Transcriptomic and proteomic analysis reveals mechanisms of embryo abortion during chrysanthemum cross breeding

Abstract

Embryo abortion is the main cause of failure in chrysanthemum cross breeding, and the genes and proteins associated with embryo abortion are poorly understood. Here, we applied RNA sequencing and isobaric tags for relative and absolute quantitation (iTRAQ) to analyse transcriptomic and proteomic profiles of normal and abortive embryos. More than 68,000 annotated unigenes and 700 proteins were obtained from normal and abortive embryos. Functional analysis showed that 140 differentially expressed genes (DEGs) and 41 differentially expressed proteins (DEPs) were involved in embryo abortion. Most DEGs and DEPs associated with cell death, protein degradation, reactive oxygen species scavenging, and stress-response transcriptional factors were significantly up-regulated in abortive embryos relative to normal embryos. In contrast, most genes and proteins related to cell division and expansion, the cytoskeleton, protein synthesis and energy metabolism were significantly down-regulated in abortive embryos. Furthermore, abortive embryos had the highest activity of three executioner caspase-like enzymes. These results indicate that embryo abortion may be related to programmed cell death and the senescence- or death-associated genes or proteins contribute to embryo abortion. This adds to our understanding of embryo abortion and will aid in the cross breeding of chrysanthemum and other crops in the future.

Reduced expression of selected FASCICLIN‐LIKE ARABINOGALACTAN PROTEIN genes associates with the abortion of kernels in field crops of Zea mays (maize) and of Arabidopsis seeds

“…The expression of the FKBP (FK506‐binding protein) gene positively correlated with abortion, and the immunophilin protein FKBP12 interacts with AtFIP37 (FKBP12 interacting protein 37 kD), which is required for normal embryogenesis in Arabidopsis (Vespa et al, ). Genes associated to cell death and reactive oxygen species scavenging are significantly up‐regulated in abortive embryos of chrysanthemum (Zhang et al, ). In addition, proper regulation of cell death is required for normal embryo development (Zhao et al, ) and stress (drought) can delay the normal advance to programmed cell death in the central endosperm close to the embryo (Yu & Setter, ).…”

Identification of MicroRNAs and their Targets Associated with Embryo Abortion during Chrysanthemum Cross Breeding via High-Throughput Sequencing

“…Interspecific crosses were performed according to previously described methods [ 13 ]. Sample collection was performed as described previously [ 31 ]. Briefly, 60 chrysanthemum plants were planted in three planting areas, with 20 plants in each area.…”

“…A total of 615,312 contigs and 116,697 unigenes were identified, and all of them had the Nr, Nt, COG, GO and KEGG annotation. More details have been previously described in an article about chrysanthemum embryo transcriptomic analysis [ 31 ]. Genes were classified according to KEGG functional annotations using the DAVID bioinformatics resources [ 38 ].…”

Transcriptome Analysis of Hamelia patens (Rubiaceae) Anthers Reveals Candidate Genes for Tapetum and Pollen Wall Development

“…If the unigenes contained in the distinct clusters were treated as single unigenes, then the total number of annotated unigenes would be 27,562, and the annotated proportion would be 41.0%, which is close to the proportion of unigenes in the same cluster treated as independent unigenes. Non-BLASTable ( E -value > 1e-5) sequences have been reported in all studied plant transcriptomes, with the proportion varying from 13.0 to 80.0%, depending on the species, the sequencing depth and the parameters of the BLAST search (Parchman et al, 2010; Blanca et al, 2011; Ness et al, 2011; Zhang et al, 2012, Zhang F.J. et al, 2014). Non-BLASTable (E-value > 1e-5) sequences might result from biological factors, including rapidly evolved genes with divergent sequences, species-specific genes, and the persistence of non-coding fractions derived mainly from untranslated regions (Logacheva et al, 2011; Zhang et al, 2012).…”

“…Further, the number of H. patens unigenes is an estimate, since the genome is unknown and unigenes sharing sequence similarities were classified as different unigenes, in consideration of alternative splicing events. High numbers of unigenes have also been reported for species with no reference genomes such as for the fruit transcriptome of Triadica sebifera with 92,550 unigenes (Divi et al, 2016), the embryo transcriptome of chrysanthemum with 116,697 unigenes (Zhang F.J. et al, 2014) and the leaf transcriptome of Lycium chinense with 61,595 unigenes (Wang et al, 2015). Finally, each developmental stage of H. patens anther contains about 20% of transcripts with RPKM ≤ 1, which most likely would not be detected with microarrays.…”