Academic journal article Genetics

Gene-Expression Novelty in Allopolyploid Cotton: A Proteomic Perspective

Academic journal article Genetics

Gene-Expression Novelty in Allopolyploid Cotton: A Proteomic Perspective

Article excerpt

POLYPLOIDY is now recognized as a fundamental process in plant evolution, and all flowering plant genomes are known to have experienced several or more rounds of genome doubling in their evolutionary history (Jiao et al. 2011). Compared to the intraspecific genome duplication of autopolyploidy, the formation of allopolyploids entails the merging and doubling of diverged genomes, which has been proposed as an important mechanism of functional and phenotypic evolution driven by structural and regulatory divergence between parental genomes and the attendant duplication of genetic materials (Wendel 2000; Wendel and Doyle 2004; Comai 2005; Doyle et al. 2008; Leitch and Leitch 2008; Soltis and Soltis 2009; Finigan et al. 2012; Madlung 2013; Madlung andWendel 2013; Ainouche and Wendel 2014).

A large and growing body of literature has demonstrated that allopolyploidy is accompanied by a series of non- Mendelian interactions and processes, including chromosomal rearrangement and variation (Ramsey and Schemske 2002; Szadkowski et al. 2010; Xiong et al. 2011; Chester et al. 2012), DNA sequence elimination (Shaked et al. 2001; Ozkan et al. 2003; Blanc and Wolfe 2004; Han et al. 2005; Skalicka et al. 2005; Anssour et al. 2009; Buggs et al. 2009; Tate et al. 2009; Schnable et al. 2011), recombination between homeologous chromosomes (Gaeta et al. 2007; Szadkowski et al. 2010) and genes (Salmon et al. 2010; Flagel et al. 2012), epigenetic modification (Madlung et al. 2002; Salmon et al. 2005; Bottley et al. 2006; Chen 2007; Gaeta et al. 2007; Kovarik et al. 2008; Ni et al. 2009; Bottley 2014), and differences in small RNA regulation (Kovarik et al. 2008; Ha et al. 2009; Kenan-Eichler et al. 2011; Ng et al. 2011; Woodhouse et al. 2014). With respect to gene expression, a common observation is that the increase of genetic information in allopolyploids leads to different transcriptomic repatterning relative to parental species (Grover et al. 2012a). In particular, nonadditive expression has been studied in allopolyploid species from the perspectives of expression-level dominance, transgressive expression, and homoelog expression bias (reviewed in Yoo et al. 2014). The first two phenomena describe the total expression of a homeolog pair and up-/down-regulation relative to the diploid parents, whereas homeolog expression bias quantifies cases of unequal contribution of two homeologs to total gene expression (Grover et al. 2012a; Yoo et al. 2014).

The advent and subsequent widespread use of microarray and next-generation sequencing technologies have led to a rapid increase in exploration of gene expression at the transcriptional level (Adams et al. 2003; Hegarty et al. 2005; Bottley et al. 2006; Wang et al. 2006; Gaeta et al. 2007; Flagel et al. 2008; Hovav et al. 2008; Chaudhary et al. 2009; Rapp et al. 2009; Buggs et al. 2010a; Buggs et al. 2010b; Chague et al. 2010; Chelaifa et al. 2010; Flagel and Wendel 2010; Koh et al. 2010; Bardil et al. 2011; Chelaifa et al. 2013; Yoo et al. 2013). However, the transcriptome itself is insufficient for understanding the end products of gene expression and phenotypic outcomes (Rose et al. 2004; Thelen and Peck 2007; Karr 2008; Vogel and Marcotte 2012; Ponnala et al. 2014). Because proteins are the major catalysts of cellular activities, the phenotype of an organism arguably may be more directly related to protein abundance and function than to transcriptional abundance (Karr 2008; Diz et al. 2012). Thus, comparative proteomics offers an important perspective on evolutionary processes.

Only a few studies have examined the outcome of gene expression at the protein level in allopolyploids with respect to their diploid progenitors. Using a two-dimensional gel electrophoresis (2-DE) approach or isobaric tags for relative and absolute quantitation (iTRAQ), interspecific comparisons of protein presence and abundance have been performed in wheat (Bahrman and Thiellement 1987; Islam et al. 2003), Brassica napus (Albertin et al. …

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