Allelic genome structural variations in maize detected by array comparative genome hybridization

Abstract

DNA polymorphisms such as insertion/deletions and duplications affecting genome segments larger than 1 kb are known as copy-number variations (CNVs) or structural variations (SVs). They have been recently studied in animals and humans by using array-comparative genome hybridization (aCGH), and have been associated with several human diseases. Their presence and phenotypic effects in plants have not been investigated on a genomic scale, although individual structural variations affecting traits have been described. We used aCGH to investigate the presence of CNVs in maize by comparing the genome of 13 maize inbred lines to B73. Analysis of hybridization signal ratios of 60,472 60-mer oligonucleotide probes between inbreds in relation to their location in the reference genome (B73) allowed us to identify clusters of probes that deviated from the ratio expected for equal copy-numbers. We found CNVs distributed along the maize genome in all chromosome arms. They occur with appreciable frequency in different germplasm subgroups, suggesting ancient origin. Validation of several CNV regions showed both insertion/deletions and copy-number differences. The nature of CNVs detected suggests CNVs might have a considerable impact on plant phenotypes, including disease response and heterosis.

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

“…1A), which is present in 11 of 25 domesticated maize lines and 3 of 14 teosinte lines, and absent in other genotypes. This region was previously identified as present in B73 and absent in Mo17 (Springer et al 2009) as well as several other genotypes (Belo et al 2010). This insertion/deletion variant also segregates among teosinte individuals, suggesting that this large insertion/deletion is not a result of selection or inbreeding that has occurred during maize domestication or improvement.…”

“…For example, Wang and Dooner (2006) documented that only 25%-84% of bases within a ;100-kb region were shared among eight haplotypes. The frequency of CNV and PAV between the reference genome (B73) and a second genotype (Mo17) has been assayed using BAC libraries ) and comparative genomic hybridization (CGH) (Springer et al 2009;Belo et al 2010). These scans have identified hundreds of copy number variants as well as several thousand sequences present in the reference genome but absent in Mo17 (PAVs).…”

The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82

“…Collectively, these data suggest that the true number of PAV and rearranged genes between Wm82-SGC-01 and Wm82-ISU-01 may be substantially greater than the 25 genes we identified using the stringent criteria described above. Gene content differences in the form of PAV have been extensively documented in maize inbred line comparisons, and there is speculation that these may significantly contribute to maize phenotypic variation (Springer et al, 2009;Beló et al, 2010;Swanson-Wagner et al, 2010). Likewise, it will be critical to evaluate the extent and consequences of such structural variation and presence/absence gene variants in providing phenotypic plasticity in soybean lines and breeding populations.…”

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

“…Recent studies in maize (Zea mays) have explored the exceptionally high rates of SV between inbred accessions (Springer et al, 2009;Beló et al, 2010;SwansonWagner et al, 2010). The maize profile indicates that there are continuously high levels of SV between accessions throughout all 10 chromosomes, interspersed by relatively small regions of conservation thought to be regions of identity by descent.…”