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

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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.

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Change history

  • 22 January 2020

    Correction to: Journal of Plant Biochemistry and Biotechnology

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

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Acknowledgements

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

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Authors and Affiliations

  1. Division of Fruits and Horticultural Technology, IARI, New Delhi, India

    Ashok Yadav & K. Usha

  2. National Research Centre for Plant Biotechnology, New Delhi, India

    Pawan K. Jayaswal, K. Venkat Raman & Nagendra K. Singh

  3. Centre for Environment Science and Climate Resilient Agriculture, IARI, New Delhi, India

    Bhupinder Singh

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  1. Ashok Yadav
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  2. Pawan K. Jayaswal
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  3. K. Venkat Raman
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  4. Bhupinder Singh
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  5. Nagendra K. Singh
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  6. K. Usha
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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.

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Correspondence to K. Usha.

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Yadav, A., Jayaswal, P.K., Venkat Raman, K. et al. Transcriptome analysis of flowering genes in mango (Mangifera indica L.) in relation to floral malformation. J. Plant Biochem. Biotechnol. 29, 193–212 (2020). https://doi.org/10.1007/s13562-019-00541-z

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