Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.)

Background. Starch branching enzyme (SBE) is one of the key enzymes in starch biosynthetic metabolism and determines the structure of amylopectin. Methods. Full length of SBE genes were cloned by reverse transcription PCR (RT-PCR) technology, and used neighbor-joining (NJ) tree for phylogenetic anal...

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Published inPeerJ preprints
Main Authors Zhu, Fenglin, Sun, Han, Diao, Ying, Zheng, Xingwen, Xie, Keqiang, Hu, Zhongli
Format Journal Article
LanguageEnglish
Published San Diego PeerJ, Inc 27.04.2019
Subjects
Affinity
Amylopectin
Amylose
Developmental stages
Domestication
Enzymatic activity
Enzymes
Genetic analysis
Genetic diversity
Isoenzymes
Isoforms
Nelumbo nucifera
Phylogenetics
Phylogeny
Polymerase chain reaction
Reverse transcription
Single-nucleotide polymorphism
Starch
Starch-branching enzymes
Ultrastructure
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Summary:Background. Starch branching enzyme (SBE) is one of the key enzymes in starch biosynthetic metabolism and determines the structure of amylopectin. Methods. Full length of SBE genes were cloned by reverse transcription PCR (RT-PCR) technology, and used neighbor-joining (NJ) tree for phylogenetic analysis. The single nucleotide polymorphisms (SNPs) were determined to assess the genetic polymorphisms and variation indexes between individuals and clusters. Quantitative real time PCR (qRT-PCR) was performed to analyse spatial and temporal expression of SBE genes. Effect of NnSBE genes on fine structure of amylopectin was explore by affinity and enzyme activity analysis of two isoforms in amylopectin and amylose. Results. In this study, two SBE family genes, NnSBEI and NnSBEIII were identified from lotus (Nelumbo nucifera Gaertn.). Phylogenetic analysis divided the NnSBEI into SBE family B and NnSBEIII was belong to SBE family A. The homozygous haplotype (AA GG GG AA GG) of NnSBEIII was observed in seed lotus. During the seed embryo development stage, NnSBEIII reached the peak in middle of development stage and while NnSBEI increased in mid-late developmental stage. The different affinity activity of two isozymes bind amylopectin and amylose assay indicated NnSBEI has higher activity and wider affinity. Discussion. This study showed that NnSBE genes received artificial selection during the process of cultivation and domestication in seed lotus especially. Furthermore, the expression pattern and affinity activity analysis indicated that NnSBE genes was related to chain length of amylopectin.
ISSN:2167-9843
DOI:10.7287/peerj.preprints.27689v1