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. 2022 Feb 28;12(1):3346.
doi: 10.1038/s41598-022-07318-w.

High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids

Chia-Chi Hsu #  1   2 , Shu-Yun Chen #  1   3 , Shang-Yi Chiu  1 , Cheng-Yuan Lai  3 , Pei-Han Lai  1 , Tariq Shehzad  4 , Wen-Luan Wu  1 , Wen-Huei Chen  5 , Andrew H Paterson  4 , Hong-Hwa Chen  6   7
Affiliations

High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids

Chia-Chi Hsu et al. Sci Rep. .

Abstract

Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker-trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Distribution of flower aesthetic traits in P. Intermedia (a–l). For flower: a, e, I, m; for sepal: b, f, j, n; for petal: c, g, k, o; for lip: d, h, l, p. The aesthetic traits of width (a–d), length (e–h), and area (i–l). Frequency distribution of flower color-related traits in P. Intermedia (m–p). The color-related traits are magenta area in petal (m), magenta color in petal (n), red color in lip (o), and yellow color in lip (p).
Figure 2
Figure 2
Correlation coefficients for all floral aesthetic traits. The yellow and green colors represent the positive and negative correlation coefficients estimated by Pearson correlation. *,**,***P < 0.05, 0.01, 0.001, respectively.
Figure 3
Figure 3
The genetic linkage map for Phalaenopsis that contains 19 potential homologous groups (HGs). The 19 HGs were assembled from 27 linkage groups (LGs) based on P. equestris BAC-end sequences (BESs).
Figure 4
Figure 4
Genome-wide association study (GWAS) of lip yellow color. (a) Manhattan plot of lip yellow color, (b) difference in lip yellow color level by single nucleotide polymorphism (SNP) type at position S5-24984925, (c) SNP type at position S5-23606179, (d) SNP type at position S5-10776122, (e) SNP type at position S9-14147427. N indicates the individual number of this SNPs.
Figure 5
Figure 5
GWAS of lip magenta color. (a) Manhattan plot of lip magenta color, (b) difference in lip Magenta color level by SNP type at position S5-43867748, (c) SNP type at position S5-46455357. N indicates the individual number of this SNPs.
Figure 6
Figure 6
GWAS of petal magenta color. (a) Manhattan plot of petal magenta color, (b) difference in petal magenta color level by SNP type at position S5-46455357, (c) SNP type at position S5-45647571, (d) SNP type at position S5-43867748, (e) SNP type at position S5-45345022. N indicates the individual number of this SNPs.
Figure 7
Figure 7
GWAS of petal magenta area. (a) Manhattan plot of petal magenta area, (b) difference in petal magenta area by SNP type at position S2-195281745, (c) SNP type at position S5-43867748, (d) SNP type at position S5-46455357, (e) SNP type at position S5-45345022, (f) SNP type at position S5-43813578. N indicates the individual number of this SNP.
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