Degree Type


Date of Award


Degree Name

Master of Science


Genetics, Development and Cell Biology

First Advisor

Patrick S. Schnable


Maize (Zea mays subsp mays) was domesticated from teosinte (Z. mays subsp parviglumis) in southern Mexico between 6,000 and 9,000 years ago (Matsuoka et al., 2002; Sluyter and Dominguez, 2006). Both domestication and crop improvement involved selection of specific alleles at genes, resulting in reduced genetic diversity in the genes controlling key morphological and agronomic traits. This is termed the "genetic bottleneck". We coupled the approaches of molecular population genetics with reverse genetics to associate genes with phenotypes. More than 16,000 primer pairs were subjected to gel and temperature gradient capillary electrophoresis (TGCE)-based assays. This screen identified 73 genes that contain zero sequence diversity (ZSD) fragments. They are monomorphic among 59 diverse maize lines, but polymorphic among 9 teosinte lines. Therefore, they are candidate domestication-related genes. Using 3,000 Mutator-insertion lines, a large-scaled screen for Mu transposon insertions in domestication candidate genes was performed. Our data supports the bottleneck model and at least 0.5% of maize genes are under selection during maize domestication based on our test. Phenotypic analysis of plants homozygous for the Mu-insertion alleles of the domestication candidate genes are underway.

We also detected two other interesting features in the maize genome: First, the existence of nearly identical paralogs (NIPs) and "orphan" genes. Our data suggested that at least ~1% of maize genes are members of a NIP family, defined as paralogous genes that exhibit >=98% identity (Emrich et al. 2007). Members of a NIP family are expressed and in some instances, members of a given NIP family exhibit differential patterns of gene expression. NIPs may have played important roles during the evolution and domestication of maize. NIPs expression data supports subfunctionalization model for duplicated genes. Besides, NIPs were also detected in other maize inbred lines. Second, ~400 "orphan" transcripts were captured via 454 sequencing of cDNA, isolated using laser capture microdissection (LCM) from functionally important shoot apical meristems (SAMs). The expression of 27 randomly picked cDNA was validated via RT-PCR. Expression of 20 of these SAM-expressed genes (~74%) were not detected in meristem-rich immature ears.

454 sequenced cDNAs, isolated by LCM from B73 and Mo17 SAM, enabled us to detect gene-associated SNPs, which escaped previous tests.

Copyright Owner

Li Li



Date Available


File Format


File Size

98 pages