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

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 F 1 progenies using genotyping by sequencing (GBS) and co-segregated with inflorescence type (χ 2 = 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.

Detection of Reproducible Major Effect QTL for Petal Traits in Garden Roses

“…Very few publications have recently reported markers derived from association studies that are based on a larger number of unrelated genotypes and therefore have a much broader genetic base and use a large number of molecular markers covering the genome [ 17 , 19 , 25 , 26 ].…”

Identification of Chilling Accumulation-Associated Genes for Litchi Flowering by Transcriptome-Based Genome-Wide Association Studies

“…A larger population size has been used for association analysis in field crops, such as rice ( Huang et al, 2012 ), soybean ( Zhou et al, 2015 ), and maize ( Maldonado et al, 2019 ). GWAS has also been identified in trait-related candidate genes or SNPs in horticultural plants using populations less than 100, such as rose ( Schulz et al, 2016 ), chestnut ( Kang et al, 2019 ), chrysanthemums ( Su et al, 2019 ), and bigleaf hydrangea ( Wu and Alexander, 2020 ). In this research, we used 87 litchi accessions for the transcriptome-based GWAS and obtained 1,411 lead SNPs and 1,115 AGs.…”

Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map

“…GBS has been widely used in popular ornamental crops, such as roses [20], for linkage mapping and subsequent quantitative trait loci (QTL) analyses. In hydrangea, valuable traits such as inflorescence shape, double flower, and recurrent blooming are thought to be quantitatively inherited and suitable for QTL studies to identify markers for MAS [13,23]. The genotyping of two hydrangea cultivars and their F 1 progeny identified 3923 SNP markers through a GBS approach, providing the possibility to facilitate construction of a high-density linkage map for future QTL studies in hydrangea.…”

“…GBS has been employed for linkage mapping in woody ornamentals such as roses [20] and apples [21]. In hydrangea, it has been used for genetic diversity [22] and association mapping studies [23,24], but no linkage map was constructed with this method.…”