title: Molecular tools for exploring polyploid genomes in plants.
abstract: Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.
authors.affiliation: Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Aversano
authors.affiliation: Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy.
authors.forename: Maria Raffaella
authors.initials: MR
authors.lastname: Ercolano
authors.affiliation: Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy.
authors.forename: Immacolata
authors.initials: I
authors.lastname: Caruso
authors.affiliation: Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Fasano
authors.affiliation: Department of Applied Biology, University of Perugia, Borgo XX Giugno 74, Perugia 06121, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Rosellini
authors.affiliation: Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy.
authors.forename: Domenico
authors.initials: D
authors.lastname: Carputo
mesh_terms: D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D010641:Phenotype; D010944:Plants / Q000235:genetics*; D011123:Polyploidy