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

Abstract

Cotton is not only the most important fiber crop but also the fifth most important oilseed crop in the world because of its oil‐rich seeds as a byproduct of fiber production. By comparative transcriptome analysis between two germplasms with diverse oil accumulation, we reveal pieces of the gene expression network involved in the process of oil synthesis in cottonseeds. Approximately, 197.16 Gb of raw data from 30 RNA sequencing samples with 3 biological replicates were generated. Comparison of the high‐oil and low‐oil transcriptomes enabled the identification of 7682 differentially expressed genes (DEGs). Based on gene expression profiles relevant to triacylglycerol (TAG) biosynthesis, we proposed that the Kennedy pathway (diacylglycerol acyltransferase‐catalyzed diacylglycerol to TAG) is the main pathway for oil production, rather than the phospholipid diacylglycerol acyltransferase‐mediated pathway. Using weighted gene co‐expression network analysis, 5312 DEGs were obtained and classified into 14 co‐expression modules, including the MEblack module containing 10 genes involved in lipid metabolism. Among the DEGs in the MEblack module, GhCYSD1 was identified as a potential key player in oil biosynthesis. The overexpression of GhCYSD1 in yeast resulted in increased oil content and altered fatty acid composition. This study may not only shed more light on the underlying molecular mechanism of oil accumulation in cottonseed oil, but also provide a set of new gene for potential enhancement of oil content in cottonseeds.

Oil candidate genes in seeds of cotton (Gossypium hirsutum L.) and functional validation of GhPXN1

“…Remarkably, the peak period of cottonseed oil content in H6053 occurred earlier (at 25 DPA) compared to L2052 (at 30 DPA). Based on previous reporters [ 6 , 10 ], 330 genes were identified involving in oil synthesis (Additional file 1 : Table S3). Notably, the expression levels of these genes were consistently higher in H6053 compared to L2052 during cotton ovule development (Fig.…”

“…Sucrose is the primary carbon source for seed storage oil biosynthesis [ 9 ]. De novo FA synthesis is catalyzed by a complex of several enzymes in plastids [ 10 ]. Briefly, free FA chains are released from FA acyl carrier protein (acyl-ACP) under the catalysis of FA acyl-ACP thioesterase in plastids, and then transported into the endoplasmic reticulum (ER) for functional modifications, such as the elongation and desaturation of acyl chains [ 11 ].…”

“…With the development of next-generation sequencing (NGS) technologies, an increasing number of studies on oil traits have been conducted in various crops. For instance, a novel key regulatory gene GhCYSD1 is associated with oil synthesis [ 10 ]. Integration of comparative transcriptome and population mapping identified 21 candidate genes associated with oil accumulation in G. barbadense and G. hirsutum , such as GbSWEET and GbACBP6 [ 6 ], GhKASII [ 17 ], GhSAD [ 18 ], GhWRI1 [ 19 ] and GmPEPC1 [ 20 ].…”

Multi‐omics‐driven advances in the understanding of triacylglycerol biosynthesis in oil seeds

“…Moreover, differential expression analysis and co‐expression analysis are straightforward and popular methods to study the transcriptional response to distinct cell types/organs, developmental stages, growth conditions, and contrasted genotypes (Bashir et al., 2019; Lim et al., 2022; MovahedI et al., 2012; Ng et al., 2020; Seyfferth et al., 2021). For example, high‐resolution spatiotemporal transcriptome profiles were constructed at different developmental stages of seeds or embryos from fertilization to maturity in soybean, peanut, cotton, and maize (Chen et al., 2014; Collakova et al., 2013; Machado et al., 2020; Song et al., 2022; Yang, Miao, et al., 2019) and early seed development stages from 0 to 144 h after pollination in maize (Yi et al., 2019). Six co‐expression modules were identified to associate with soybean SOC.…”

Genome-Wide Identification and Expression Analyses of the Cotton AGO Genes and Their Potential Roles in Fiber Development and Stress Response

“…Cotton has been grown as the most important natural fiber crop and provides approximately 35% of the total fiber consumed worldwide [ 18 ]. It is also a vital oilseed and feed crop in the world owing to the high contents of oil and protein in cottonseeds [ 19 ]. However, cotton production is severely constrained by several biotic and abiotic stresses such as Verticillium wilt, salt, and drought, which result in decreased yields and inferior harvest quality.…”