Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Genetics, Development and Cell Biology

First Advisor

Patrick S. Schnable


Whole-genome array-based comparative genomic hybridization (aCGH) was used to study structural variation between two elite maize inbred lines, B73 and Mo17. Several hundred Copy Number Variants (CNVs) as well as several thousands of Present Absent Variants (PAVs) were discovered. This high level of structural variation among haplotypes is unprecedented among higher eukaryotes. Haplotype-specific PAVs that encompass hundreds of single-copy, expressed genes may contribute to heterosis and the extraordinary phenotypic diversity of this important crop. aCGH can be also used for genotyping complex genomes, such as that of maize. Approximately 200,000 oligonucleotide probes whose hybridization signals exhibit significant differences between B73 and Mo17 were used to genotype two Recombinant Inbred Lines (RILs) derived from a cross between these two inbreds. The resulting genotyping scores are highly consistent with marker data from previous experiments generated using alternative technologies. A careful analysis of the aCGH data from the two RILs relative to their inbred parents revealed the presence of several hundred apparently de novo CNVs. Further analyses revealed that these recurrent apparently de novo CNVs were caused by the segregation of single-copy homologous sequences that are located in non-allelic positions in the two parental inbreds. These changes in genome content of RILs were validated via both PCR and whole genome shotgun sequencing experiments.

Copyright Owner

Kai Ying



File Format


File Size

99 pages


Appendix_A.PDF (101 kB)
Appendix A

Appendix_B.PDF (2149 kB)
Appendix B