Functional genomics of intraspecific variation in carbon and phosphorus kinetics in Daphnia

Abstract

Understanding how the genome interacts with the environment to produce a diversity of phenotypes is a central challenge in biology. However, we know little about how traits involved in nutrient processing interact with key ecological parameters, such as the supply of mineral nutrients, particularly in animals. The framework of ecological stoichiometry uses information on the content of key elements such as carbon (C) and phosphorus (P) in individuals to predict the success of species. Nevertheless, intraspecific variation in content and the underlying mechanisms that generate such variation has been poorly explored. We studied two genotypes (G1 and G2) of Daphnia pulex that exhibit striking genotype × environment (G × E) interaction in response to shifts in dietary stoichiometry (C:P). G1 had higher fitness under C:P ∼ 100 diet, while G2 performed better in C:P ∼ 800. Dual (14) C/(33) P radiotracer assays show that G1 was more efficient in C processing, while G2 was more efficient in P use. Microarrays revealed that after 3 days of incubation, the genotypes differentially expressed ∼ 25% (7,224) of the total genes on the array under C:P ∼ 100 diet, and ∼ 30% (8,880) of genes under C:P ∼ 800. These results indicate large differences in C and P use between two coexisting genotypes. Importantly, such physiological differences can arise via differential expression of the genome due to alterations in dietary stoichiometry. Basic frameworks such as ecological stoichiometry enable integration of physiological and transcriptomic data, and represent initial steps toward understanding the interplay between fundamental ecological parameters such as nutrient supply and important evolutionary processes such as G × E interactions.

Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS)

“…It has also been reported that phosphorus supply drives rapid turnover of membrane phospholipids in phytoplankton30. Particularly, in Daphnia it has been shown that under low quality food (i.e., high carbon – C to low phosphorus – P ratio: C:P), this organism can maintain P-homeostasis by reducing C-uptake and/or increasing P-retention, which is in agreement with stoichiometric theory31. Additionally, it has been suggested (and assessed) that the role of organismal C:P ratios may be functionally related to the structural and copy number variation of ribosomal-RNA genes16.…”

“…Additionally, it has been suggested (and assessed) that the role of organismal C:P ratios may be functionally related to the structural and copy number variation of ribosomal-RNA genes16. Recent studies have reported large differences in gene expression levels under different P-diets in Daphnia at the intra-specific level1731. These previous studies have found hundreds of differentially expressed genes in a comparison between genotypes run under low and high P environmental conditions.…”

Interactive effects of dietary phosphorus and iron on Daphnia life history

“…b). This decrease in retention efficiency in D. pulex under limitation is surprising, considering that previous work has found that, for certain genotypes, P limitation yields an increase in nutrient retention (Roy Chowdhury et al ). However, studies have also found that D. pulex has significantly increased electron transport chain activity compared with D. pulicaria (Simcic and Brancelj ).…”

Sex-specific nutrient use and preferential allocation of resources to a sexually selected trait in Hyalella amphipods

“…Nevertheless, radiolabeling has been shown to be a reliable indicator of the physiological kinetics of both C and P (e.g. DeMott et al, 1998;He and Wang, 2007;Roy Chowdhury et al, 2014).…”