Evidence map›Paper›PMID 41042266›Full record

ArticleRice (New York, N.Y.)2025

Natural variation of the MIR168a promoter influences its activity and miR168a abundance in rice.

Zhi-Xue Zhao, Xiu-Lian Yan, Rong Liao, Dai-Ming Guo, Ya-Ping Tang, Mao-Lin Guo, Si-Jia Yang, Xiao-Xiao Yin, Beenish Hassan, De-Qiang Li and 8 more

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Article in Rice (New York, N.Y.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

18 authors.

Zhi-Xue Zhao *State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China. zhixuezhao@sicau.edu.cn.
Xiu-Lian Yan *State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Rong Liao *State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Dai-Ming Guo *Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
Ya-Ping TangState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Mao-Lin GuoState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Si-Jia YangState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Xiao-Xiao YinState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Beenish HassanState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
De-Qiang LiState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Jing FanState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Yan-Yan HuangState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Ji-Wei ZhangState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
He WangState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Guo-Bang LiState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Yong ZhuState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Yan LiState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Wen-Ming WangState Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China. j316wenmingwang@sicau.edu.cn.

Funding

National Natural Science Foundation of China 32101728National Natural Science Foundation of China 32350410431National Natural Science Foundation of China U19A2033Open Project Program of State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China SKL-KF202423Sichuan Province Breeding Project 2021YFYZ0021
6 · The paper itself

Abstract

miR168a, a plant-specific microRNA (miRNA) derived from the MIR168a gene, plays a pivotal role in modulating rice blast disease resistance and critical agronomic traits such as flowering time and yield. However, the regulatory mechanisms governing the MIR168a promoter remain poorly understood. This study identified a 1661 bp upstream fragment of the mature miR168a as highly active in promoter function. Sequence alignments revealed substantial variation in MIR168 promoters across plant species. Analysis of over 4000 rice accessions showed that while the MIR168a promoter exhibited abundant SNPs and InDels, miR168a itself had no such polymorphisms. Based on promoter polymorphisms, the MIR168a promoter was classified into three haplotypes, with Hap2 and Hap3 showing higher activity than Hap1. Through DNA fragment swapping and site-directed mutagenesis, the T site in Hap2 and the A site in Hap3 were identified as critical determinants of promoter activity. Rice accessions containing these sites exhibited significantly higher miR168a abundance compared to Hap1 accessions. Population genetic and evolutionary analyses revealed that highly active MIR168a promoters in Hap2 and Hap3 predominantly occur in indica accessions and trace their origins to wild rice. Furthermore, the nucleotide diversity of the MIR168a promoter in cultivated rice was markedly lower than in wild rice, likely reflecting artificial selection during domestication and artificial selection. Breeders may have favored rice lines harboring MIR168a promoter variants with reduced activity, such as Hap1 accessions, underscoring its potential for breeding programs. Additionally, miR168a expression was induced in all three haplotypes following infection with Magnaporthe oryzae. These findings illuminate the natural variation in MIR168a promoter sequences and their influence on miR168a expression activity, offering new insights for rice improvement strategies.

Indexed as

HaplotypemiR168Oryza sativaPolymorphismPromoter

Identifiers

PMID41042266
PMCPMC12495017

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.