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Identification of a Sidwf1 gene controlling short internode length trait in the sesame dwarf mutant dw607

  • Hongmei Miao
  • Chun Li
  • Yinghui Duan
  • Libin Wei
  • Ming Ju
  • Haiyang ZhangEmail author
Original Article
  • 44 Downloads

Abstract

Key message

SiDWF1 encodes a gibberellin receptor GID1B-like protein controlling the internode length and plant height in sesame.

Abstract

Sesame is a high-height crop. Here we systematically analyzed the morphological and genetic characters of the sesame dwarf mutant dw607 (dwf1 type). The plant height and the internode length of dw607 significantly declined, while the thousand seed weight (TSW) significantly increased (P < 0.01). The cell size of stem parenchyma and pith tissue reduced, and vascular bundle cells and parenchyma tissue arranged much tighter in the dwarf mutant. Based on the cross-population association mapping of a RIL population of the cross ‘dw607 (dwf1) × 15N41 (wt type),’ the target interval linked to the short internode length was located on C9.scaffold2 of SiChr.4 in sesame. We further screened the 58 variants using the genomic variant data of 824 germplasm and BSA DNA pools and determined the target gene Sidwf1. The SNP mutation of C1057 to T1057 resulted in the amino acid change of P150 (proline) to S150 (serine) in SiDWF1. SiDWF1 gene allele is 1,638 bp and encodes a gibberellin receptor GID1B-like protein. Transcription profile assay reflected that Sidwf1 is highly expressed in leaf, stem, bud, and capsule tissues. The dynamic variation in endogenous GA3 content in dw607 and the wild type was also monitored in this study. The results revealed the molecular genetic mechanism of the internode length and plant height trait in sesame for the first time. The findings supply the theoretical and material basis for developing the marker-assisted selection (MAS) breeding in sesame.

Abbreviations

ABA

Abscisic acid

BR

Brassinosteroid

BSA

Bulked segregant analysis

DAS

Days after sowing

ELISA

Enzyme-linked immunosorbent assay

EMS

Ethyl methanesulfonate

Ep

Epidermis

FAA

Formalin–glacial acetic acid–alcohol

GAs

Gibberellins

GID1

Gibberellin-insensitive dwarf 1

GLM

General linear model

GWAS

Genome-wide association studies

IAA

Indole-3-acetic acid

InDel

Insertion–deletion

LG

Linkage group

JA

Jasmonate

KEGG

Kyoto Encyclopedia of Genes and Genomes

MAS

Marker-assisted selection

NGS

Next-generation sequencing technology

NR

Non-redundant

PC

Parenchyma cell

PE

Paired end

Pi

Pith

qRT-PCR

Quantitative real-time PCR

QTL

Quantitative trait loci

RIL

Recombinant inbred line

SNP

Single-nucleotide polymorphism

TSW

Thousand seed weight

VC

Vascular bundle cells

Notes

Acknowledgements

This work was supported by the Key Laboratory of Specific Oilseed Crops Genomics of Henan Province. This work was financially supported by the earmarked fund for China Agriculture Research System (CARS-14), the Plan for Scientific Innovation Talent of Henan Province (184200510002), the Key Project of Science and Technology in Henan Province (151100111200), the Henan Province Specific Professor Position Program (SPPP2016), the Distinguished Professor Program of Institutions of Higher Learning in Henan Province (DPPIHL2017), the Innovation Scientists and Technicians Troop Construction Projects of Henan Province (ISTTCPHP2016), the Henan Natural Science Foundation (162300410159), and the International Cooperation and Exchanges Project of Henan Province (182102410040).

Author contribution

ZH conceived the technical route and guided the manuscript for publishing. MH guided the experiments, performed the data analysis, and drafted the manuscript. LC and DY conducted the main data analysis and experiments. WL and JM performed the genetic experiments and participated in result validation. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

122_2019_3441_MOESM1_ESM.xlsx (21.4 mb)
Supplementary Table 1 Growth profile comparison of dw607 and Yuzhi11. * Data are collected at Yuanyang experimental station in 2013; Supplementary Table 2 Variant information of the candidate interval controlling the short internode length trait in sesame; Supplementary Table 3 Variants information of 824 sesame germplasm accessions in target region; Supplementary Table 4 Information of candidate variants screened using genome resequencing data of 824 sesame germplasm accessions; Supplementary Table 5 Genome re-sequencing information of the BSA pools for internode length trait. a: The genome coverage is calculated based on the sesame genome size of 354 Mb estimated by K-mer (Zhang et al. 2013); Supplementary Table 6 Information of the five candidate variants for short internode length trait in sesame; Supplementary Table 7 Primer pair information of the SNP marker design of Sidwf1 gene alleles; Supplementary Table 8 Primer pair information of the cDNA and DNA sequences of SiDWF1 Supplementary file1 (XLSX 21888 kb)
122_2019_3441_MOESM2_ESM.pdf (533 kb)
Supplementary Figure 1 Comparison of plant height of dw607 and Yuzhi 11 during cycle life. Data are collected at Yuanyang experimental station in 2013; Supplementary Figure 2 Amplification validation of the SiSNPdwf1 marker using the test population and germplasm accessions. M: DNA marker; Lane 1–10: F2-3 individuals with short internode length trait (dwf1 type); Lane 11–20: F2-3 individuals with normal internode length trait (wt); Lane 21–40: 20 sesame accessions with normal internode length trait (wt); Supplementary Figure 3 Dynamic content variation of GA3, IAA, ABA, BR and ZR in shoot tip, root tip, and leaf of dw607 and Yuzhi11. a-c: Dynamic variation of GA3 content in shoot tip, root tip, and leaf of dw607 and Yuzhi11, respectively; d-f: Dynamic variation of IAA content in shoot tip, root tip, and leaf of dw607 and Yuzhi11, respectively; g-i: indicate the dynamic variation of ABA content in shoot tip, root tip, and leaf of dw607 and Yuzhi11, respectively; j-l: Dynamic variation of BR content in shoot tip, root tip, and leaf of dw607 and Yuzhi11, respectively Supplementary file2 (PDF 532 kb)

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Copyright information

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

Authors and Affiliations

  • Hongmei Miao
    • 1
  • Chun Li
    • 1
  • Yinghui Duan
    • 1
  • Libin Wei
    • 1
  • Ming Ju
    • 1
  • Haiyang Zhang
    • 1
    Email author
  1. 1.Henan Sesame Research CenterHenan Academy of Agricultural SciencesZhengzhouPeople’s Republic of China

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