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Association mapping in Populus reveals the interaction between Pto-miR530a and its target Pto-KNAT1

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Abstract

Main conclusion

We used transcript profiling and multi-SNP association to investigate the genetic regulatory relationship between miRNA Pto-miR530a and its target Pto-KNAT1, identifying additive, dominant, and epistatic effects.

MicroRNAs (miRNAs) play crucial roles in the post-transcriptional regulation of plant growth and development; indeed, many studies have described the importance of miRNA–target interactions in herbaceous species. However, elucidation of the miRNA–target interactions in trees may require novel strategies. In the present study, we describe a strategy combining expression profiling by reverse transcription quantitative PCR (RT-qPCR) and association mapping with multiple single nucleotide polymorphisms (SNPs) to evaluate the interaction between Pto-miR530a and its target Pto-KNAT1 in Populus tomentosa. RT-qPCR analysis showed a negative correlation (r = −0.62, P < 0.05) between expression levels of Pto-miR530a and Pto-KNAT1 in eight tissues. We used a Bayesian hierarchical model to identify allelic variants of Pto-miR530a and Pto-KNAT1 that associated with eight traits related to growth and wood properties, in a population of 460 unrelated individuals of P. tomentosa. This analysis identified 27 associations, with the proportions of phenotypic variance (R 2) contributed by each SNP ranging of 0.82–15.81 %, the additive effects of each SNP ranging of 0.16–18.09, and the dominant effects ranging from −14.09 to 19.00. Epistatic interaction models showed a strong interaction among SNPs in the miRNA target with R 2 of 0.1–3.56 %, and information gain of significant SNP pairs of −3.09 to 0.93 %, representing the regulatory interactions between the miRNA and the mRNA. Thus, we used a new strategy that combines association genetics and expression profiling based on SNPs to study the regulatory relationship between this miRNA and its target mRNA, thereby providing novel advances in our understanding of the genetic architecture of important traits.

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Abbreviations

5′-UTR:

5′-untranslated region

DBH:

Diameter at breast height

FL:

Fiber length

FW:

Fiber width

fGWAS:

Functional genome-wide association studies

HC:

Holocellulose content

IG:

Information gain

LC:

Lignin content

LD:

Linkage disequilibrium

MFA:

Microfiber angle

miRNAs:

MicroRNAs

MDR3.0.2:

Multifactor dimensionality reduction 3.0.2

PCN :

POPCORONA

PCA:

Principle component analysis

RT-qPCR:

Reverse transcription quantitative PCR

SNP:

Single nucleotide polymorphism

V:

Stem volume

H:

Tree height

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Acknowledgments

We owe thanks to Prof. Rongling Wu and Dr. Zhong Wang (Center for Statistical Genetics, Pennsylvania State University, Hershey, Pennsylvania) for advice on statistical analysis. This work was supported by the National ‘863’ Plan Project (No. 2013AA102702), the State Key Basic Research Program of China (No. 2012CB114506), and the Project of the National Natural Science Foundation of China (No. 31170622, 30872042).

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Correspondence to Deqiang Zhang.

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Yang, X., Du, Q., Chen, J. et al. Association mapping in Populus reveals the interaction between Pto-miR530a and its target Pto-KNAT1 . Planta 242, 77–95 (2015). https://doi.org/10.1007/s00425-015-2287-3

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