Comparative transcriptomics in alternate bearing cultivar Dashehari reveals the genetic model of flowering in mango

Abstract

Flowering is a complex developmental process, with physiological and morphological phases influenced by a variety of external and internal factors. Interestingly, many mango cultivars tend to bear fruit biennially because of irregular flowering, and this has a negative impact on mango flowering and the subsequent yield, resulting in significant economic losses. In this article, transcriptome analysis was carried out on four tissues of mango cv. Dashehari (bearing tree leaf, shoot apex, inflorescence, and non-bearing tree leaf). De novo transcriptome assembly of RNA-seq reads of Dashehari using the Trinity pipeline generated 67,915 transcripts, with 25,776 genes identified. 85 flowering genes, represented by 179 transcripts, were differentially expressed in bearing vs. non-bearing leaf tissues. Gene set enrichment analysis of flowering genes identified significant upregulation of flowering related genes in inflorescence tissues compared to bearing leaf tissues. The flowering genes FT, CO, GI, ELF 4, FLD, FCA, AP1, LHY, and SCO1 were upregulated in the bearing leaf tissues. Pathway analysis of DEGs showed significant upregulation of phenylpropanoid and sucrose and starch pathways in non-bearing leaf tissue compared with bearing leaf tissue. The comparative transcriptome analysis performed in this study significantly increases the understanding of the molecular mechanisms driving the flowering process as well as alternative bearing in mango.

Keywords: Dashehari mango; RNA-seq; alternate bearing; floral development; flowering genes.

FIGURE 1

Dashehari mango samples used for RNA isolation: (A) shoot apex; (B) immediate mature leaf (within 50 cm of the shoot apex); and (C) inflorescence.

FIGURE 2

Functional annotation of de novo Dashehari assembly using the non-redundant (nr) database.

FIGURE 3

GO classification of the annotated Mango transcripts categorized into cellular component, molecular function, and biological process.

FIGURE 4

Venn diagram of differentially expressed genes with different comparisons of the bearing and non-bearing leaf, apex, and inflorescence. DL—Dashehari bearing leaf; DLNB—Dashehari non-bearing leaf; DA—Dashehari shoot apex; DI—Dashehari Inflorescence.

FIGURE 5

Flor-ID flowering genes—binned into circadian clock, photoperiod, aging, vernalization, autonomous and temperature related pathway—expressed in bearing vs. non-bearing Dashehari leaf tissue.

FIGURE 6

(A) KEGG binning analysis showing phenylpropanoid pathway up regulation in Dashehari non-bearing leaf. (B) Gene Set Enrichment Analysis (GSEA)—Upregulation of phenylpropanoid pathway genes in the non-bearing Dashehari compared to bearing leaf.

FIGURE 7

KEGG binning analysis shows-sucrose and starch pathway has shown up-regulation in Dashehari non-bearing leaf.

FIGURE 8

Gene Set Enrichment Analysis-Upregulation of flower development pathway genes in Dashehari inflorescence compared to bearing leaf.

FIGURE 9

Quantitative real time (qRT-PCR) expression of eight flowering genes (FT, FTIP, GI, CO, T6P, Sucrose synthase, BR1, SOC1) in leaf, apex, inflorescence and non-bearing leaf of Dashehari. Mi-Actin is used as an internal reference. The fold change data is normalized to Dashehari bearing leaf (DL). Tissue types compared are Dashehari bearing leaf vs. Dashehari apex, Dashehari bearing leaf vs. Dashehari inflorescence, Dashehari bearing leaf vs. Dashehari non-bearing leaf, Dashehari apex vs. Dashehari inflorescence. Error bars represents ± Standard error with n = 3.