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.
","abstract_html":"<p>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 <em>amylose extender 1 (ae1)</em> and the polymorphism responsible for this QTL was additive (semi-dominant). Located within the QTL interval is <em>starch branching enzyme 1 (sbe1)</em>, which makes it a candidate gene. In order to test whether a polymorphism in <em>sbe1</em> is the source of this QTL, we crossed a plant homozygous for <em>ae1</em> and <em>sbe1-Mu</em> onto a GEMS-0067/H99ae hybrid to test whether this allele would eliminate additivity in the progeny. The<em> sbe1-Mu</em> allele is null and acts as a simple recessive against a functional <em>Sbe1</em> allele. PCR markers were used to distinguish homozygous wild <em>(Sbe1-G/Sbe1-G or Sbe1- H/Sbe1-H)</em>, heterozygous <em>(Sbe1-G/ sbe1-Mu or Sbe1-H/ sbe1-Mu)</em> and homozygous mutant <em>(sbe1-Mu/ sbe1-Mu)</em>. 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 <em>sbe1-Mu</em> eliminated additivity and dominance relationship was revealed. This establishes that allelic differences of <em>sbe1</em> between H99ae and GEMS-0067 as the source of the QTL. The gene for <em>starch branching enzyme 1 (sbe1)</em> 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 <em>sbe1</em> 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 <em>starch branching enzyme 1 (sbe1)</em>, 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<em> sbe1</em> 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 <em>sbe1</em> revealed that <em>sbe1</em> in a high amylose line, GEMS-007, is ancestral as it lies together in group with teosintes.</p>","abstract_has_math":false,"creators":["Gyawali, Abiskar"],"institution":null,"degree_name":"Master of Science (MS)","degree_level":"Thesis - Open Access","degree_discipline":"Biology and Microbiology","degree_department":null,"school":null,"contributors":["Donald Auger"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-01-01T08:00:00Z","date_published":"2016-01-01T08:00:00Z","updated_at":"2026-07-24T04:28:30Z","subjects":["amylopectin","amylose","endosperm","starch","starch branching enzyme","Biology"],"languages":["en"],"rights":[],"rights_urls":["http://rightsstatements.org/vocab/InC/1.0/"],"identifier_entries":[]},"links":{"outbound_url":"https://openprairie.sdstate.edu/etd/1037","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Donald Auger"]},{"key":"dc:creator","label":"Author","values":["Gyawali, Abiskar"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2016-08-16T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biology and Microbiology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis - Open Access"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science (MS)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["amylopectin","amylose","endosperm","starch","starch branching enzyme","Biology"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["http://rightsstatements.org/vocab/InC/1.0/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://openprairie.sdstate.edu/etd/1037"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["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.
"]},{"key":"dc:title","label":"Title","values":["Analysis of Starch Branching Enzyme 1 (SBE1) Gene in Maize"]}]}],"canonical_facts":{"dc:contributor":["Donald Auger"],"dc:creator":["Gyawali, Abiskar"],"dc:date.available":["2016-08-16T07:00:00Z"],"dc:description.abstract":["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.
"],"dc:identifier":["https://openprairie.sdstate.edu/etd/1037"],"dc:language":["en"],"dc:rights":["http://rightsstatements.org/vocab/InC/1.0/"],"dc:subject":["amylopectin","amylose","endosperm","starch","starch branching enzyme","Biology"],"dc:title":["Analysis of Starch Branching Enzyme 1 (SBE1) Gene in Maize"],"thesis:degree_discipline":["Biology and Microbiology"],"thesis:degree_level":["Thesis - Open Access"],"thesis:degree_name":["Master of Science (MS)"]},"updated_at":"2026-07-24T04:28:30Z"}