Genetic Diversity and Population Structure Analysis of Bigleaf Hydrangea Using Genotyping-by-sequencing

in Journal of the American Society for Horticultural Science

Hydrangea macrophylla (bigleaf hydrangea) is one of the most important floral and nursery crops worldwide. However, breeding of new bigleaf hydrangea cultivars has been hampered by a long breeding cycle and lack of genetic resources. This study investigated the genetic diversity and population structure of 82 bigleaf hydrangea cultivars using single-nucleotide polymorphisms (SNPs) originated from genotyping-by-sequencing. A total of 5803 high-quality SNPs were discovered in a bigleaf hydrangea cultivar panel. A phylogenetic analysis and analysis of molecular variance based on discovered SNPs concluded the taxonomic classification of H. macrophylla ssp. serrata as a subspecies of H. macrophylla. Principal component analysis confirmed ‘Preziosa’ as a hybrid between H. macrophylla ssp. macrophylla and H. macrophylla ssp. serrata. In addition, the cultivar Lady in Red was also found to be a hybrid between the two subspecies. The population structure analysis identified three groups among the 82 cultivars. All H. macrophylla ssp. serrata cultivars belonged to one group, and two groups were revealed within H. macrophylla ssp. macrophylla. The separation within H. macrophylla ssp. macrophylla indicated a second gene pool due to breeding efforts that have targeted similar breeding goals for bigleaf hydrangea. The discovered SNPs and the phylogenetic results will facilitate further exploitation and understanding of phylogenetic relationships of bigleaf hydrangea and will serve as a reference for hydrangea breeding improvements.

Contributor Notes

Corresponding author. E-mail: Lisa.Alexander@ars.usda.gov.

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    Numbers and percentages of polymorphic single-nucleotide polymorphism (SNP) loci generated by genotyping-by-sequencing (GBS) of 82 Hydrangea macrophylla cultivars. (A) Numbers of nucleotide substitutions for the total 5803 SNPs. (B) Observed percentage of transition and transversion SNP types in H. macrophylla cultivars.

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    Dendrogram of 82 Hydrangea macrophylla cultivars from two subspecies based on similarity calculated from 5803 genome-wide single-nucleotide polymorphisms. Subspecies macrophylla is represented by diamonds, subspecies serrata is represented by circles. Two proposed hybrids are colored red.

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    Principal component (PC) analysis based on 5803 single-nucleotide polymorphisms from 82 Hydrangea macrophylla cultivars. Subspecies are color-coded; the three detected clusters are indicated by circles.

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    Population structure analysis of 82 Hydrangea macrophylla cultivars based on 5803 single-nucleotide polymorphisms developed using genotyping-by-sequencing. Each individual is represented by a vertical bar reflecting assignment probabilities in each of the three groups. Group I: green bars; group II: blue bars; group III: red bars. (A) Phylogenetic tree based on the neighbor-joining method in MEGA 7 (Kumar et al., 2016). (B) Population structure based on a mixed-model analysis using STRUCTURE software (Pritchard et al., 2000). (C) Plot of the ΔK value with the number of subpopulations (K) from 2 to 10 based on the Evanno test (Evanno et al., 2005). Phylogenetic studies corresponded to population structure groups; ssp. serrata (green) agreed with group I, ssp. macrophylla was separated into two clades (blue and red) and corresponded to group II and group III, respectively.

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