A global survey of the gene network and key genes for oil accumulation in cultivated tetraploid cottons

Abstract

Summary To enrich our knowledge about gene network of fatty acid biosynthesis in cottonseed, we conducted comparative transcriptome to reveal the differences in gene expression between Gossypium hirsutum and Gossypium barbadense during cottonseed development. The prolonged expression period and increased expression abundance of oil‐related genes are the main reasons for producing high seed oil content (SOC) in G. barbadense, which manifested as the bias of homeologous gene expression in Dt‐subgenome after 25 day postanthesis (DPA). The dynamic expression profile showed that SAD6 and FATA are more important for oil biosynthesis in G. barbadense than that in G. hirsutum. Three key transcription factors, WRI1, NF‐YB6 and DPBF2, showed their elite roles in regulating seed oil in cotton. We observed that sequence variations in the promoter region of BCCP2 genes might contribute to its divergence in expression level between the two species. Based on the quantitative trait loci (QTL) information of the seed oil content and utilizing additional G. barbadense introgression lines (ILs), we propose 21 candidate genes on the basis of their differential expression level, of which the GbSWEET and the GbACBP6 showed the potential functional to improve the oil content. Taken together, studying the different expression of oil‐related genes and their genetic regulation mechanisms between G. hirsutum and G. barbadense provide new insights to understanding the mechanism of fatty acid biosynthesis network and fatty acid genetic improving breeding in cotton.

Transcriptome analysis and identification of genes associated with oil accumulation in upland cotton

“…RNA‐seq is a useful tool to discover the differential gene expression genome‐wide and identify key candidate genes involved in oil biosynthesis (Li et al, 2019). Different from previous studies (Zhao et al, 2018; Zhu et al, 2021), a high‐resolution gene expression network in developing cottonseed was constructed based on deep RNA sequencing to facilitate the molecular analysis of the genetic regulation of lipid metabolism in high‐oil and low‐oil genotypes, which led to the identification of an important candidate gene that may play a vital role in oil biosynthesis.…”

Evolutionary and Functional Characterization of Cytochrome P450 in Cotton Reveal the Role of Subgenome Expression of GhCYP78A for Cotton Fiber Initiation

“…Other two GhCYP78A, namely GhCYP78A194_A and GhCYP78A197_D displayed high normalized value in C6 cluster representing their crucial role in SCW synthesis through the fatty acid elongation process [52]. Quantitative trait loci demonstrated the role of GhCYP78A194_A in seed development as well as in high seed oil content in cotton [53]. The dual functionality of GhCYP78A has been validated through one of its orthologs, GhCYP78A198_A, whose expression was relatively high at -3 DPA and 21 DPA (Fig.…”

Genetics, Breeding and Genetic Engineering to Improve Cottonseed Oil and Protein: A Review

“…Currently, there is a profound understanding on the biochemical and molecular functions of most steps in the lipid biosynthetic pathway, as well as the inheritance of phenotypic performance of various mutants corresponding to these metabolic steps in model plants ( Byrne et al, 1996 ; McMullen et al, 1998 ). With the advent of numerous high quality genome sequence databases derived from cotton and associated Gossypium species, attempts have been made to identify key genes and their interactive gene networks that are involved in oil biosynthesis in cotton ( Liu et al, 2009 ; Jiao et al, 2013 ; Hovav et al, 2015 ; Hu et al, 2016 ; Xu et al, 2016 ; Zhao et al, 2018c ; Ma et al, 2021 ; Zhu et al, 2021 ). The current understanding for the general biosynthetic pathway of cottonseed oil is shown in Figure 1 .…”

“…In congruence, WRI1 and NF-YB6 were highly expressed and displayed coordinated temporal patterns with oil accumulation in cottonseeds ( Zhao et al, 2018b ). That the key genes involved in de novo fatty acid biosynthesis, such as SAD6 and FATA , showed clear differential expression concomitant with oil accumulation, which were substantially highly expressed in G. barbadense than in G. hirsutum , highlighting the divergence between these two closely related allotetraploid cottons ( Zhu et al, 2021 ). Some other enzymes in plastids, such as GhPEPC1 , are not only involved in photosynthesis but also key to the inflowing of carbon turnover to fatty acid biosynthesis attributable to the accumulation of cottonseed oil ( Xu et al, 2016 ).…”

“… Cui et al (2017) showed that overexpression of GhACCase subunits resulted in increased cottonseed oil content by 17–22%. A large number of oil-related genes, such as fatty acyl-ACP thioesterase B ( FATB ), acyl carrier protein 5 ( ACP5 ) ( Yuan et al, 2018 ) and KASIII ( Du et al, 2018a ), have been identified by various approaches including GWAS (e.g., Du et al, 2018a , b ), gene expression studies (e.g., Ma et al, 2021 ; Zhu et al, 2021 ), cloning and sequence-based in silico analysis ( Zhang et al, 2009 ; Yu et al, 2011 ; Yurchenko et al, 2014 ; Shang et al, 2016 ; Cui et al, 2020 ). Among GhSAD genes coding for stearoyl-acyl carrier protein desaturase, GhSAD4 was found to stand out as the most relevant to determine the relative ratio of oleic acid and linoleic acid ( Shang et al, 2017 ).…”