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Functional & Integrative Genomics

, Volume 18, Issue 6, pp 613–625 | Cite as

Starch content differences between two sweet potato accessions are associated with specific changes in gene expression

  • Songtao Yang
  • Xiaojing Liu
  • Shuai Qiao
  • Wenfang Tan
  • Ming Li
  • Junyan Feng
  • Cong Zhang
  • Xiang Kang
  • Tianbao Huang
  • Youlin Zhu
  • Lan Yang
  • Dong Wang
Original Article

Abstract

Sweet potato (Ipomoea batatas (L.) Lam.) is one of the most important root crops in the world. Initial formation and development of storage roots (SRs) are key factors affecting its yields. In order to study the molecular mechanism and regulatory networks of the SRs development process, we have analyzed root transcriptomes between the high and low starch content sweet potato accessions at three different developmental stages. In this study, we assembled 46,840 unigenes using Illumina paired-end sequencing reads and identified differentially expressed genes (DEGs) between two accessions. The numbers of DEGs were increased with the development of SRs, indicating that the difference between two accessions is enlarging with the maturation. DEGs were mainly enriched in starch biosynthesis, plant hormones regulatory, and genetic information processing pathways. Then, expression patterns of DEGs that are most significant and starch biosynthesis related were validated using qRT-PCR. Our results provide valuable resources to future study on molecular mechanisms of SRs development and candidate genes for starch content improvement in sweet potato.

Keywords

Gene regulation RNA-Seq Storage root Starch content Sweet potato 

Notes

Author contributions

Experiments were designed by STY, LY, and DW. XJL and STY conducted experiments, and all authors analyzed the data. LY and DW wrote the manuscript, and all authors edited the manuscript. All authors read and approved the final manuscript.

Funding information

This work was funded by the China Agriculture Research System (CARS-10-B5), National Science Foundation of China (31401077), Sichuan Breeding Cooperation Project (2016NYZ0032), Sichuan Financial Innovation Project (2016ZYPZ-012), and Natural Science Foundation of Jiangxi Province (20171ACB20001).

Supplementary material

10142_2018_611_Fig11_ESM.gif (15 kb)
Fig. S1

PCA analysis was performed to show overall gene expression similarity among different RNA-sequencing data. (GIF 15 kb)

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High resolution image (TIFF 1314 kb)
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Fig. S2

Correlation between RNA-seq and qRT-PCR results for 12 DEGs. The log2 value of FPKM extracted for RNA-seq results and the qRT-PCR results obtained from the comparative CT method were displayed. (GIF 12 kb)

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High resolution image (TIFF 590 kb)
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Fig. S3

Validation of relative expression levels of DEGs by qRT-PCR which identified using the recent public reference genome. (GIF 11 kb)

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High resolution image (TIF 76 kb)
10142_2018_611_MOESM4_ESM.xlsx (11 kb)
Table S1 General information about RNA sequence libraries used in this study. (XLSX 10 kb)
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Table S2 Functional annotation of Ipomoea batatas unigenes. (XLSX 10726 kb)
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Table S3 Similarity of unigenes sequences between Ipomoea batatas and other species. (XLSX 33 kb)
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Table S4 Kyoto Encyclopedia of Genes and Genomes classification of Ipomoea batatas unigenes. (XLSX 68 kb)
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Table S5 Functional annotation and transcriptional levels of DEGs. (XLSX 2636 kb)
10142_2018_611_MOESM9_ESM.xlsx (20 kb)
Table S6 DEGs enriched by GO and KEGG analyses. (XLSX 20 kb)
10142_2018_611_MOESM10_ESM.xlsx (12 kb)
Table S7 Primers used in qRT-PCR. (XLSX 12 kb)
10142_2018_611_MOESM11_ESM.xlsx (10 kb)
Table S8 Statistics of reads mapping rate for each sample to the recent public reference genome. (XLSX 10 kb)
10142_2018_611_MOESM12_ESM.xlsx (2.2 mb)
Table S9 DEGs between the high and low starch content sweetpotato accessions using the recent public reference genome. (XLSX 2281 kb)
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Table S10 DEGs enriched by GO and KEGG for the new analyses using recent public reference genome. (XLSX 19 kb)
10142_2018_611_MOESM14_ESM.xlsx (3.1 mb)
Table S11 Comparison of our de novo assembled unigenes with the gene sets in the recent public reference genome. (XLSX 3209 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Crop Research InstituteSichuan Academy of Agricultural SciencesChengduChina
  2. 2.Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life ScienceNanchang UniversityNanchangChina
  3. 3.Institute of Biotechnology and Nuclear TechnologySichuan Academy of Agricultural SciencesChengduChina
  4. 4.Jiangxi Institute of Red SoilNanchangChina

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