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.

Keywords: gene expression; genome doubling; microarrays; molecular markers; next generation sequencing; transcriptomics.

Figure 1

Phenotypic variation between diploids and tetraploids in Solanum commersonii (a, b) and in Medicago sativa (c, d). A diploid (2n = 2× = 24) clone of S. commersonii was subjected to oryzaline treatment, an antimitotic drug commonly employed to induce chromosome doubling in plants. The autotetraploid (2n = 4× = 48) genotype displayed larger size at both whole plant (a) and leaf (b) level. (c) Diploid M. sativa subsp. coerulea (2n = 2× = 16, left) and its cultivated tetraploid counterpart, M. sativa subsp. sativa (2n = 4× = 32, right) differ clearly for flower size. (d) Leaves of diploid (upper row) and tetraploid (bottom row) plants obtained from crossing two diploid M. sativa plants producing both n and 2n gametes. Leaves are the best qualitative component of forage: tetraploid M. sativa has larger leaves and is cultivated.