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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 F₁ 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.

SUBMITTER: Wu X

PROVIDER: S-EPMC7049302 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:The ornamental crop Hydrangea macrophylla develops highly attractive lacecap (wild type) or mophead inflorescences. The mophead trait, which is mostly favored by consumers, is recessively inherited by the INFLORESCENCE TYPE locus (INF). If lacecap cultivars are crossed with mophead cultivars, then either 50% or all progenies develop lacecap inflorescences, depending on the zygosity at the INF locus. For most cultivars, the zygosity at the INF locus is unknown. Furthermore, the determination of the inflorescence type in offspring populations is time-consuming, because seedlings flower the first time in the 2nd year after sowing. Within this study, we aimed to develop DNA-based markers that allow to determine the zygosity at the INF locus of prospective parental plants and to predict the inflorescence phenotype of seedlings already in the non-flowering stage. RESULTS:By crossing a mophead and a lacecap cultivar of H. macrophylla, we produced a pseudo-backcross F1 population consisting of 422 plants. These plants segregated into 279 lacecap, 73 mophead, 3 intermediate and 67 non-flowering plants, differing significantly from the expected 1:1 segregation ratio. Surprisingly, 75% of these plants were triploid, although both parents were diploid. We found that the lacecap parent produced unreduced pollen, which induced the formation of triploids. 380 randomly selected F1 plants were genotyped by genotyping-by-sequencing (GbS). Using a genome assembly of cultivar 'Sir Joseph Banks', we performed subsequently a bulk sequence analysis with pooled GbS data of diploid versus mophead plants. We identified directly 2 markers tightly linked with the INF locus, each of them explaining 99.7% of the inflorescence phenotype. Using a collection consisting of 56 diploid, triploid or tetraploid H. macrophylla varieties, we detected 6 sequence variants for one of these markers. Two variants were associated with the mophead phenotype. Furthermore, we found by marker analysis a co-segregation between the mophead and the non-flowering trait, which indicates a major flowering time locus next to the INF locus. CONCLUSION:Through bulk sequence analysis of pooled GbS data from diploid and polyploid F1 plants, we identify rapidly tightly linked markers for the inflorescence type, a dominant-recessively inherited trait in the non-model plant species H. macrophylla.

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

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