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

Abstract

Background: In 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 hours after pollination (HAP). Moreover, some regulatory genes and functional proteins that may cause low pollen-pistil compatibility in Nymphaea were identified. Results: RNA-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 8,789 (4,680 were up-regulated), 6,401 (3,020 were up-regulated), and 11,284 (6,148 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. Conclusions: Our 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.

Comparative analysis of the complete chloroplast genome of seven Nymphaea species

“…Our results are consistent with the results presented by Dkhar et al [8]. The genetic relationship between subgenus Nymphaea and subgenus Brachyceras, subgenus Brachyceras and subgenus Anecphya, subgenus Hydrocallis and subgenus Lotos is relatively close, which is also supported by their cross compatibility [40][41][42].…”

Comparative analysis of the complete chloroplast genome of seven Nymphaea species

“…However, the relationship between species in the genus Nymphaea is still unclear and needs further study. In this study, subgenus Anecphya, subgenus Hydrocallis, and subgenus Lotos form separate branches indicating support for these subgenera, but subgenus Nymphaea and subgenus Brachyceras showed which is also supported by their cross compatibility [40][41][42].…”

Transcriptomic Insight into Viviparous Growth in Water Lily

“…Viviparity in Water Lily. The extrachromosomal genome [38], transcriptome, and proteome [10] analyses for various morphological and physiological traits have been reported in water However, this is the first research focused on the molecular basis of viviparous growth in water lilies. We generated the whole transcriptome sequence from leaf tissues at various plant developmental stages, assembled the sequencing data and annotated the differentially expressed for functional assessment.…”

“…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].…”