domestication, crop species undergo intense selective pressures that alter their genomes. The process of selection during domestication has largely focused on core traits that have come to define domesticated species. In seed or grain crops, these hallmark traits include increases in seed size, a reduction in natural seed dispersal, reduced lateral branching, and an annual life cycle. The genes that code for these traits have been elucidated in some species, such as the maize tb1 gene, which controls for lateral branching, using classical genetic techniques as well as genomics. However, traditional Mendelian genetics which examines inheritance patterns on an individual trait basis is limited to traits or phenotypes that cleanly segregate into distinct classes. Genomics is able to overcome this limitation through the comparison of the genomes of individuals exhibiting a trait or phenotype of interest to a reference genome which enables the identification differences between the two genomes such as single-nucleotide polymorphisms (SNP), the movement of transposable elements (or retrotransposons) or deletions, among other genetic changes. Coding DNA Genomics offers insight into coding DNA as well as noncoding DNA. By comparing the sequence of a previously isolated section of chromosome 8 in rice between fragrant and non-fragrant varietals researchers were able to determine their genetic difference. The aromatic and fragrant rices, including basmati and jasmine are derived from an ancestral rice domesticate that suffered a deletion in exon 7 and as a result sequence coding for betaine aldehyde dehydrogenase (BADH2) was altered. Noncoding DNA However, looking solely at genes, or coding DNA, can be ineffective when examining certain traits or studying the evolution of a species during the domestication process. Genes that are vital for cellular process are often highly conserved and mutations at these locations can prove fatal. Areas of the genome that are noncoding can be prone to much higher mutation rates. Because of this, these noncoding genes provide vital information when studying the divergence of wild and domestic species. Since core genes are conserved between and among species, examining DNA sequences for these genes in multiple individuals of a species may be unable to provide much information on the diversity present in a population or species that is young. The estimated age of domesticated animal and plant species tends to be less than 10,000 years, which on an evolutionary timescale, is relatively short. Because of this, highly variable noncoding DNA, such as microsatellites, that mutate frequently,