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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #380890

Research Project: Improving Crop Efficiency Using Genomic Diversity and Computational Modeling

Location: Plant, Soil and Nutrition Research

Title: Identification of miRNA-eQTLs in maize mature leaf by GWAS

item CHEN, SHU-YUN - Cheng Kung University
item MEI-HSIU, SU - Academia Sinica
item KREMLING, KARL - Cornell University
item Lepak, Nicholas
item ROMAY, MARIE - Cornell University
item SUN, QI - Cornell University
item Bradbury, Peter
item Buckler, Edward - Ed
item KU, HSIN-MEI - Chung Hsing University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/14/2020
Publication Date: 10/6/2020
Citation: Chen, S., Mei-Hsiu, S., Kremling, K.A., Lepak, N.K., Romay, M.C., Sun, Q., Bradbury, P., Buckler IV, E.S., Ku, H. 2020. Identification of miRNA-eQTLs in maize mature leaf by GWAS. Biomed Central (BMC) Genomics. 21(689).

Interpretive Summary: MicroRNA (miRNA) is a small RNA molecule than regulates one or more target genes in both plants and animals. Differences in miRNA abundance has been shown to affect plant height in cotton and flowering time in Arabidopsis. In maize, they have been implicated in kernel development, response to stress, and grain yield and, as a result, have potential economic importance. Although miRNAs are known to be important gene regulators for a variety of functions, little is known about which genes affect miRNA levels in plants. This study used genome wide association (GWAS) to identify genes that affect miRNA abundance. The GWAS found specific genetic variants that had statistically different miRNA expression levels in plants that carried those variants compared to plants that did not. The variants associated with miRNA expression are called eQTLs. This paper is the first to report miRNA eQTLs in maize. The study was conducted by measuring miRNA levels in 200 maize inbred lines and used the HapMap v.3.2.1 dataset that has information on genetic variants at millions of sites in the genome.

Technical Abstract: Background MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different plant accessions, developmental stages, and tissues. Little is known about the content within the plant genome contributing to the variations in plants. This study aims to identify miRNA expression-related quantitative trait loci (miR-QTLs) in the maize genome. Results The miRNA expression level from next generation sequencing (NGS) small RNA libraries derived from mature leaf samples of the maize panel (200 maize lines) was estimated as phenotypes, and maize Hapmap v3.2.1 was chosen as the genotype for the genome-wide association study (GWAS). A total of four significant miR-eQTLs were identified contributing to miR156k-5p, miR159a-3p, miR390a-5p and miR396e-5p, and all of them are trans-eQTLs. In addition, a strong positive coexpression of miRNA was found among five miRNA families. Investigation of the effects of these miRNAs on the expression levels and target genes provided evidence that miRNAs control the expression of their targets by suppression and enhancement. Conclusions These identified significant miR-eQTLs contribute to the diversity of miRNA expression in the maize penal at the developmental stages of mature leaves in maize, and the positive and negative regulation between miRNA and its target genes has also been uncovered.