Transcriptomic and proteomic analysis reveals mechanisms of low pollen-pistil compatibility during water lily cross breeding

Abstract

BackgroundIn water lily (Nymphaea) hybrid breeding, breeders often encounter non-viable seeds, which make it difficult to transfer desired or targeted genes of different Nymphaea germplasm. We found that pre-fertilization barriers were the main factor in the failure of the hybridization of Nymphaea. The mechanism of low compatibility between the pollen and stigma remains unclear; therefore, we studied the differences of stigma transcripts and proteomes at 0, 2, and 6 h after pollination (HAP). Moreover, some regulatory genes and functional proteins that may cause low pollen-pistil compatibility in Nymphaea were identified.ResultsRNA-seq was performed for three comparisons (2 vs 0 HAP, 6 vs 2 HAP, 6 vs 0 HAP), and the number of differentially expressed genes (DEGs) was 8789 (4680 were up-regulated), 6401 (3020 were up-regulated), and 11,284 (6148 were up-regulated), respectively. Using label-free analysis, 75 (2 vs 0 HAP) proteins (43 increased and 32 decreased), nine (6 vs 2 HAP) proteins (three increased and six decreased), and 90 (6 vs 0 HAP) proteins (52 increased and 38 decreased) were defined as differentially expressed proteins (DEPs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs and DEPs were mainly involved in cell wall organization or biogenesis, S-adenosylmethionine (SAM) metabolism, hydrogen peroxide decomposition and metabolism, reactive oxygen species (ROS) metabolism, secondary metabolism, secondary metabolite biosynthesis, and phenylpropanoid biosynthesis.ConclusionsOur transcriptomic and proteomic analysis highlighted specific genes, incuding those in ROS metabolism, biosynthesis of flavonoids, SAM metabolism, cell wall organization or biogenesis and phenylpropanoid biosynthesis that warrant further study in investigations of the pollen-stigma interaction of water lily. This study strengthens our understanding of the mechanism of low pollen-pistil compatibility in Nymphaea at the molecular level, and provides a theoretical basis for overcoming the pre-fertilization barriers in Nymphaea in the future.

Quantitative Proteomics of Maize Roots Treated with a Protein Hydrolysate: A Comparative Study with Transcriptomics Highlights the Molecular Mechanisms Responsive to Biostimulants

“…It is evident from our results (Figure ) and numerous other reports that the gene expression level and protein abundance do not sufficiently correlate to orthogonally validate each other. − There was no correlation between the FC of DEGs and their corresponding DAPs in our study as the Spearman correlation coefficients were −0.516 and 0.330 for A1/2 and A1 data sets, respectively. Majority of this non-correlative discrepancies are a manifestation of the complexity of biological regulation by post-transcriptional and post-translational modifications and may not be attributed to platform-specific errors or measurement bias.…”

Transcriptomic Insight into Viviparous Growth in Water Lily

“…The extrachromosomal genome [ 38 ], transcriptome, and proteome [ 10 ] analyses for various morphological and physiological traits have been reported in water lilies. However, this is the first research focused on the molecular basis of viviparous growth in water lilies.…”

“…Currently, researchers mainly focus on evolution and taxonomic status, regulation of flower color, floral fragrance, flowering period, and reproduction of water lilies [ 10 ]. With the progress in genome sequencing tools, the use of transcriptome technology may provide a new way for mining the genes related to viviparous growth in water lilies [ 10 ]. In particular, transcriptome sequencing is a useful method for identifying novel transcripts and analyzing gene expression [ 11 ].…”

“…RNA-seq or transcriptome studies have extensively been used to evaluate many plant species [ 12 , 13 ] for various traits including early maturity [ 14 ] and seed dormancy [ 15 ]. The viviparity trait was investigated based on transcriptome analysis in mangrove plants [ 15 , 16 ] and Ophiorrhiza mungos L. [ 4 ], but limited transcriptome data exists in water lilies [ 10 ].…”

Gene coexpression analysis reveals key pathways and hub genes related to late-acting self-incompatibility in Camellia oleifera

“…and Theobroma cacao , in which the pollen tube can grow successfully in the styles, but the inhibition occurs either prezygotically or postzygotically ( Hao et al., 2012 ). Many studies have been performed to identify the key factors involved in the LSI response, but the mechanism remains unclear ( Chen et al., 2012 ; Sun et al., 2019 ). The genetic basis of LSI was hypothesized to be gametophytic under genetic control ( Zhou and Zheng, 2015 ; Zhang et al., 2016 ).…”