Structural Variants

A structural variant is a difference in two individuals DNA that is larger than just a few nucleotides. These include, inversions, large deletions or insertions, translocations etc.

Structural variants can have significant effects on an organisms genetic makeup, therefore, they have great potential to alter an organisms phenotype. 

Map Analysis for Structural Variation

Optical mapping allows us to have a broader picture of DNA than nucleotide sequence will give us. When you are working with nucleotide sequence, it’s like being in the forest, when you are working with optical maps, its like you are surveying the forest from a helicopter.

Optical mapping is a technique for constructing ordered, genome-wide, high-resolution restriction maps from single, stained molecules of DNA, called "optical maps". By mapping the location of restriction enzyme sites (or sequence motifs aka nick sites) along the unknown DNA of an organism, the spectrum of resulting DNA fragments collectively serve as a unique "fingerprint" or "barcode" for that sequence.  These pieces can then be assembled into a whole genome map.

Once you have the genome map for a wild-type individual. You can map non-wild type individuals genomes and can compare the two to each other. You can see if the two have any major differences, or structural variants. This technique can also be used to understand how speciation may have occurred in the past. You can map and compare many different species of a genus and see what major differences the DNA has there. (what we are doing with Cotton)

The reason why bio nano technology is different is that it requires no fragmenting or amplifying of DNA before reading it on the machine. This allows for higher, SV, CNV detection and more accurately sized gaps in your scaffolds. The sequence of events to make an optical map are as follows. Create a denovo assembly of all the reads creating contigs. Then align the in silico digested contigs to the consensus optical map. last, join neighboring contig sequences to create supercontigs on the basis of their location.  

The following info is from a paper published in Giga science by Haibao Tang, Eric Lyons, and Christopher Town entitled Optical mapping in comparative genomics.

[Local adaptation of plant varieties is reflected in traits, such as flower development, photo-sensitivity, disease resistance and stress tolerance. All of these traits have been shown to be associated with SVs in various taxa. Some SVs may have been under intense natural and/or artificial selection. For example, the PROG1 gene was found to be deleted in several rice species, leading to prostrate rather than erect growth that differentiates rice species. Due to the limitations of sequencing-based approaches, the impact of SVs on the diversification of plant varieties may still be under-estimated, but could be clarified via optical mapping.

Some important agronomic traits are directly caused by structural variations which could be studied with a whole genome association framework across varieties or diversity panels. For example, the SUN gene that controls elongated fruit shape of tomato results from long-terminal repeat (LTR) retrotransposon-mediated gene duplication. Current studies mostly focus on single nucleotide polymorphisms (SNPs) or short indels as markers of association genetics, but have largely ignored the large SVs which often have significant genomic and functional impact. With the recent decrease in cost, we could conduct optical mapping on genetic mutants and re-sequencing lines to directly identify those critical SVs that are linked to the varietal differences.

In addition to agronomic traits, a wide range of studies in plants, including domestication, polyploidy, population history and natural selection could benefit from optical mapping. Long et al.uncovered large structural variants that are associated with selective sweeps in Arabidopsis lines from Sweden, based on a suite of methods from ‘manual’ detection of breakpoints to de novoassembly. They acknowledged that many polymorphisms may be complex and difficult to resolve using short-read sequencing data. Re-sequencing studies have also revealed that SVs in the maize genome are particularly enriched in regions important for domestication, although many candidate SVs remain to be validated using an independent approach, such as optical mapping.

The application of optical mapping could reveal structural changes following polyploidy events in plants that might be difficult to study using other techniques. Studies show that homeologous exchanges (HEs) occur frequently between subgenomes inside polyploid genomes and often involve large chromosomal segments. This was studied in the Brassica napus genome, an allotetraploid merged from two diploid Brassica genomes. Each HE was characterized by the replacement of a particular region with a duplicated copy from another subgenome. Specific HEs have contributed to the deletions of genes responsible for glucosinolate catabolism, probably selected as a result of intense breeding. While read mapping provided the initial clues about HEs, the precise locations and boundaries of HEs across a set of lines were difficult to assess based on read mapping, thereby requiring a tedious validation procedure based on PCR and targeted sequencing in the study reported. The direct application of optical mapping could therefore help pinpoint the precise breakpoint and further validate segmental loss and exchanges among homeologous chromosomes, which are important aspects of polyploid genome evolution.]

The study of structural variants can be taken one step further. It can be use to look at structural variants role in evolution of a genus or species. You can compare the maps of many different species of a genus to see if they differ at all. Especially, you could look for structural variations between them. You can then analyze the similarities, and differences between them and see if they give any clues to the evolutionary history of that genus. This is what we are doing with our multiple species of cotton.