Abstract
BackgroundTRIANGULAR HULL1 (TH1), a member of the rice ALOG gene family, has been characterized as a rice lemma/palea-related gene. To understand the gene regulatory network that controlled by TH1, we analyzed the transcriptome from a TH1 knock out (KO) line, which was generated by CRISPR/Cas9. Our study may shed some light on the molecular mechanism of lemma/palea development.ResultsWe obtained 20 T0th1-C transgenic plants by CRISPR/Cas9. Among the 20 plants, there were eight bi-allelic mutations, five homozygous mutations, three heterozygous mutations, and four Non-KO plants. By comparing with the wild type and the heterozygous knock out (KO) line, the homozygous KO lines showed defects in lemma/palea development as well as in grain filling. Further more, we studied the gene regulatory network that controlled by TH1 by comparing the transcriptome of a homozygous TH1 KO line with its Non-KO line as a control. A total of 622 genes were identified as differentially expressed genes (DEGs), of which 297 genes were significantly up-regulated while 325 genes were down-regulated. One hundred thirty eight of the DEGs were assigned to the 59 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Among these annotated DEGs, 15 genes were related to plant hormone signal transduction, eight genes were related to starch and sucrose metabolism. These were the two largest groups of DEGs according to the KEGG pathway analysis.ConclusionsOur results indicated that hormone related genes and starch/sucrose metabolism related genes might act as downstream targets of TH1; they might be responsible for lemma/palea development and grain filling respectively.
Highlights
TRIANGULAR HULL1 (TH1), a member of the rice ALOG gene family, has been characterized as a rice lemma/palea-related gene
Its expression is restricted to the lemma, its function on lemma development remains unknown (Yamaguchi et al 2004; Ishikawa et al 2009); MOSAIC FLORAL ORGANS1 (MFO1)/MADS6 is a member of MADS-box gene family that specifies palea identity
In our RNA-seq experiment, eight genes related to starch and sucrose metabolism were differentially expressed between knock out (KO) and Non-KO plants (Fig. 4), the altered expression levels of these genes might result in the defection for grain filling in the homozygous KO line
Summary
TRIANGULAR HULL1 (TH1), a member of the rice ALOG gene family, has been characterized as a rice lemma/palea-related gene. A number of genes involved in lemma and palea development have been identified. DROOPING LEAF (DL), a member of the YABBY gene family, is expressed in the lemma, but not in the palea, it involves in leaf midrib formation and carpel specification. Its expression is restricted to the lemma, its function on lemma development remains unknown (Yamaguchi et al 2004; Ishikawa et al 2009); MOSAIC FLORAL ORGANS1 (MFO1)/MADS6 is a member of MADS-box gene family that specifies palea identity. Research showed that genes involved in the small RNA pathway including SHOOT ORGANIZATION1 (SHO1), SHOOTLESS2 (SHL2), SHO2/SHOOTLESS4 (SHL4) and WAVY LEAF1 (WAF1) participate in determining the polarity of the lemma and palea (Itoh et al 2000; Nagasaki et al 2007; Abe et al 2010)
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