Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium)

Abstract

Background: Reactive oxygen species (ROS) play a prominent role in signal transduction and cellular homeostasis in plants. However, imbalances between generation and elimination of ROS can give rise to oxidative stress in growing cells. Because ROS are important to cell growth, ROS modulation could be responsive to natural or human-mediated selection pressure in plants. To study the evolution of oxidative stress related genes in a single plant cell, we conducted comparative expression profiling analyses of the elongated seed trichomes ("fibers") of cotton (Gossypium), using a phylogenetic approach.

Results: We measured expression changes during diploid progenitor species divergence, allopolyploid formation and parallel domestication of diploid and allopolyploid species, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes in progenitor diploid species revealed significant up-regulation of ROS scavenging and potential signaling processes in domesticated G. arboreum. Similarly, in two independently domesticated allopolyploid species (G. barbadense and G. hirsutum) antioxidant genes were substantially up-regulated in comparison to antecedent wild forms. In contrast, analyses of three wild allopolyploid species indicate that genomic merger and ancient allopolyploid formation had no significant influences on regulation of ROS related genes. Remarkably, many of the ROS-related processes diagnosed as possible targets of selection were shared among diploid and allopolyploid cultigens, but involved different sets of antioxidant genes.

Conclusion: Our data suggests that parallel human selection for enhanced fiber growth in several geographically widely dispersed species of domesticated cotton resulted in similar and overlapping metabolic transformations of the manner in which cellular redox levels have become modulated.

Figure 1

Evolutionary history of diploid and allotetraploid cotton (Gossypium). Phylogeny of the genus is shown, with the history of repeated domestication at both the diploid (n = 13) and polyploid (n = 26) levels. The ancestral A- and D-genome diploids are inferred to have diverged from a common ancestor ~5–10 million years ago, prior to genomic merger in a common polyploid nucleus ~1–2 million years ago [32]. The newly evolved allopolyploid lineage subsequently diversified into five species (three used for microarray analysis are shown). Two allotetraploid species, G. hirsutum (source of 'upland cotton') and G. barbadense (source of 'Pima cotton'), and the diploid species G. arboreum were domesticated by humans within the past ~7000 years [35,36]. In the present study, we used models of the two progenitor diploids, G. arboreum (A-genome) and G. raimondii (D-genome), and both wild and domesticated forms of G. hirsutum and G. barbadense. We also included G. tomentosum, a wild allopolyploid from Hawaii. A representative image of a single seed at maturation is also shown for each species, with attached trichomes ("cotton fiber") with average fiber length (G. raimondii = 1.6 cm; G. arboreum = 3.0 cm; wild G. hirsutum = 2.0 cm; domesticated G. hirsutum = 3.9 cm; wild G. barbadense = 2.4 cm; domesticated G. barbadense = 4.3 cm; G. tomentosum = 1.2 cm) (modified from Applequist et al. [31]. Arrows denote microarray comparisons between species, with graphs designating the number of differentially up-regulated genes (P < 0.05 and FDR < 0.01) in each species, using the same color codes as in the seed image outlines.

Figure 2

Protein blot analysis from wild and domesticated diploid and polyploid species. It is to show levels of thylakoid bound and cytosolic ascorbate peroxidase (tylAPX and cytAPX), Cu/Zn-Superoxide dismutase (CSD) and HSP70 proteins in 2 dpa fiber extracts. All experiments were repeated twice and representative results are shown.

Figure 3

Venn diagrams of gene expression evolution in allopolyploid cotton. The numbers indicate genes classified as up-regulated in any wild polyploid species in comparison to the mid-parent values (MPV; estimated from a 1:1 RNA mix from the diploids G. arboreum and G. raimondii). Intersections denote genes shared by two or more of the three wild forms of the allopolyploids (wild G. hirsutum, wild G. barbadense and G. tomentosum).

Figure 4

Differential gene expression patterns for some ROS-related genes. These genes are differentially up-regulated in G. arboreum and the domesticated polyploids in contrast to their relative wild relatives or ancestors. Each point on the polygons represents a gene and the scale corresponds to relative expression levels in the diploid model progenitor genomes (G. arboreum and G. raimondii) and the wild and domesticated forms of: (a) G. hirsutum; and (b) G. barbadense.