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

文献类型： 外文期刊

作者： Xu, Pengfei 1 ; Zhu, Yantao 3 ; Zhang, Yanfeng 3 ; Jiang, Jianxia 4 ; Yang, Liyong 4 ; Mu, Jianxin 3 ; Yu, Xiang 5 ; He, 1 ;

作者机构： 1.Chinese Acad Sci, CAS Ctr Excellence Mol Plant Sci, Shanghai Inst Plant Physiol & Ecol, Natl Key Lab Plant Mol Genet, Shanghai, Peoples R China

2.Univ Chinese Acad Sci, Beijing, Peoples R China

3.Hybrid Rape Res Ctr Shaanxi Prov, Yangling, Shaanxi, Peoples R China

4.Shanghai Acad Agr Sci, Crop Breeding & Cultivat Res Inst, Shanghai, Peoples R China

5.Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Shanghai, Peoples R China

关键词： rapeseed; miRNA target site; genetic variant; agronomic trait; correlation analysis

期刊名称：FRONTIERS IN GENETICS （ 影响因子：4.599； 五年影响因子：4.888 ）

ISSN：

年卷期： 2021 年 12 卷

页码：

收录情况： SCI

摘要： 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.

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