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Transcriptome analysis of flowering genes in mango (Mangifera indica L.) in relation to floral malformation

  • Ashok Yadav
  • Pawan K. Jayaswal
  • K. Venkat Raman
  • Bhupinder Singh
  • Nagendra K. Singh
  • K. UshaEmail author
Original Article
  • 39 Downloads

Abstract

Flowering is a complicated developmental process of physiological and morphological stages under the control of a number of external signals and internal factors. Floral malformation occurring during flower development stage is serious constraint having crippling effect on mango flowering and production leading to heavy economic losses. In mango there is lack of information about the gene expression profile during flower development. We therefore performed transcriptome analysis of Mangifera indica cultivar Amrapalli, by isolating total RNA from different stages of bud development in healthy and malformed tissues. The next generation sequencing were performed using 2 × 150 PE chemistry on the Illumina NextSeq platform resulting in 20.31, 20.77, 20.32, 27.92 and 18.59 million PE reads in MB-1, MB-2, MB-3, HB-1 and HB-2 stages respectively. Higher differential expressions copy numbers of seven flowering genes (MYB30, TPL, bHLH, FTIP1, CDKC2, CPK33, and ATH1) were observed in both the healthybud and panicle development stages as compared to malformed bud development stages. Among the other differentially expressed pattern of flowering genes in six possible combinations, the highly upregulated genes are UBP12, EFS, AGL8, AGL14, AGL20, AGL24, KIN10, MYB30, SUS2, FTIP1, CCT and LDL2 and down regulated genes were like TIL1, TIC, DCL3, GA20OX3, CCT, AP1, AGL6, AGL8, MYB30, AGL8, GCT and GA3OX1. The data set provides information on transcripts putatively associated with embryonic flower, earlier flowering, flowering time control, terminal flower and mads-box protein in healthy and malformed tissues. Out of the observed differentially expressed genes, the transcript profiles of GA20OX3, AGL24 and LDL2, the key genes regulating floral transition and differentiation, were validated through qRT-PCR. Our study provides a resource for exploring the complex molecular mechanisms in flower development and malformations in mango.

Keywords

Differentially expressed genes (DEG’s) Flowering Mango Malformation Transcriptome Metabolic pathways 

Abbreviations

AGL

Agamous-Like

AP2

Apetala2

ATH1

Arabidopsis thaliana Homeobox Gene 1

bHLH

Basic Helix–Loop–Helix

CCT

CO, CO-like and Timing of Cab

CDF1

Cycling DOF Factor 1

CDKC2

Cyclin-Dependent Kinase

CLF

Curly Leaf

COP1

Constitutive Photomorphogenic 1

CPK6

Calcium Dependent Protein Kinase 6

CRY2

Cryptochrome 2

CUL3

Cullin 3A

DCL3

Dicer-Like 3

DEGs

Differentially expressed genes

EFS

Early flowering in short days

ELF3

Early Flowering 3

EMF2

Embryonic Flower 2

FC

Fold change

FY

Flowering time control protein FY

FKF1

Flavin-Binding Kelch Repeat F box Protein

FLK

Flowering locus KH domain

FTIP1

FT-Interacting Protein 1

GA20ox3

Gibberellin20-Oxidase 3

GA2-ox

GA2-oxidase

GA3-ox

GA2-oxidase

GCT

Grand Central

GI

Gigantea

GID1A

Gibberellin Insensitive Dwarf1A

GID1B

GA Insensitive Dwarf 1B

GID1C

GA Insensitive Dwarf 1C

HB-1

Healthy bud stage 1

HB16

Homeobox Protein 16

HB-2

Healthy bud stage 2

HUB1

Histone Mono-Ubiquitination 1

INO80

Inositol Requiring 80

JMJ14

Jumonji 14

KIN10

Kinase 10

LDL2

Lysine Specific Demethylase Like 1

LHY

Late Elongated Hypocotyl

LFY

Leafy

LRB1

Light-Response BTB 1

LWD2

Light-Regulated WD 2

MB-1

Single swollen malformed bud stage 1

MB-2

Multiple malformed bud stage 2

MB-3

Multiple malformed panicle development stage 3

MBD9

Methyl-CPG-Binding Domain 9

NF-YB1

Nuclear Factor Y Subunit B1

NUC

Nut-Cracker

PIF

Phytochrome-Interacting Factor

PIL6

Phytochrome-Interacting Factor Like

PRR3

Pseudo-Response Regulator 3

RAP2.7

Related to AP2.7

REF6

Relative to Early Flowering

RFI2

Red and Far-Red Insensitive 2

RVE2

Reveille 2

SDG25

Set Domain Protein 25

SPL5

Squamosa Promoter Binding Protein-LIKE 5

SPL9

Squamosa Promoter Binding Protein-Like 9

SUS2

Sucrose Synthase 2

SUS4

Sucrose Synthase 4

SUVR5

SU(VAR)3-9-Related Protein 5

SVP

Short Vegetative Phase

TEM1

Tempranillo 1

TIC

Time for Coffee

TIL1

Tilted 1

TPL

Topless

TPS1

Trehalose-6-Phosphate Synthase 1

UBC1

Ubiquitin Carrier Protein 1

UBP12

Ubiquitin-Specific Protease 12

UGT

UDP-Glucosyl Transferase

VOZ1

Vascular Plant one Zinc Finger Protein 1

Notes

Acknowledgements

The authors thank Director, ICAR—Indian Agricultural Research Institute, New Delhi for financial support provided for conducting the studies.

Authors Contributions

UK, BS performed the experiment and manuscript drafting. PKJ and AY carried out bioinformatics analysis of functional annotation, GO, KEGG pathway analysis, TF’s analysis, DEG’s analysis and approval of final version of manuscript was done by NKS, UK, PKJ, and NT. All authors have read and approved the final manuscript. VR and BS had performed validation using qRT-PCR.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

13562_2019_541_MOESM1_ESM.xlsx (35 kb)
Supplementary material 1 (XLSX 34 kb)
13562_2019_541_MOESM2_ESM.docx (31 kb)
Supplementary material 2 (DOCX 31 kb)
13562_2019_541_MOESM3_ESM.pptx (534 kb)
Supplementary material 3 (PPTX 534 kb)

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Copyright information

© Society for Plant Biochemistry and Biotechnology 2019

Authors and Affiliations

  1. 1.Division of Fruits and Horticultural TechnologyIARINew DelhiIndia
  2. 2.National Research Centre for Plant BiotechnologyNew DelhiIndia
  3. 3.Centre for Environment Science and Climate Resilient AgricultureIARINew DelhiIndia

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