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. 2022 Jan 4:12:802738.
doi: 10.3389/fgene.2021.802738. eCollection 2021.

A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia

Yang Cui  1 , Baolian Fan  1 , Xu Xu  1 , Shasha Sheng  1 , Yuhui Xu  2 , Xiaoyun Wang  1
Affiliations

A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia

Yang Cui et al. Front Genet. .

Abstract

The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F1 population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F1 individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.

Keywords: QTL; gardenia; genetic map; genotyping-by-sequencing; growth-and leaf-related traits; synteny.

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Conflict of interest statement

YX was employed by Adsen Biotechnology Co., Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Part of the trait measurement schematic diagram.
FIGURE 2
FIGURE 2
Variation and Pearson pairwise correlation analyses of growth-related and leaf-related traits of the F1 population. (A), (B) and (C) represent the variation and Pearson pairwise correlations in 2019, 2020 and 2021, respectively. The correlations were calculated with Spearman correlation coefficients, and the p values are indicated as follows: *, p < 0.05; **, p < 0.01; and ***, p < 0.001. The abbreviations given in the histograms are as follows: CD: crown diameter; BSBN: basal stem branch number; SI: stem inclination; PH: plant height; MSH: main stem height; SBD: stem base diameter; LNS: leaf number on stem; LNP: leaf number per plant; LLLS: longest leaf length on stem; LLWS: longest leaf width on stem; SLLS: shortest leaf length on stem; and SLWS: shortest leaf width on stem.
FIGURE 3
FIGURE 3
The distributions of SNP marker segregation patterns.
FIGURE 4
FIGURE 4
High-density sex-average genetic map of gardenia.
FIGURE 5
FIGURE 5
Repeatable QTLs for three dynamic phenotyping time points.
FIGURE 6
FIGURE 6
Potential pleiotropism QTLs.
FIGURE 7
FIGURE 7
Synteny analyses between the genetic map of gardenia and the genomes of Coffea arabica (A), Coffea canephora (B), and Ophiorrhiza pumila (C).
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