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Heterosis and differential gene expression in hybrids and parents in Bombyx mori by digital gene expression profiling - PubMed

  • ️Thu Jan 01 2015

Heterosis and differential gene expression in hybrids and parents in Bombyx mori by digital gene expression profiling

Hua Wang et al. Sci Rep. 2015.

Abstract

Heterosis is a concern to all breeders, but the mechanism of heterosis remains unknown. In F1 organisms, genetic material is inherited from the two parents and theoretically, heterosis might be caused by differences in gene expression or modification. Differential gene expression was analyzed in hybrids and parents in Bombyx mori. The results showed that there were significant changes in gene expression in the fat body involving biological regulation, cellular and metabolic processes. Consistent trends in expression patterns covering different hybrid combinations were seen in 74 genes. Moreover, these differential gene expression patterns included overdominance, dominance, and additive effects. By correlating these patterns with economic traits, a potential relationship was found. Differential gene expression was seen in different cross combinations and in different sexes. In addition, a regulatory mechanism involving metabolism and ErbB signaling pathways was also found, suggesting that such a network might also be related to heterosis in Bombyx mori. Together, our data provide a comprehensive overview and useful resource for transcriptional analysis of heterosis of Bombyx mori.

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Figures

Figure 1
Figure 1. Distributions of tags and genes.

(A) Data on reference genes in this study. (B) Distribution of distinct clean tags and genes. (C) Positional distribution of all tags that could be mapped to a gene. Position distribution vector (scalar figure) of the distance of a tag aligned to a reference gene from a 3′-end restriction site. Insert: vector of changes in tag types increased with sequencing number. (D) Distribution of distinct clean tag copy numbers from the eight libraries. The error bars indicate standard deviation.

Figure 2
Figure 2. Venn diagram and GO analysis of shared genes.

(A) and (B) Venn diagram of unique and shared genes among the eight libraries. “a1”, “a2”, “b1”, “b1” displayed the detail venn diagram between F1 and parents. (C) GO analysis of all shared conserved genes by WEGO (

http://wego.genomics.org.cn/cgi-bin/wego/index.pl

).

Figure 3
Figure 3. Gene expression patterns clustered by hybrid combination.

(A) Distribution of eight patterns by gender and combination. The eight differential expression patterns were No Difference(ND), Over Parents(OPS), Under Parents(UPS), Under Female(UF), Under Male(UM), Over Female(OF), Over Male(OM), Between Female and Male(FAM), Between Male and Female(MAF). (B) Trends in gene expression patterns. The differential expression pattern of F1 males and F1 females with the greatest number was consistently OM, while the most common pattern for crosses was UM. In both of the two hybrids, the patterns with the lowest numbers were MAF and FAM. “A-F1-Co” indicated the co-expression genes in reciprocal cross group, “C-F1-Co” indicated the co-expression genes in cross group, “C&A-F1-Co” indicated the co-expression genes in cross and reciprocal cross group. (C) Clustering figure for 74 consistently trending genes. All the vertical axis shows the number of genes.

Figure 4
Figure 4. GO and KEGG pathway enrichment analysis of OPS genes in different combinations.

(A) GO analysis of differentially expressed genes between cross and F1. (B) GO analysis of differentially expressed genes between reciprocal crosses and F1. (C) KEGG analysis of differentially expressed genes between cross and reciprocal crosses.“C-F1-♂” indicated the co-expression genes in cross F1 males, “C-F1-♀” mean cross F1 females.“A-F1-♂” indicated the co-expression genes in reciprocal cross F1 males, “A-F1-♀” mean reciprocal cross F1 females.

Figure 5
Figure 5. Validation of 12 B. mori gene expression levels using qPCR.

Known genes were (A) BGIBMGA010975 (B. mori homologous FRG1 protein). (B) BGIBMGA010172 (B. mori transcription initiation factor subunit 12). (C) BGIBMGA014427 (serine protease precursor). (D) BGIBMGA007230 (B. mori elongation factor 1A2). (E) BGIBMGA003210 (B. mori Yokozuna transposon). (F) BGIBMGA010722 (B. mori facilitated trehalose transporter-like protein Tret1). (G) BGIBMGA010275. (H) BGIBMGA012774. (I) BGIBMGA011868. (J) BGIBMGA012524. (K) BGIBMGA013545. (L) BGIBMGA010732. The error bars indicate standard deviation. All the vertical axis shows the Relative expression of genes.

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