Transcriptome Analysis Suggests That Chromosome Introgression Fragments from Sea Island Cotton (Gossypium barbadense) Increase Fiber Strength in Upland Cotton (Gossypium hirsutum)

Abstract

As high-strength cotton fibers are critical components of high quality cotton, developing cotton cultivars with high-strength fibers as well as high yield is a top priority for cotton development. Recently, chromosome segment substitution lines (CSSLs) have been developed from high-yield Upland cotton (Gossypium hirsutum) crossed with high-quality Sea Island cotton (G. barbadense). Here, we constructed a CSSL population by crossing CCRI45, a high-yield Upland cotton cultivar, with Hai1, a Sea Island cotton cultivar with superior fiber quality. We then selected two CSSLs with significantly higher fiber strength than CCRI45 (MBI7747 and MBI7561), and one CSSL with lower fiber strength than CCRI45 (MBI7285), for further analysis. We sequenced all four transcriptomes at four different time points postanthesis, and clustered the 44,678 identified genes by function. We identified 2200 common differentially-expressed genes (DEGs): those that were found in both high quality CSSLs (MBI7747 and MBI7561), but not in the low quality CSSL (MBI7285). Many of these genes were associated with various metabolic pathways that affect fiber strength. Upregulated DEGs were associated with polysaccharide metabolic regulation, single-organism localization, cell wall organization, and biogenesis, while the downregulated DEGs were associated with microtubule regulation, the cellular response to stress, and the cell cycle. Further analyses indicated that three genes, XLOC_036333 [mannosyl-oligosaccharide-α-mannosidase (MNS1)], XLOC_029945 (FLA8), and XLOC_075372 (snakin-1), were potentially important for the regulation of cotton fiber strength. Our results suggest that these genes may be good candidates for future investigation of the molecular mechanisms of fiber strength formation and for the improvement of cotton fiber quality through molecular breeding.

Keywords: DEG; GenPred; Genomic Selection; Shared Data Resources; cotton; fiber strength; secondary cell wall synthesis; transcriptome.

Figure 1

Statistical analysis of transcript profiling data. Z, S, L, and Y indicate CCRI45, MBI7561, MBI7747, and MBI7285, respectively. 15, 15 DPA; 20, 20 DPA; 25, 25 DPA; and 28, 28 DPA. (A) Pearson correlation coefficients of all samples. (B) Self-Organizing Tree Algorithm clustering of all genes across all samples. (C) Functional annotations of genes in more highly expressed at 15 DPA than later (orange bars) and those more highly expressed at 28 DPA than earlier (blue bars). DEG, differentially-expressed gene; DPA, days postanthesis.

Figure 2

Overview of DEGs. Z, S, L, and Y indicate CCRI45, MBI7561, MBI7747, and MBI7285, respectively. 15, 15 DPA; 20, 20 DPA; 25, 25 DPA; and 28, 28 DPA. (A) Heatmap of all common DEGs at 15, 20, 25, and 28 DPA. (B) Expression pattern of common DEGs over the four time points as compared to the recurrent parent CCRI45. DEG, differentially-expressed gene; DPA, days postanthesis.

Figure 3

Functional associations of common differentially-expressed genes (DEGs). (A) Biological processes associated with upregulated common DEGs. (B) Biological processes associated with downregulated common DEGs.

Figure 4

Cluster analysis of the common DEGs. Z, S, L, and Y indicate CCRI45, MBI7561, MBI7747, and MBI7285, respectively. 15, 15 DPA; 20, 20 DPA; 25, 25 DPA; and 28, 28 DPA. (A) Venn diagram of significant DEGs found in MBI7561 and CCRI45 across various time points. (B) Heatmap of common DEGs. (C) Self-Organizing Tree Algorithm clustering of all significant DEGs between CCRI45 and MBI7561 at all four time points. (D) Heatmap analysis of the expression of all significant DEGs between CCRI45 and MBI7561 at all four time points. (E) Functional annotations of significant DEGs: green bars indicate genes highly expressed at 15 DPA; orange bars indicate genes highly expressed at 20 DPA; gold bars indicate genes highly expressed at 25 DPA; and blue bars indicate genes highly expressed at 28 DPA. ATP, adenosine triphosphate; DEG, differentially-expressed gene; DPA, days postanthesis.

Figure 5

Common DEGs related to fiber strength. Z, S, L, and Y indicate CCRI45, MBI7561, MBI7747, and MBI7285, respectively. 15, 15 DPA; 20, 20 DPA; 25, 25 DPA; and 28, 28 DPA. (A) Heatmap of common DEGs related to fiber strength. (B) Numbers of common DEGs involved in processes related to fiber strength. DEG, differentially-expressed gene; DPA, days postanthesis.

Figure 6

Biological functions associated with selected DEGs in MBI7561. Z, S, L, and Y indicate CCRI45, MBI7561, MBI7747, and MBI7285, respectively. 15, 15 DPA; 20, 20 DPA; 25, 25 DPA; and 28, 28 DPA. (A) Biological processes of genes at 15 DPA. (B) Biological processes of genes at 20 DPA. (C) Biological processes of genes at 25 DPA. (D) Biological processes of genes at 28 DPA. DEG, differentially-expressed gene; DPA, days postanthesis.

Figure 7

Quantitative real-time polymerase chain reaction validation of 10 DEGs. DPA, days postanthesis.