Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla

Xingbo Wu,Lisa W Alexander

doi:10.1038/s41438-020-0255-y

Xingbo Wu, Lisa W Alexander

Open Access

https://doi.org/10.1038/s41438-020-0255-y

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Abstract

Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea (Hydrangea macrophylla L.) and both are recessively inherited. Molecular marker-assisted selection (MAS) can greatly reduce the time necessary to breed cultivars with desired traits. In this study, a genome-wide association study (GWAS) using 5803 single-nucleotide polymorphisms (SNPs) was performed using a panel of 82 bigleaf hydrangea cultivars. One SNP locus (Hy_CAPS_Inflo) associated with inflorescence type was identified with general linear model (GLM) and mixed linear model (MLM) methods that explained 65.5% and 36.1% of the phenotypic variations, respectively. Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM. The SNP locus (Hy_CAPS_Inflo) was converted to a cleaved amplified polymorphic sequence (CAPS) marker that showed absolute identification accuracy (100%) of inflorescence type in a validation panel consisting of eighteen H. macrophylla cultivars. The SNP was investigated in 341 F1 progenies using genotyping by sequencing (GBS) and co-segregated with inflorescence type (χ2 = 0.12; P = 0.73). The SNP was subsequently used for breeding selection using kompetitive allele specific PCR (KASP) technology. Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed. The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy in H. macrophylla. The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.

Highlights

Hydrangea macrophylla L. is a popular cultivated horticultural crop widely grown throughout America, Asia, and Europe[1,2]
Genetic diversity and population structure A neighbor-joining phylogenetic tree based on 5803 discovered single-nucleotide polymorphisms (SNPs) classified the 82 cultivated hydrangeas into two major clades according to their subspecies category (Fig. 2a)
genome-wide association study (GWAS) was performed in 82 hydrangea accessions and a major SNP locus was identified to be associated with inflorescence type, which was known to be under single-gene control[8]

Summary

Introduction

Hydrangea macrophylla L. is a popular cultivated horticultural crop widely grown throughout America, Asia, and Europe[1,2]. Breeding landscape hydrangeas focuses on whether the plant forms a rounded or mounded shrub composed of erect, unbranched stems, whereas florist hydrangea breeding programs target stem strength and durability[4]. Flowering traits are always considered as a priority for any hydrangea breeding program, as flowers present the key horticultural attraction for hydrangea as for many other ornamental crops. Inflorescence type, and the timing of flower bud initiation are the most important flowering traits in hydrangea. While flower color changes in hydrangea have been shown to be a result of internal detoxification of Al under low-pH conditions[5], inflorescence type and the timing of flower bud initiation are largely under genetic control[6,7,8]

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