genes may function in endoreplication and regulate the development of reproductive organs. These results may provide valuable information for future studies of the functions of the SMR family in maize. SN - 1471-2148 UR - https://www.unboundmedicine.com/medline/citation/32727363/Genome_wide_evolutionary_characterization_and_expression_analysis_of_SIAMESE_RELATED_family_genes_in_maize_ L2 - https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-020-01619-2 DB - PRIME DP - Unbound Medicine ER -