Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

Pengfei Xu; Yantao Zhu; Yanfeng Zhang; Jianxia Jiang; Liyong Yang; Jianxin Mu; Xiang Yu; Yuke He

doi:10.3389/fgene.2021.741858

Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

Front Genet. 2021 Sep 14:12:741858. doi: 10.3389/fgene.2021.741858. eCollection 2021.

Authors

Pengfei Xu^{1

2}, Yantao Zhu³, Yanfeng Zhang³, Jianxia Jiang⁴, Liyong Yang⁴, Jianxin Mu³, Xiang Yu⁵, Yuke He^{1

2}

Affiliations

¹ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai, China.
² University of the Chinese Academy of Sciences, Beijing, China.
³ Hybrid Rape Research Center of Shaanxi Province, Yangling, China.
⁴ Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
⁵ School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.

Abstract

MicroRNAs (miRNAs) and their target genes play vital roles in crops. However, the genetic variations in miRNA-targeted sites that affect miRNA cleavage efficiency and their correlations with agronomic traits in crops remain unexplored. On the basis of a genome-wide DNA re-sequencing of 210 elite rapeseed (Brassica napus) accessions, we identified the single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) in miRNA-targeted sites complementary to miRNAs. Variant calling revealed 7.14 million SNPs and 2.89 million INDELs throughout the genomes of 210 rapeseed accessions. Furthermore, we detected 330 SNPs and 79 INDELs in 357 miRNA target sites, of which 33.50% were rare variants. We also analyzed the correlation between the genetic variations in miRNA target sites and 12 rapeseed agronomic traits. Eleven SNPs in miRNA target sites were significantly correlated with phenotypes in three consecutive years. More specifically, three correlated SNPs within the miRNA-binding regions of BnSPL9-3, BnSPL13-2, and BnCUC1-2 were in the loci associated with the branch angle, seed weight, and silique number, respectively; expression profiling suggested that the variation at these 3 miRNA target sites significantly affected the expression level of the corresponding target genes. Taken together, the results of this study provide researchers and breeders with a global view of the genetic variations in miRNA-targeted sites in rapeseed and reveal the potential effects of these genetic variations on elite agronomic traits.

Keywords: agronomic trait; correlation analysis; genetic variant; miRNA target site; rapeseed.