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

Abstract

<jats:p><jats:italic>Hydrangea macrophylla</jats:italic> (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 <jats:italic>H. macrophylla</jats:italic> ssp. <jats:italic>serrata</jats:italic> as a subspecies of <jats:italic>H. macrophylla</jats:italic>. Principal component analysis confirmed ‘Preziosa’ as a hybrid between <jats:italic>H. macrophylla</jats:italic> ssp. <jats:italic>macrophylla</jats:italic> and <jats:italic>H. macrophylla</jats:italic> ssp. <jats:italic>serrata</jats:italic>. 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 <jats:italic>H. macrophylla</jats:italic> ssp. <jats:italic>serrata</jats:italic> cultivars belonged to one group, and two groups were revealed within <jats:italic>H. macrophylla</jats:italic> ssp. <jats:italic>macrophylla</jats:italic>. The separation within <jats:italic>H. macrophylla</jats:italic> ssp. <jats:italic>macrophylla</jats:italic> 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.</jats:p>

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

“…To date, SSR markers are still the most popular molecular marker type in hydrangea breeding programs, but their usefulness remains limited by low marker numbers 40 . Recently, a large number of SNPs were developed using GBS technology for ongoing genomic and breeding applications in hydrangea 29 .…”

“…Genotyping of the hydrangea cultivar panel was carried out via GBS as described by Elshire et al 28 . A total of 5803 highquality SNPs discovered and described previously 29 were used to perform genome-wide association analysis in the present study.…”

“…Genomic DNA was prepared and submitted for GBS following the same protocol as stated above. SNPs were called via the TAS-SEL UNEAK pipeline using the same parameters described by Wu and Alexander 29 . Inflorescence type (mophead or lacecap) was investigated for genotype-phenotype association using chi-squared analysis.…”

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

“…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.…”

Ploidy Level Influences Pollen Tube Growth and Seed Viability in Interploidy Crosses of Hydrangea macrophylla

“…The fruit of a hydrangea is a capsule containing dozens to hundreds of ovules that are capable of maturation into viable seeds (Hufford, 2001). Hybrid seed production is often low in H. macrophylla, possibly due to inbreeding in the cultivated gene pool (Wu and Alexander, 2019). Jones et al (2007) reported from 0 to 20 seeds/ capsule while other researchers have reported as little as 0-5 seeds/ capsule resulting from crosses among H. macrophylla cultivars (Venturieri et al, 2017).…”