Genome and GWAS analysis identified genes significantly related to phenotypic state of Rhododendron bark

Abstract

As an important horticultural plant, Rhododendron is often used in urban greening and landscape design. However, factors such as the high rate of genetic recombination, frequent outcrossing in the wild, weak linkage disequilibrium, and the susceptibility of gene expression to environmental factors limit further exploration of functional genes related to important horticultural traits, and make the breeding of new varieties require a longer time. Therefore, we choose bark as the target trait which is not easily affected by environmental factors, but also has ornamental properties. Genome-wide association study (GWAS) of Rhododendron delavayi (30 samples), R. irroratum (30 samples) and their F₁ generation R. agastum (200 samples) was conducted on the roughness of bark phenotypes. Finally, we obtained 2416.31 Gbp of clean data and identified 5 328 800 high-quality SNPs. According to the P-value and the degree of linkage disequilibrium of SNPs, we further identified 4 out of 11 candidate genes that affect bark roughness. The results of gene differential expression analysis further indicated that the expression levels of Rhdel02G0243600 and Rhdel08G0220700 in different bark phenotypes were significantly different. Our study identified functional genes that influence important horticultural traits of Rhododendron, and illustrated the powerful utility and great potential of GWAS in understanding and exploiting wild germplasm genetic resources of Rhododendron.

Acknowledgements

We thank Hong Yang for phenotypic data collection. This research was supported by the ZIAT-Special Project (ZJKJT-2022-01) and the Science and Technology Talent and Platform Program of Yunnan Province (202105 AC160017), the Yunnan Province Agriculture joint special project (202101BD070001-010), and the China Agriculture Research System of MOF and MARA (CARS-23-G56).

Author contributions

C.Z. and J.W conceived the study and participated in revision and discussion; Q.Y., Q.L., Y.Z., and Y.J. executed formal analysis, methodology and project administration; Z.W., Y.H., and Y.J. helped in investigation, data curation and resources; L.Z. conducted experiments; Q.Y., L.Z., and C.Z. drafted the manuscript with significant participation of Y.M. All authors read and approved the final manuscript.

Data availability

The authors confirm that the data supporting the findings of this study are available within the article and its supplementary materials.

Conflict of interest

The authors have no conflicts of interest to declare.

Supplementary data

Supplementary data is available at Horticulture Research online.

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