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Genome-wide investigation of the MADS gene family and dehulling genes in tartary buckwheat (Fagopyrum tataricum)

  • Moyang Liu
  • Qiankun Fu
  • Zhaotang Ma
  • Wenjun Sun
  • Li Huang
  • Qi Wu
  • Zizhong Tang
  • Tongliang Bu
  • Chenglei Li
  • Hui Chen
Original Article
  • 68 Downloads

Abstract

Main conclusion

Genome-wide identification, expression analysis and potential functional characterization of previously uncharacterized MADS family of tartary buckwheat, emphasized the importance of this gene family in plant growth and development.

The MADS transcription factor is a key regulatory factor in the development of most plants. The MADS gene in plants controls all aspects of tissue and organ growth and reproduction and can be used to regulate plant seed cracking. However, there has been little research on the MADS genes of tartary buckwheat (Fagopyrum tataricum), which is an important edible and medicinal crop. The recently published whole genome sequence of tartary buckwheat allows us to study the tissue and expression profiles of the MADS gene in tartary buckwheat at a genome-wide level. In this study, 65 MADS genes of tartary buckwheat were identified and renamed according to the chromosomal distribution of the FtMADS genes. Here, we provide a complete overview of the gene structure, gene expression, genomic mapping, protein motif organization, and phylogenetic relationships of each member of the gene family. According to the phylogenetic relationship of MADS genes, the transcription factor family was divided into two subfamilies, the M subfamily (28 genes) and the MIKC subfamily (37 genes). The results showed that the FtMADS genes belonged to related sister pairs and the chromosomal map showed that the replication of FtMADSs was related to the replication of chromosome blocks. In different tissues and at different fruit development stages, the FtMADS genes obtained by real-time quantitative PCR (RT-qPCR) showed obvious expression patterns. A comprehensive analysis of the MADS genes in tartary buckwheat was conducted. Through systematic analysis, the potential genes that may regulate the growth and development of tartary buckwheat and the genes that may regulate the easy dehulling of tartary buckwheat fruit were screened, which laid a solid foundation for improving the quality of tartary buckwheat.

Keywords

Tartary buckwheat MADS genes Genome-wide Fruit development Expression patterns Easy dehulling 

Abbreviations

AUX

Auxin

ARF

Auxin response factor

cDNA

ComplementaryDNA

CDS

Coding sequence length

Ft

Fagopyrum tataricum

PI

Isoelectric point

PF

Pfam

GSDS

Gene structure display server

HMM

Hidden Markov model

LSD

Least significant difference

MCScanX

Multiple collinear scanning toolkits

MW

Molecular weight

NJ

Neighbor-joining

RT-qPCR

Real-time quantitative polymerase chain reaction

SL

Sequence length

TBGP

Tartary buckwheat genome project

Notes

Acknowledgments

We are very grateful to the editor and reviewers for critically evaluating the manuscript and providing constructive comments for its improvement.

Funding

This research was supported by the National Natural Science Foundation of China (31500289), and the National Key R&D Program of China (2018YFD1000706).

Compliance with ethical standards

Conflict of interest

We certify that there is no conflict of interest with any financial organization regarding the materials discussed in the manuscript.

Supplementary material

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Supplementary material 1 (XLS 128 kb)
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Supplementary material 2 (XLS 37 kb)
425_2019_3089_MOESM3_ESM.xls (56 kb)
Supplementary material 3 (XLS 55 kb)
425_2019_3089_MOESM4_ESM.xls (33 kb)
Supplementary material 4 (XLS 33 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.College of Life ScienceSichuan Agricultural UniversityYa’anChina

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