Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole-genome duplication

Abstract

Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization. To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization. Hybridization played a major role in shaping the relative expression pattern of the neo-allopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility. In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.

Keywords: Capsella bursa-pastoris; gene expression; hybridization; neopolyploid lines; polyploidy.

Fig. 1

The even groups of synthetic or natural Capsella plants used in this study. Synthetic diploid hybrids, autotetraploids, and allotetraploids were generated with the diploid Capsella orientalis and Capsella grandiflora. Whole‐genome duplication (WGD) was induced by colchicine treatments. Capsella orientalis served as maternal plant in all interspecific crosses. Group abbreviations are highlighted in bold.

Fig. 2

Phenotypes of the seven plant groups. (a) Stem length. (b) Flowering time. (c) Estimated pollen grain number per flower, averaged between the two flowers of each individual. (d) The proportion of viable pollen grains, calculated by examining > 300 pollen grains per flower, and averaged between two flowers. (e) The number of normal and abnormal seeds in 10 fruits. Error bars show the group mean ± SE. (f) The proportion of normal seeds (normal seeds/total seeds). Individuals with < 10 fruits were excluded from the analysis. For boxplots and violin plots, sample size (number of examined individuals) is shown above the groups. When one‐way ANOVA and Tukey's HSD test were applied (plots a–c and number of normal seeds in plot e), group difference at a significance level of α < 0.05 is indicated by letters. Groups with the same letter are not significantly different. Within each box plot, the bold horizontal line represents the median value; box range means values within interquartile range (IQR) from first quartile (Q1) to third quartile (Q3); up and down whiskers indicate 1.5 IQR above the Q3 (Q3+1.5 IQR) and 1.5 IQR below the Q1 (Q1−1.5 IQR), separately; circles representative outliers.

Fig. 3

Transcriptome‐wide expression pattern visualized by multidimensional scaling (MDS) plots. The plots were made with (a) all samples, (b) only the flower samples, or (c) only the leaf samples. Genes with transcripts per million (TPM) > 2 in at least three samples were used for the analysis, and the expression levels were normalized with the trimmed mean of M‐values (TMM) method.

Fig. 4

Venn diagram analyses of nonadditively expressed genes in the three hybrid groups (F2, Allo‐d, and Allo‐h), compared with parental expression‐differential (PED) genes (Cg2–Co2 DEG). Both nonadditively expressed genes and PED genes were identified by differential expression analyses (fold‐change > 2, false discovery rate (FDR) < 0.05). Genes showing complete expression level dominance (ELD) or transgressive expression (TRE) in each group were considered as nonadditive gene expression and were compared in flowers (a) or leaves (b).

Fig. 5

Extremely expressed genes per individual. The number of extremely expressed genes (rank 1 or 42) was counted for each of the 42 individuals from the seven groups, using all the genes with count‐per‐million (CPM) > 1 in at least two samples (a, b), or only the genes which were not differentially expressed between the Co2 and Cg2 groups (c, d). Each dot represents one individual. Within each box plot, the bold horizontal line represents the median value; box range means values within interquartile range (IQR) from first quartile (Q1) to third quartile (Q3); up and down whiskers indicate 1.5 IQR above the Q3 (Q3+1.5 IQR) and 1.5 IQR below the Q1 (Q1−1.5 IQR), separately; circles representative outliers.

Fig. 6

Abundance of transposable elements (TE) in transcriptomes. The proportion of annotated RNA‐sequencing reads that were mapped to TE sequences (reads mapped to TEs/reads mapped to genes or TEs) was calculated for each individual and compared among the seven plant groups in flowers (a) and leaves (b). Each dot represents one individual. Within each box plot, the bold horizontal line represents the median value; box range means values within interquartile range (IQR) from first quartile (Q1) to third quartile (Q3); up and down whiskers indicate 1.5 IQR above the Q3 (Q3+1.5IQR) and 1.5 IQR below the Q1 (Q1−1.5 IQR), separately; circles representative outliers.