Analysis of differentially expressed genes and pathways associated with male sterility lines in watermelon via bulked segregant RNA-seq

Abstract

Genic male sterility (GMS) is a common and important trait, which is widely used for the production of hybrid seeds. However, the molecular mechanism of GMS in watermelon remains poorly understood. In this study, we comparatively analyzed the transcriptome profiles of sterile and fertile floral buds using the bulked segregant analysis (BSA) and transcriptome sequencing (RNA-seq). A total of 2507 differentially expressed genes (DEGs) including 593 up-regulated and 1914 down-regulated, were identified to be related to male sterility in watermelon line Se18. Gene ontology (GO) analysis showed that 57 GO terms were significantly enriched, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed plant hormone signal transduction, glycolysis/gluconeogenesis, starch and sucrose metabolism, plant-pathogen interaction, phenylpropanoid biosynthesis pathways were obviously enriched. Furthermore, the efficiency of the RNA-seq analysis was validated by quantitative real-time PCR (qRT-PCR). Among the DEGs, some valuable candidate genes involved in pollen development were identified, such as gene Cla000029, a bHLH transcription factor and homologous to MS1 in Arabidopsis. Moreover, other DEGs including MYB gene Cla012590 (MYB26), Cla017100 (MYB21), etc., also provide useful information for further understanding the function of key genes involved in pollen development. This study provides new insights into the global network of male sterility in watermelon.

Keywords: BSR-seq; Degs; Male sterile; Transcriptome; Watermelon.

Fig. 1

Morphologic characteristics of flowers and buds of fertile and sterile watermelon lines. a Se18-MF, genic male fertile; b Se18-MS, genic male sterile. Floral buds are marked by red arrows. Bar = 10 mm

Fig. 2

Gene Ontology Classification of DEGs of the watermelon floral bud transcriptome. The x-axis indicates the GO term. The right side of the y-axis shows the numbers of genes, while the left side of the y-axis shows the percent of genes

Fig. 3

Cluster of Orthologous Groups (COG) categories of differentially expressed genes

Fig. 4

Classification based on the categories of KEGG pathways. The x-axis indicates the number of DEGs in a function class and the number of gene accounts for the total number of genes in the annotation; the y-axis indicates the function classes

Fig. 5

Family assignment of the 210 differentially expressed TFs

Fig. 6

Validation of gene expression via qRT-PCR. The relative expression levels of 20 DEGs are shown. Student’s t test: *P < 0.05. Error bars indicate mean ± SE

Fig. 7

Proposed model for sterility of watermelon