Author's School

Graduate School of Arts & Sciences

Author's Department/Program

Biology and Biomedical Sciences: Evolution, Ecology and Population Biology


English (en)

Date of Award

January 2009

Degree Type


Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

Barbara Schaal


The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized biosynthesis pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication and subsequent crop improvement. In this study, I have examined six key genes in the rice endosperm starch biosynthesis pathway to investigate the evolution of this pathway before rice domestication and during rice domestication. Oryza rufipogon is the wild ancestor of cultivated rice: Oryza sativa). Oryza sativa has five variety groups: aus, indica, tropical japonica, temperate japonica and aromatic. I have sequenced five genes: shrunken2, Sh2; brittle2, Bt2; waxy, Wx; starch synthase IIa, SsIIa; starch branching enzyme IIb, SbeIIb; and isoamylase1, Iso1) in 70 O. rufipogon accessions, 99 cultivated rice accessions: aus, 10; indica, 34; tropical japonica, 26; temperate japonica, 21; aromatic rice, 8) and two accessions of two closely related species, O. barthii, O. meridionalis. The published sequence data for Wx in rice are included in the analysis as well. The difficulty of detecting selection is often caused by the complex demographic history of a species. Genome-wide sequence data in a species would mainly reflect its demographic history. I have compared the pattern of nucleotide variation at each starch gene with published genome-wide sequence data and with a standard neutral model for detecting selection. Results show no evidence of deviations from neutrality at these six starch genes in O. rufipogon and no evidence of deviations from neutrality at four starch genes in O. sativa. Evidence of selection is observed at Wx in tropical japonica and temperate japonica, and at Wx and SbeIIb in aromatic rice. Starch quality is one of the most important agronomic traits in rice. Starch synthase IIa: SsIIa) has been mapped as a gene which contributes to the starch quality variation in cultivated rice, O. sativa. Within the gene, three nonsysnonymous mutations in the exon 8 region were shown to affect its enzyme activity in Escherichia coli. In order to identify the mutation in SsIIa exon 8 region that is responsible for starch quality variation in rice, I have sequenced SSIIa exon 8 region and recorded the alkali spreading score in 57 O. rufipogon accessions and 151 cultivated rice accessions: aus, 8; indica, 51; tropical japonica, 55; temperate japonica, 29; aromatic, 8). Starch alkali spreading score is used to quantify rice endosperm starch quality and has been shown to be significantly associated with SsIIa enzyme activity in rice. Both a general linear model and nested clade analysis were used to detect an association between the three nonsynonymous mutations in SSIIa exon 8 and the alkali spreading score. In order to avoid the effect of population structure on the association analysis, both association analyses are conducted within each rice variety group. Among the previously identified nonsynonymous mutations, my results show strong evidence of association at one nonsynonymous mutation: SNP3, see Fig 2 of Chapter 2), and evidence of no association at another nonsynonymous mutation. Tests of association for the other nonsynonymous mutation are inconclusive with current samples and will require further investigation. This dissertation reveals the relative role of evolutionary forces in shaping the variation pattern of six starch genes in O. sativa and its wild ancestor, O. rufipogon. It also reveals an association between a nonsynonymous mutation in SSIIa exon 8 and rice endosperm starch quality.



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