Microarray analysis reveals differential gene expression in hybrid sunflower species

Abstract

This paper describes the creation of a cDNA microarray for annual sunflowers and its use to elucidate patterns of gene expression in Helianthus annuus, Helianthus petiolaris, and the homoploid hybrid species Helianthus deserticola. The array comprises 3743 ESTs (expressed sequence tags) representing approximately 2897 unique genes. It has an average clone/EST identity rate of 91%, is applicable across species boundaries within the annual sunflowers, and shows patterns of gene expression that are highly reproducible according to real-time RT-PCR (reverse transcriptionpolymerase chain reaction) results. Overall, 12.8% of genes on the array showed statistically significant differential expression across the three species. Helianthus deserticola displayed transgressive, or extreme, expression for 58 genes, with roughly equal numbers exhibiting up-or down-regulation relative to both parental species. Transport-related proteins were strongly overrepresented among the transgressively expressed genes, which makes functional sense given the extreme desert floor habitat of H. deserticola. The potential adaptive value of differential gene expression was evaluated for five genes in two populations of early generation (BC 2 ) hybrids between the parental species grown in the H. deserticola habitat. One gene (a G protein-coupled receptor) had a significant association with fitness and maps close to a QTL controlling traits that may be adaptive in the desert habitat.

Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm

“…Moreover, as for the WLM þ EUR allotetraploid, they observed that most of the genes with non-additive expression were part of those displaying significant differentiation of parental expression. Downregulation of interspecific hybrid genes was also observed for sunflower (Lai et al, 2006). However, at intraspecific level in maize, Swanson-Wagner et al (2006) observed that only 22% of the differentially regulated genes exhibited non-additive modes of gene expression.…”

“…However, the nucleolar dominance of A. arenosa over A. thaliana (Pikaard, 1999) is associated with the overall suppression of A. thaliana phenotype in new allotetraploids and in natural A. suecica (Wang et al, 2006b). Results regarding H. deserticola suggest that nonadditive gene regulation and particularly transgressive expression of transport-related proteins should be related with its high adaptability to water-stress conditions (Lai et al, 2006).…”

“…A microarray study of Senecio allopolyploid and hybrid species showed that the expression of genes with no particular functional category was overly affected, although genes involved in floral or pollen development were slightly over-represented (Hegarty et al, 2006). Similarly, a microarray study of the homoploid hybrid species Helianthus deserticola showed differential regulation of genes in various functional categories in the hybrid (Lai et al, 2006). A microarray study of Arabidopsis neo-polyploids also showed differential expression of genes in a variety of functional categories (Wang et al, 2006b).…”

Evaluating the role of natural selection in the evolution of gene regulation

“…Genome-wide measurements have revealed high rates of genetic variation in gene expression (typically 410% of genes) in humans (Enard et al, 2002;Rockman and Wray, 2002;Bray et al, 2003;Lo et al, 2003;Whitney et al, 2003;Morley et al, 2004;Pastinen et al, 2004;Radich et al, 2004), mice (Cowles et al, 2002;Schadt et al, 2003;Shockley and Churchill, 2006), fish (Oleksiak et al, 2002(Oleksiak et al, , 2005, flies (Jin et al, 2001;Wayne and McIntyre, 2002;Meiklejohn et al, 2003;Rifkin et al, 2003;Nuzhdin et al, 2004;Ranz et al, 2004), yeast (Cavalieri et al, 2000;Brem et al, 2002;Townsend et al, 2003;Yvert et al, 2003;Fay et al, 2004), plants (Kirst et al, 2005;Vuylsteke et al, 2005;Lai et al, 2006) and bacteria (Le et al, 2005). Patterns of expression divergence have also been compared between sexes (Jin et al, 2001;Ranz et al, 2003;Gibson et al, 2004), across developmental stages (Rifkin et al, 2003), among tissue types (Enard et al, 2002;Whitehead and Crawford, 2005;Khaitovich et al, 2005a, b) and over different environments (Fay et al, 2004;Landry et al, 2006).…”

Ecological genomics in Daphnia: stress responses and environmental sex determination

“…This situation is starting to change owing to increased ecological study of these model organisms. Second, molecular genetic and genomic studies are initiated using organisms that have wellunderstood ecologies and evolutionary histories (Crawford, 2001;Strauss and Martin, 2004;Lai et al, 2006), of which the water flea, Daphnia, is one. Here, we outline the progress in the use of Daphnia as a model in evolutionary and ecological functional genomics.…”