Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.)
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Abstract
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.
Cite this as
2019. Genetic diversity, functional properties and expression analysis of NnSBE genes involved in starch synthesis of lotus (Nelumbo nucifera Gaertn.) PeerJ Preprints 7:e27689v1 https://doi.org/10.7287/peerj.preprints.27689v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Supplemental Information
The names and SNPs of 45 individual lotus of four clusters
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Fenglin Zhu conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Han Sun performed the experiments, approved the final draft.
Ying Diao authored or reviewed drafts of the paper, approved the final draft.
Xingwen Zheng contributed reagents/materials/analysis tools, approved the final draft.
Keqiang Xie contributed reagents/materials/analysis tools, approved the final draft.
Zhongli Hu conceived and designed the experiments, approved the final draft.
Data Deposition
The following information was supplied regarding data availability:
The data of SNP was provided in supplement 1.
The names of 45 individual which belong to four clusters of lotus. All SNPs of NnSBEⅢ was displaying in table.
Funding
This work was supported by the National Science and Technology Supporting Program (No. 2012BAD27B01). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
