Integrated SMRT Technology with UMI RNA-Seq Reveals the Hub Genes in Stamen Petalody in Camellia oleifera

Abstract

Male sterility caused by stamen petalody is a key factor for a low fruit set rate and a low yield of Camellia oleifera but can serve as a useful genetic tool because it eliminates the need for artificial emasculation. However, its molecular regulation mechanism still remains unclear. In this study, transcriptome was sequenced and analyzed on two types of bud materials, stamen petalody mutants and normal materials, at six stages of stamen development based on integrated single-molecule real-time (SMRT) technology with unique molecular identifiers (UMI) and RNA-seq technology to identify the hub genes responsible for stamen petalody in C. oleifera. The results show that a large number of alternative splicing events were identified in the transcriptome. A co-expression network analysis of MADSs and all the differentially expressed genes between the mutant stamens and the normal materials showed that four MADS transcription factor genes, CoSEP3.1, CoAGL6, CoSEP3.2, and CoAP3, were predicted to be the hub genes responsible for stamen petalody. Among these four, the expression patterns of CoAGL6 and CoSEP3.2 were consistently high in the mutant samples, but relatively low in the normal samples at six stages, while the patterns of CoSEP3.1 and CoAP3 were initially low in mutants and then were upregulated during development but remained relatively high in the normal materials. Furthermore, the genes with high connectivity to the hub genes showed significantly different expression patterns between the mutant stamens and the normal materials at different stages. qRT-PCR results showed a similar expression pattern of the hub genes in the RNA-seq. These results lay a solid foundation for the directive breeding of C. oleifera varieties and provide references for the genetic breeding of ornamental Camellia varieties.

Characterization and comprehensive evaluation of phenotypic characters in wild Camellia oleifera germplasm for conservation and breeding

“…In addition, the stamen petalody was a surprising phenomenon during our investigation ( Figure 3B ). The stamen of the male sterile mutant shows remarkable petalody, increasing whorls of petals and generating different flower forms, which are extremely important traits for ornamental value and serve as a useful genetic tool because they eliminates the need for artificial emasculation ( Li et al., 2021 ).…”

Genome-Wide Analysis of MYB Transcription Factors and Screening of MYBs Involved in the Red Color Formation in Rhododendron delavayi

“…High-throughput RNA sequencing (RNA-Seq) can generate information-rich sequence and expression data sets to characterize the abundance of related genes in plants [18,19]. RNA-Seq using a unique molecular identifier (UMI) strategy can eliminate quantitative interference by polymerase chain reaction (PCR) amplification preferences, leading to more accurate expression results [20,21]. Hub genes associated with a certain trait can be identified using the weighted gene co-expression network analysis (WGCNA) of RNA-Seq genes based on the UMI strategy associated with trait phenotypic data [22][23][24].…”

Tree Genetics: Molecular and Functional Characterization of Genes

“…In particular, [6] analyzes Camellia oleifera, which is used for oil production; [7] Liriodendron sino-americanum, a relevant ornamental and afforestation species; and [3] Handeliodendron bodinieri, a rare and endangered species, which is also important for bio-energy, landscaping, and water and soil conservation. The of [4] focuses on Picea likiangensis, one of the dominant tree species in the subalpine forest southwest China, with an important ecological in soil and water and carbon storage; [8] reports findings on Pinus massoniana, a relevant timber well as loblolly and slash pines studied in [9].…”

“…Reproductive biology, sensu lato, Issue, with a total of five papers. In [6], transcriptome sequencing was used to study the male sterility caused by stamen petalody in Camellia oleifera, whose molecular regulation mechanism remains unclear. The results showed that four MADS transcription factor genes are predicted to be involved to different extents.…”