BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN PRUNUS MUME

Highlights

• Five QTLs associated with weeping traits on chromosome 7 were identified by BSR-seq.

• The novel allele PmUGT72B3 has a synonymous transition of T⁶⁶ (upright) to C (weeping) in the coding sequence and a 470-bp deletion in the promoter region.

• PmUGT72B3 was associated with hormone and lignin regulation by WGCNA.

Abstract

Weeping species are used both as ornamental plants and for breeding dwarf plant types. However, exploration of casual genes controlling weeping traits is rather limited. Here, we identified individuals with contrasting phenotypes from an F₁ bi-parental mapping population of Prunus mume which was developed from a cross between the upright cultivar ‘Liuban’ and the weeping cultivar ‘Fentai Chuizhi’. Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified. The Pm024074 (PmUGT72B3) allele, belonging to the UDP-glycosyltransferase superfamily containing the coniferyl-alcohol glucosyltransferase domain, was identified in a genomic region overlapping with a previously identified QTL, and had a synonymous transition of T⁶⁶ (upright) to C (weeping) in the coding sequence and a 470-bp deletion in the promoter region. Pm024074 had exceptionally high expression in buds and stems of weeping P. mume. Weighted correlation network analysis indicates that genes neighboring Pm024074 were significantly associated with plant architecture. In addition, a reliable single nucleotide polymorphism marker was developed based on the variation in the Pm024074 gene, providing precise marker-assisted breeding for weeping traits. This study provides insights into the genetic mechanism governing the weeping trait in P. mume, and indicates potential applications for the manipulation of tree architecture.

Graphical abstract

Keywords

BSR-seq / PmUGT72B3 / Prunus mume / UDP-glycosyltransferase / weeping shoots / WGCNA

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Supplementary materials

The online version of this article at https://doi.org/10.15302/J-FASE-2020379 contains supplementary materials.

Acknowledgements

The research was funded by the National Key Research and Development Program of China (2018YFD1000401), the program for Science and Technology of Beijing (No. Z181100002418006), the National Natural Science Foundation of China (No. 31870689) and the Special Fund for Beijing Common Construction Project.

Compliance with ethics guidelines

Xiaokang Zhuo, Tangchun Zheng, Zhiyong Zhang, Suzhen Li, Yichi Zhang, Lidan Sun, Weiru Yang, Jia Wang, Tangren Cheng, and Qixiang Zhang declare that they have no conflicts of interest or financial conflicts to disclose. This article does not contain any studies with human or animal subjects performed by any of the authors.

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The Author(s) 2020. Published by Higher Education Press. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0)