Development of DNA Markers Linked to Double-Flower and Hortensia Traits in &lt;i&gt;Hydrangea macrophylla&lt;/i&gt; (Thunb.) Ser.

Waki, Takamitsu; Kodama, Masashi; Akutsu, Midori; Namai, Kiyoshi; Iigo, Masayuki; Kurokura, Takeshi; Yamamoto, Takatsugu; Nashima, Kenji; Nakayama, Masayoshi; Yagi, Masafumi

doi:10.2503/hortj.okd-096

Cited by 14 publications

(23 citation statements)

References 32 publications

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“…Mophead inflorescence was reported to be a recessive characteristic controlled by a single recessive gene located on linkage group 4 8,50 . Even though little information is known about the physiological and genetic mechanisms causing the mophead phenotype, the GWAS and segregation of the discovered SNP in the F 2 population does support the hypothesis that the appearance of the mophead phenotype is a qualitative rather than a quantitative change in H. macrophylla, as proposed by Uemachi and Okumura 8 .…”

Section: Discussionmentioning

confidence: 99%

“…An insertion of a long terminal repeat retrotransposon into the locus controlling inflorescence type was also proposed by the same research group through an observation of lacecap hydrangea cultivar mutation, but such a finding was not able to be connected to the current study due to limited genomic information. While genetic markers linked to inflorescence type in bigleaf hydrangea have been reported previously 46,50 , the single marker discovered and utilized herein has advantages for use in MAS. The previously published markers must be used in combination for marker-assisted selection while the SNP detailed here can be used alone.…”

Section: Discussionmentioning

confidence: 99%

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

Wu¹,

Alexander

2020

Hortic Res

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

Wu¹,

Alexander

2020

Hortic Res

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“…Previous studies have suggested that the double flower phenotype is a recessive trait controlled by a single major gene. 4 , 5 Suyama et al 4 found that crosses between the progeny of ‘Sumidanohanabi’ and the progeny of ‘Jogasaki’ produced only single flower descendants. Thus, it was also suggested that the genes controlling the double flower phenotype are different.…”

Section: Introductionmentioning

confidence: 99%

“…Thus, it was also suggested that the genes controlling the double flower phenotype are different. 4 We named the double flower locus d su as the locus controlling the double flower phenotype of ‘Sumidanohanabi’ and the double flower locus d jo as the locus controlling the double flower phenotype of ‘Jogasaki.’ Waki et al 5 identified d su on the genetic linkage map. They also found that the DNA marker STAB045 was the closest marker to d su and that STAB045 could help distinguish flower phenotypes with a high degree of agreement.…”

Section: Introductionmentioning

confidence: 99%

Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype

et al. 2020

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Owing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single-molecule real-time sequencing data followed by a Hi-C analysis was employed. Two haplotype-phased sequences were obtained from the heterozygous genome of hydrangea. One assembly consisted of 3,779 scaffolds (2.256 Gb in length and N50 of 1.5 Mb), the other also contained 3,779 scaffolds (2.227 Gb in length, and N50 of 1.4 Mb). A total of 36,930 genes were predicted in the sequences, of which 32,205 and 32,222 were found in each haplotype. A pair of 18 pseudomolecules was constructed along with a high-density SNP genetic linkage map. Using the genome sequence data, and two F2 populations, the SNPs linked to double flower loci (djo and dsu) were discovered. DNA markers linked to djo and dsu were developed, and these could distinguish the recessive double flower allele for each locus, respectively. The LEAFY gene is a very likely candidate as the causative gene for dsu, since frameshift was specifically observed in the double flower accession with dsu.

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“…A phylogenetic tree of Hydrangea species was established to study the possibility of interspecific hybridization by using 13 highly polymorphic chloroplast markers (Mendoza et al, 2013). Recently, Waki et al (2018) screened 768 SSR primer pairs in 93 F 2 progeny to identify markers linked to double-flower and hortensia (mophead) traits in H. macrophylla; they found that both traits are each controlled by a single recessive gene. Many SSRs were developed through transcriptome sequencing and used for genetic mapping of powdery mildew resistance, remontancy, and flower type in hydrangea, but they were insufficient for linkage mapping due to the lack of marker density (Rinehart et al, 2018).…”

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confidence: 99%

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

Wu¹,

Alexander²

2019

J. Amer. Soc. Hort. Sci.

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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.

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Development of DNA Markers Linked to Double-Flower and Hortensia Traits in <i>Hydrangea macrophylla</i> (Thunb.) Ser.

Cited by 14 publications

References 32 publications

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

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

Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype

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

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