Genetic architecture of microhabitat adaptation traits in a pair of sympatric Primulina species

Figures & data

Figure 1. Fully expanded leaves of P. depressa (1), P. danxiaensis (2), the F₁ hybrid (3) and some individuals of the F₂ population (4–8).

Table 1. Means and standard deviations for the four studied traits in P. depressa and P. danxiaensis and F₁ hybrids, and phenotypic values range of F₂ population.

Trait	P. depressa population (n = 10)	P. danxiaenesis population (n = 9)	Paternal individual	Maternal individual	F1 (n = 3)	F2 phenotypic range	t-test (two-sided)
Maximum leaf area (LA; cm2)	55.76 ± 10.76	23.56 ± 7.30	55.76 ± 10.76	23.56 ± 7.30	43.37 ± 7.45	6.01-51.72	t = 3.1824 p < 0.05
Leaf length-width ratio (LWR)	2.47 ± 0.032	0.83 ± 0.025	2.47 ± 0.032	0.83 ± 0.025	0.96 ± 0.10	0.75-1.44	t= −14.884 p < 0.001
Specific leaf area (SLA; cm^2/g)	241.78 ± 35.99	414.06 ± 37.84	241.78 ± 35.99	414.06 ± 37.84	284.31 ± 4.99	223.07-532.79	t= −2.9769 p < 0.05
Flowering time (FT; days)	257.30 ± 13.64	312.60 ± 12.70	257.30 ± 13.64	312.60 ± 12.70	170	229-326	t= −12.667 p < 0.05

Figure 2. Histograms of the four analyzed traits in the F₂ population. Phenotypic means for P. depressa, P. danxiaensis and F₁ hybrids are indicated with blue, red and orange arrows, respectively.

Figure 3. Correlations between and within the four traits (LA: maximum leaf area; LWR: leaf length-width ratio; SLA: specific leaf area; FT: flowering time) in the F₂ population. Scatterplots of all traits are given below the diagonal and Spearman’s correlation coefficients and associated significance are given above the diagonal.

Figure 4. Genome location of significant QTLs for four traits. Confidence intervals of the QTLs are illustrated on the right side of the linkage groups.

Figure 5. The phenotypic variance explained value of QTLs for four traits. LA: maximum leaf area; LWR: leaf length-width ratio; SLA: specific leaf area; FT: flowering time.

Table 2. Summary of significant epistatic interaction between QTLs.

Interacted loci ID	LOD	Var (%)	F value	p value	Significance level
LA02&LA10	2.677006	2.930819	2.700273	0.031979	*
LA03&LA04	2.552528	2.798692	2.570812	0.039315	*
LA06&LA07	2.983151	3.254096	3.020333	0.019114	*
LA08&LA10	2.408477	2.645293	2.421479	0.049819	*
LWR03&LWR05	3.208731	3.770538	3.257681	0.013011	*
LWR05&LWR06	2.585602	3.060950	2.605173	0.037222	*
SLA02&SLA08	2.440450	3.308638	2.545490	0.040930	*
SLA03&SLA09	2.757467	3.724322	2.887280	0.023689	*
SLA04&SLA08	2.502818	3.390668	2.612525	0.036788	*
FT01&FT06	3.025253	5.027619	3.217425	0.014197	*
FT01&FT07	2.649116	4.425249	2.802542	0.027583	*

Epistasis analysis among the identified QTLs was conducted with R/qtl. Only QTLs that had significant epistatic interactions are shown. Var (%), F value and p value represent percentage of variance explained, F statistics and F distribution, respectively.

*p < 0.05.

Figure 6. Proportion of phenotypic variation explained by all of the single QTLs and epistatic interactions. LA: maximum leaf area; LWR: leaf length-width ratio; SLA: specific leaf area; FT: flowering time.

Data availability statement

All the data and plant material are available from the first author (CF) upon reasonable request. Traits data for analysis are available at the FIGSHARE repository: Feng C, Feng C, Yang L, Kang M, Rausher M. qtlST script and phenotypic data. figshare. Dataset; 2019. https://doi.org/10.6084/m9.figshare.7270715.v3