Abstract
Copy number variants (CNVs) are genomic rearrangements resulting from gains or losses of DNA segments. Typically, the term refers to rearrangements of sequences larger than 1 kb. This type of polymorphism has recently been shown to be a key contributor to intra-species genetic variation, along with single-nucleotide polymorphisms and short insertion-deletion polymorphisms. Over the last decade, a growing number of studies have highlighted the importance of copy number variation (CNV) as a factor affecting human phenotype and individual CNVs have been linked to risks for severe diseases. In plants, the exploration of the extent and role of CNV is still just beginning. Initial genomic analyses indicate that CNVs are prevalent in plants and have greatly affected plant genome evolution. Many CNV events have been observed in outcrossing and autogamous species. CNVs are usually found on all chromosomes, with CNV hotspots interspersed with regions of very low genetic variation. Although CNV is mainly associated with intergenic regions, many CNVs encompass protein-coding genes. The collected data suggest that CNV mainly affects the members of large families of functionally redundant genes. Thus, the effects of individual CNV events on phenotype are usually modest. Nevertheless, there are many cases in which CNVs for specific genes have been linked to important traits such as flowering time, plant height and resistance to biotic and abiotic stress. Recent reports suggest that CNVs may form rapidly in response to stress.
Highlights
It was assumed that single-nucleotide polymorphisms (SNPs) and small insertion-deletion polymorphisms were the main types of DNA alterations underlying intra-species genomic variation
nonallelic homologous recombination (NAHR) usually involves low-copy repeats (LCRs)—DNA segments larger than 1 kb that are generated during ancient duplication events
Depending on the LCR location, NAHR can lead to intrachromatid, interchromatid or interchromosomal rearrangements
Summary
It was assumed that single-nucleotide polymorphisms (SNPs) and small insertion-deletion polymorphisms (indels) were the main types of DNA alterations underlying intra-species genomic variation. The ability of the assay to detect a particular region in the tested genome depends on its homology to the array probes For this reason, CGH is always biased toward the detection of deletions (relative to the reference genome sequence), whereas DNA segments present in the tested genome but not in the reference remain undetected due to a lack of representative probes. Analysis of relative increases and decreases in sequence coverage by short reads (readdepth method) provides information about duplications and deletions It allows for calculating the absolute copy numbers of genomic segments. Due to the CGH array design, the detected variants more often indicated decrease in copy number or complete deletion in the tested genome, relative to the B73 reference. The CGH method has been applied to CNV detection in several model plant species and— to the maize studies—has provided mainly examples of gene copy loss in the tested genomes.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have