Genomic aspects of research involving polyploid plants

Abstract

Almost all extant plant species have doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been developed during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomic diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. Polyploids will be a focus of genomic research in the future as rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

First record of a natural hexaploid population for Valeriana officinalis: genome size is confirmed to be a suitable indicator of ploidy level in the species

“…However, it cannot be ruled out that the population might correspond to a tetraploid or an octoploid cytotype. Indeed, gain or loss of DNA coupled with a polyploidy event, a phenomenon documented in many plant groups (Yang et al 2011, and references therein), would explain the divergence in genome size between this Pyrenean population and other populations at same ploidy level. If this assumption is verified, genome size would not be as reliable a ploidy level indicator in the species as previously thought.…”

Perennial Grain Legume Domestication Phase I: Criteria for Candidate Species Selection

“…Ploidy of potential domesticates should also be taken into consideration because sequence assembly and genotyping is much cheaper and easier in diploids than at higher ploidy levels [135]. While some molecular approaches involving allopolyploids with disomic inheritance may be similar in complexity to those performed in diploids, autopolyploids require complex approaches for marker/sequence polymorphism detection and dosage estimation [135,136].…”

“…While some molecular approaches involving allopolyploids with disomic inheritance may be similar in complexity to those performed in diploids, autopolyploids require complex approaches for marker/sequence polymorphism detection and dosage estimation [135,136]. Finally, classical breeding approaches in autopolyploids require many more plants to be grown to identify unique segregates.…”

Breeding triploid plants: a review

“…Use of triploid plants for studying genome evolution and genome plausibility Yang et al (2011) has reviewed the genomic aspects of research involving polyploid plants. Triploid plant species provide some unique characteristics for genome studies.…”