Mapping Floral Genetic Architecture in Prunus mume, an Ornamental Woody Plant

Abstract

Floral traits are both evolutionarily and economically relevant for ornamental plants. However, their underlying genetic architecture, especially in woody ornamental plants, is still poorly understood. We perform mapping experiments aimed at identifying specific quantitative trait loci (QTLs) that control the size, shape, architecture, color, and timing of flowers in mei (Prunus mume). We find that the narrow region of chromosome 1 (5-15 Mb) contains a number of floral QTLs. Most QTLs detected from this mapping study are annotated to candidate genes that regulate various biological functions toward the floral formation. We identify strong pleiotropic control on different aspects of flower morphology (including shape, petal number, pistil number, petal color, and calyx color) and flower timing, but find different genetic systems that mediate whether a flower produces pistils and how many pistils a flower produces. We find that many floral QTLs display pleiotropic effects on shoot length growth but shoot radial growth, implicating a possible association of floral display with light capture. We conduct a transcriptomic study to characterize the genomic signature of floral QTLs expressed in mei. Our mapping results about the genetic control of floral features make it promising to select superior varieties for mei carrying flowers of ornamental value.

Keywords: Prunus mume (mei); QTL; floral trait; genetic mapping; pleiotropy; transcriptomic analysis.

FIGURE 1

Differences in floral attributes between two parents, Liuban (female) and Huang LvE (male).

FIGURE 2

Identification of quantitative trait loci (QTLs) for flower size throughout the mei genome in a full-sib family of mei (L-2015 population) derived from Liuban (female) and Huang Lve (male) cultivars. (A) The Manhattan plots of significance test for floral diameter (upper panel) and pedicel length (lower panel). Solid and dashed lines represent the genome-wide critical thresholds of testcross and intercross markers, respectively, determined from 1,000 permutation tests. Single nucleotide polymorphisms (SNPs) annotated with biological functions are indicated. (B) Mean values (±SE) of different genotypes at two representative QTLs detected for floral diameter (upper panel) and pedicel length (lower panel).

FIGURE 3

Identification of QTLs for flower shape throughout the mei genome in a full-sib family of mei (L-2015 population) derived from Liuban (female) and Huang Lve (male) cultivars. (A) The Manhattan plot of a significance test. Solid and dashed lines represent the genome-wide critical thresholds of testcross and intercross markers, respectively, determined from 1,000 permutation tests. SNPs annotated with biological functions are indicated. (B) Distribution percentages of shallow bowl-shaped flowers (red) and dish-shaped flowers (yellow) for the same genotype at two representative QTLs detected.

FIGURE 4

Identification of QTLs for floral architecture throughout the mei genome in a full-sib family of mei (L-2015 population) derived from Liuban (female) and Huang Lve (male) cultivars. (A) The Manhattan plots of significance test for petal number (upper panel) and blossom bud number (lower panel). Solid and dashed lines represent the genome-wide critical thresholds of testcross and intercross markers, respectively, determined from 1,000 permutation tests. SNPs annotated with biological functions are indicated. (B) Mean values (±SE) of different genotypes at two representative QTLs detected for petal number (upper panel) and distribution percentages of progeny with a single blossom bud (red) and multiple blossom buds (yellow) at two representative QTLs detected (lower panel). (C) The Manhattan plots of significance test for pistil number (upper panel) and the occurrence of pistils (lower panel). (D) The Venn diagram of QTL numbers for the number of petals, the number of pistils, and the occurrence of pistils.

FIGURE 5

Identification of QTLs for petal color and flower timing throughout the mei genome in a full-sib family of mei (L-2015 population) derived from Liuban (female) and Huang Lve (male) cultivars. (A) The Manhattan plots of significance test for petal color (upper panel) and flower timing (lower panel). Solid and dashed lines represent the genome-wide critical thresholds of testcross and intercross markers, respectively, determined from 1,000 permutation tests. SNPs annotated with biological functions are indicated. (B) Distribution percentages of yellow flowers (red) and white flowers (yellow) for the same genotype at two representative QTLs detected for petal color (upper panel) and distribution percentages of early- (red), middle- (yellow), and late-blossomed flowers (green) for the same genotype at two representative QTLs detected for flower timing.

FIGURE 6

Identification of QTLs for shoot growth throughout the mei genome in a full-sib family of mei (L-2015 population) derived from Liuban (female) and Huang Lve (male) cultivars. (A) The Manhattan plots of significance test for shoot length growth (upper panel) and shoot diameter growth (lower panel). Solid and dashed lines represent the genome-wide critical thresholds of testcross and intercross markers, respectively, determined from 1,000 permutation tests. SNPs annotated with biological functions are indicated. (B) The Venn diagram of QTL numbers for shoot length, floral color, floral shape, floral architecture, and floral timing.

FIGURE 7

Transcriptomic signature of QTLs for petal color (A) and petal number (B) in the F-2014 population. (Upper panel) Differently expressed genes from genotype CAa to CAA for petal color and from genotype Baa to BAA for petal number. (Lower panel) The Gene Ontology (GO)-based gene enrichment analysis for genotypic differences for petal color and petal number.

FIGURE 8

Transcriptomic signature of QTLs for petal diameter. Genomic comparison is made in terms of differentiated genes and their function between the two homozygotes (A), between one homozygote and heterozygote (B), and between the alternative homozygote and homozygote (C).