To Be a Flower or Fruiting Branch: Insights Revealed by mRNA and Small RNA Transcriptomes from Different Cotton Developmental Stages

Abstract

The architecture of the cotton plant, including fruit branch formation and flowering pattern, is the most important characteristic that directly influences light exploitation, yield and cost of planting. Nulliplex branch is a useful phenotype to study cotton architecture. We used RNA sequencing to obtain mRNA and miRNA profiles from nulliplex- and normal-branch cotton at three developmental stages. The differentially expressed genes (DEGs) and miRNAs were identified that preferentially/specifically expressed in the pre-squaring stage, which is a key stage controlling the transition from vegetative to reproductive growth. The DEGs identified were primarily enriched in RNA, protein, and signalling categories in Gossypium barbadense and Gossypium hirsutum. Interestingly, during the pre-squaring stage, the DEGs were predominantly enriched in transcription factors in both G. barbadense and G. hirsutum, and these transcription factors were mainly involved in branching and flowering. Related miRNAs were also identified. The results showed that fruit branching in cotton is controlled by molecular pathways similar to those in Arabidopsis and that multiple regulated pathways may affect the development of floral buds. Our study showed that the development of fruit branches is closely related to flowering induction and provides insight into the molecular mechanisms of branch and flower development in cotton.

Light‐ and temperature‐entrainable circadian clock in soybean development

“…. In plants, time-keeping pacemakers adjust the period and phase of endogenous circadian rhythms in response to external and internal cues, conferring improved fitness (Yanovsky & Kay, 2003;Dodd et al, 2005; de Montaigu et al, 2010; Wang et al, 2011;Sun et al, 2016;Sun et al, 2018;Wang et al, 2019). In recent years, orthologs of many Arabidopsis clock-associated components have been identified in multiple agricultural crops and have been shown to function in the regulation of agronomic traits (Campoli et al, 2012;Bendix et al, 2013;Liu et al, 2015;Xie et al, 2015;Muller et al, 2016;Liew et al, 2017;Lu et al, 2017).…”

Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development

“…The balance between DNA methylation and DNA demethylation may mediate specific DNA methylation during the development of cotton tissue. To study the DNA methylation modifications that occur during cotton branch development, cotton DNA methyltransferases and demethylases were identified and expression profiles of these genes were constructed based on previously published RNA-seq data ( Sun et al, 2016 ). As shown in Table 1 , we identified a total of 22 genes encoding 16 DNA methyltransferases and six demethylases in the cotton genome based on the protein sequence homology of Arabidopsis DNA methyltransferases (including MET1 , DRM , CMT , and Dnmt2 ) and DNA demethylases (including DME , ROS1 and DML3 ) ( Fig.…”

“…Shoot apices (approximately 10 mm) were collected and stored immediately in liquid nitrogen after washing with water. The samples at three stages, including the seedling stage with two leaves (Gh1nm), the pre-squaring stage with six and seven leaves (Gh2nm) and without any visible triangular floral bud (only floral bud and fruiting branch formation), and the squaring stage with 8–10 leaves (Gh3nm) with visible triangular floral buds in the field, were used to construct libraries ( Sun et al, 2016 ). The indicated leaves refer to visual, expanded true leaves in the cotton field.…”

“…Published gene expression data (GEO accession no. ) of the same samples as used in this study were further analysed ( Sun et al, 2016 ). Gene expression profile was computed using the TopHat software package and differentially expressed genes (DEGs) were screened using the edge R package (log2|Fold Change| > 1 and FDR < 0.05).…”

“…However, little is known about the molecular mechanisms of cotton architecture development. In our previous study, high-throughput next-generation sequencing technology was used to simultaneously measure mRNA and miRNA expression profiles during fruit branch and floral bud development in cotton and identified several genes potentially related to the floral transition and branching development ( Sun et al, 2016 ). In the apple, Guo et al observed significant changes in 24 nucleotide sRNAs (RdDM pathway), suggesting that the epigenetic modifications is coupled with the floral transition ( Guo et al, 2017 ).…”