Flexibility of Parental-like or Maternal-like Gene Expression Under Diverse Environments Contributes to Combined Drought Avoidance and Drought Tolerance in a Water-saving and drought-resistance Rice Hybrid

Overview

Journal Theor Appl Genet

Publisher Springer

Specialty Genetics

Date 2024 Sep 13

PMID 39271558

Authors

Lei Wang

Xiaosong Ma

Yi Liu

Guolan Liu

Haibin Wei

Zhi Luo

Hongyan Liu

Ming Yan

Anning Zhang

Xinqiao Yu

Hui Xia

Lijun Luo

Affiliations

Soon will be listed here.

Abstract

Key Message: The hybrid rice variety (Hanyou73) exhibits the maternal-like (HH7A) gene expression in roots and parental-like (HH3) gene expression in leaves to obtain both advantages of drought avoidance and drought tolerance from its two parents.

Background: Rice is one of the most important crops in the world. Rice production consumes lots of water and significantly suffers from the water deficiency and drought stress. The water-saving and drought-resistance rice (WDR) confers good drought resistance and performs well in the water-saving cultivation.

Main Findings: A hybrid WDR variety Hanyou73 (HY73) exhibited superior drought resistance compared with its parents Hanhui3 (HH3) and Huhan7A (HH7A). Studies on drought resistance related traits revealed that HY73 performed like HH3 and HH7A on drought tolerance and drought avoidance, respectively. Transcriptomes were analyzed for samples with various phytohormone treatments and abiotic stresses, in which HY73 was closer to HH3 in leaf samples while HH7A in root samples. HY73 and its parents differed largely in DEGs and GO analysis for DEGs suggested the different pathways of drought response in HH3 and HH7A. Parent-like expression analysis revealed that the higher-parent-like expression pattern was prevailing in HY73. In addition, patterns of the parent-like expression significantly transformed between abiotic-stressed/phytohormone-treated and control samples, which might help HY73 to adapt to different environments. WGCNA analysis for those parent-like expression genes revealed some drought resistant genes that should contribute to the superior drought resistance of HY73. Genetic variation on the promotor sequence was confirmed as the reason for the flexible parent-like gene expression in HY73.

Conclusion: Our study uncovered the important roles of complementation of beneficial traits from parents and flexible gene expressions in drought resistance of HY73, which could facilitate the development of new WDR varieties.

References

Albert E, Duboscq R, Latreille M, Santoni S, Beukers M, Bouchet J . Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato. Plant J. 2018; 96(3):635-650. DOI: 10.1111/tpj.14057. View

Borah P, Sharma E, Kaur A, Chandel G, Mohapatra T, Kapoor S . Analysis of drought-responsive signalling network in two contrasting rice cultivars using transcriptome-based approach. Sci Rep. 2017; 7:42131. PMC: 5299611. DOI: 10.1038/srep42131. View

Chen Z, Li P, Jiang S, Chen H, Wang J, Cao C . Evaluation of resource and energy utilization, environmental and economic benefits of rice water-saving irrigation technologies in a rice-wheat rotation system. Sci Total Environ. 2020; 757:143748. DOI: 10.1016/j.scitotenv.2020.143748. View

Duan K, Li L, Hu P, Xu S, Xu Z, Xue H . A brassinolide-suppressed rice MADS-box transcription factor, OsMDP1, has a negative regulatory role in BR signaling. Plant J. 2006; 47(4):519-31. DOI: 10.1111/j.1365-313X.2006.02804.x. View

Garg R, Narayana Chevala V, Shankar R, Jain M . Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response. Sci Rep. 2015; 5:14922. PMC: 4598828. DOI: 10.1038/srep14922. View

Gould B, Chen Y, Lowry D . Gene regulatory divergence between locally adapted ecotypes in their native habitats. Mol Ecol. 2018; 27(21):4174-4188. DOI: 10.1111/mec.14852. View

Guo H, Mendrikahy J, Xie L, Deng J, Lu Z, Wu J . Transcriptome analysis of neo-tetraploid rice reveals specific differential gene expressions associated with fertility and heterosis. Sci Rep. 2017; 7:40139. PMC: 5223177. DOI: 10.1038/srep40139. View

He G, Zhu X, Elling A, Chen L, Wang X, Guo L . Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell. 2010; 22(1):17-33. PMC: 2828707. DOI: 10.1105/tpc.109.072041. View

Joshi R, Sahoo K, Singh A, Anwar K, Pundir P, Gautam R . Enhancing trehalose biosynthesis improves yield potential in marker-free transgenic rice under drought, saline, and sodic conditions. J Exp Bot. 2019; 71(2):653-668. PMC: 6946002. DOI: 10.1093/jxb/erz462. View

10.

Kanehisa M . Toward understanding the origin and evolution of cellular organisms. Protein Sci. 2019; 28(11):1947-1951. PMC: 6798127. DOI: 10.1002/pro.3715. View

11.

Karan R, DeLeon T, Biradar H, Subudhi P . Salt stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. PLoS One. 2012; 7(6):e40203. PMC: 3386172. DOI: 10.1371/journal.pone.0040203. View

12.

Li J, Han Y, Liu L, Chen Y, Du Y, Zhang J . qRT9, a quantitative trait locus controlling root thickness and root length in upland rice. J Exp Bot. 2015; 66(9):2723-32. DOI: 10.1093/jxb/erv076. View

13.

Li N, Wei S, Chen J, Yang F, Kong L, Chen C . OsASR2 regulates the expression of a defence-related gene, Os2H16, by targeting the GT-1 cis-element. Plant Biotechnol J. 2017; 16(3):771-783. PMC: 5814579. DOI: 10.1111/pbi.12827. View

14.

Liao Z, Zhang Y, Yu Q, Fang W, Chen M, Li T . Coordination of growth and drought responses by GA-ABA signaling in rice. New Phytol. 2023; 240(3):1149-1161. DOI: 10.1111/nph.19209. View

15.

Liu W, Wang M, Huang J, Tang H, Lan H, Zhang H . The OsDHODH1 gene is involved in salt and drought tolerance in rice. J Integr Plant Biol. 2009; 51(9):825-33. DOI: 10.1111/j.1744-7909.2009.00853.x. View

16.

Liu J, Shen Y, Cao H, He K, Chu Z, Li N . OsbHLH057 targets the AATCA cis-element to regulate disease resistance and drought tolerance in rice. Plant Cell Rep. 2022; 41(5):1285-1299. DOI: 10.1007/s00299-022-02859-w. View

17.

Lou Q, Chen L, Mei H, Xu K, Wei H, Feng F . Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice ( L.). Front Plant Sci. 2017; 8:1314. PMC: 5526896. DOI: 10.3389/fpls.2017.01314. View

18.

Love M, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. PMC: 4302049. DOI: 10.1186/s13059-014-0550-8. View

19.

Luo L . Breeding for water-saving and drought-resistance rice (WDR) in China. J Exp Bot. 2010; 61(13):3509-17. DOI: 10.1093/jxb/erq185. View

20.

Luo Z, Xiong J, Xia H, Ma X, Gao M, Wang L . Transcriptomic divergence between upland and lowland ecotypes contributes to rice adaptation to a drought-prone agroecosystem. Evol Appl. 2020; 13(9):2484-2496. PMC: 7513727. DOI: 10.1111/eva.13054. View