Identification of miRNA-eQTLs in maize mature leaf by GWAS

BMC Genomics

Hsin-Mei Ku¹  Mei-Hsiu Su²  Shu-Yun Chen³  Karl A. Kremling⁴  Edward S. Buckler⁵  M. Cinta Romay⁶  Qi Sun⁶  Nicholas K. Lepak⁷  Peter J. Bradbury⁷ 

[1] Advanced Plant Biotechnology Center, National Chung Hsing University, No 145 Xingda Rd, South Dist, 402, Taichung, Taiwan;Agricultural Biotechnology Research Center, Academia Sinica, 115, Taipei, Taiwan;Department of Life Science, National Cheng Kung University, 701, Tainan, Taiwan;Department of Plant Breeding and Genetics, Cornell University, 14850, Ithaca, NY, USA;Department of Plant Breeding and Genetics, Cornell University, 14850, Ithaca, NY, USA;United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA;Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA;Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA;United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA;

关键词: miRNA;    miR-eQTLs;    Hapmap;    Maize;    GWAS;    miRNA target gene regulation;   

DOI  :  10.1186/s12864-020-07073-0

来源: Springer

【 摘 要 】

BackgroundMiRNAs 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.ResultsThe 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.ConclusionsThese 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.

【 授权许可】

CC BY