Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)


Biology and Microbiology

First Advisor

Donald Auger


amylopectin, amylose, endosperm, starch, starch branching enzyme


A previous study revealed a quantitative trait locus (QTL) in maize on the short arm of chromosome 5 (5S) for endosperm amylose content. In that original study, both low and high amylose parental lines, H99ae and GEMS-0067 respectively, were homozygous recessive for amylose extender 1 (ae1) and the polymorphism responsible for this QTL was additive (semi-dominant). Located within the QTL interval is starch branching enzyme 1 (sbe1), which makes it a candidate gene. In order to test whether a polymorphism in sbe1 is the source of this QTL, we crossed a plant homozygous for ae1 and sbe1-Mu onto a GEMS-0067/H99ae hybrid to test whether this allele would eliminate additivity in the progeny. The sbe1-Mu allele is null and acts as a simple recessive against a functional Sbe1 allele. PCR markers were used to distinguish homozygous wild (Sbe1-G/Sbe1-G or Sbe1- H/Sbe1-H), heterozygous (Sbe1-G/ sbe1-Mu or Sbe1-H/ sbe1-Mu) and homozygous mutant (sbe1-Mu/ sbe1-Mu). Furthermore Alu1 restriction digestion was done to distinguish GEMS-0067 from H99ae. A dual wavelength iodine-binding assay was used to determine relative amylose/amylopectin content from these segregated populations. The amylose assay showed that the presence of sbe1-Mu eliminated additivity and dominance relationship was revealed. This establishes that allelic differences of sbe1 between H99ae and GEMS-0067 as the source of the QTL. The gene for starch branching enzyme 1 (sbe1) in a high amylose line, GEMS-007, would translate into a protein with six amino acid polymorphisms relative to a lower amylose line, H99ae. A review of the published sbe1 sequence data indicates that most varieties of maize are remarkably uniform, i.e., they have the same amino acid usage as found in H99ae. In Zea mays L., we studied the phylogenetic and selection analysis of starch branching enzyme 1 (sbe1), a candidate gene for high amylose QTL. The main objective of this study was to know whether or not sbe1 was subjected to selection. We compared 2797 bp of the sbe1 coding region of 17 accessions of maize and teosinte. Very low proportion of single nucleotide polymorphisms were observed relative to other genes in maize. Comparison of synonymous and nonsynonymous polymorphism revealed the effect of purifying selection in the whole species. Phylogenetic analysis of sbe1 revealed that sbe1 in a high amylose line, GEMS-007, is ancestral as it lies together in group with teosintes.

Library of Congress Subject Headings

Corn -- Genetics

Gene mapping

Starch -- Synthesis




Includes bibliographical references (pages 37-41)



Number of Pages



South Dakota State University


Copyright © 2016 Abiskar Gyawali

Included in

Biology Commons