Cataloguing Plant Genome Structural Variations

Structural variation (SV) is a type of genetic variation identified through the comparison of genome structures which often have direct and significant associations with phenotypic variations. Building on the next-generation sequencing (NGS) technologies, research on plant structural variations are gaining momentum and have revolutionized our view on the functional impact of the ‘hidden’ diversity that were largely understudied before. Herein, we first describe the current state of plant genomic SV research based on NGS and in particular focus on the biological insights gained from the large-scale identification of various types of plant SVs. Specific examples are chosen to demonstrate the genetic basis for phenotype diversity in model plant and major agricultural crops. Additionally, development of new genomic mapping technologies, including optical mapping and long read sequencing, as well as improved computational algorithms associated with these technologies have helped to pinpoint the exact nature and location of genomic SVs with much better resolution and precision. Future direction of plant research on SVs should focus on the population level to build a comprehensive catalogue of SVs, leading to full assessment of their impact on biological diversity. Introduction Structural variations (SVs) are a collection of complex genomic DNA mutations that differentiate among individuals in a certain population. In contrast to single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels), SVs typically consist of DNA changes that are relatively long in size. The initial detection of SVs before the advent of the sequencing era is often based on detection of large scale chromosomal changes from karyotypic observation under microscope, including abnormal number of chromosomes such as aneuploidies ( Jacobs et al., 1959; Edwards et al., 1960), chromosomal rearrangement (Bobrow et al., 1971) and copy number variations (CNVs) (Bailey and Eichler 2006). Karyotypic mutations larger than 3 Mb in size can often be observed with in situ hybridization. Building on the next-generation sequencing (NGS) technology, we are moving towards a new phase of variant discovery that focus on identification of SVs with their boundaries mapped at single-base resolution. Extensive studies on the human genome have revealed that SVs play important roles in human health (Spielmann and Klopocki 2013; Weischenfeldt et al., 2013). For example, Alzheimer’s disease (AD) is a chronic neurodegenerative disease that usually badly affects the elder with symptoms such as problems with Curr. Issues Mol. Biol. Vol. 27