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. 2024 Feb 7;25(1):14.
doi: 10.1186/s12863-024-01198-x.

Transcriptomic analysis of developing sorghum grains to detect genes related to cell wall biosynthesis and remodelling

Camille Costes  1 , Sergi Navarro Sanz  2   3   4 , Caroline Calatayud  2   3 , Alexandre Soriano  2   3 , Hamza Mameri  5 , Nancy Terrier  6 , Mathilde Francin-Allami  1
Affiliations

Transcriptomic analysis of developing sorghum grains to detect genes related to cell wall biosynthesis and remodelling

Camille Costes et al. BMC Genom Data. .

Abstract

Objective: Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important grain produced in the world. Interest for cultivating sorghum is increasing all over the world in the context of climate change, due to its low input and water requirements. Like other cultivated cereals, sorghum has significant nutritional value thanks to its protein, carbohydrate and dietary fiber content, these latter mainly consisting of cell wall polysaccharides. This work describes for the first time a transcriptomic analysis dedicated to identify the genes involved in the biosynthesis and remodelling of cell walls both in the endosperm and outer layers of sorghum grain during its development. Further analysis of these transcriptomic data will improve our understanding of cell wall assembly, which is a key component of grain quality.

Data description: This research delineates the steps of our analysis, starting with the cultivation conditions and the grain harvest at different stages of development, followed by the laser microdissection applied to separate the endosperm from the outer layers. It also describes the procedures implemented to generate RNA libraries and to obtain a normalized and filtered table of transcript counts, and finally determine the number of putative cell wall-related genes already listed in literature.

Keywords: Cell wall polysaccharides; Grain development; Laser microdissection; Sorghum; Transcriptome.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Number of transcripts expressed in each sample. 7_End: endosperm at 7 DAF (Days After Flowering); 13_End: endosperm at 13 DAF; 30_End: endosperm at 30 DAF; 7_OL: outer layers at 7 DAF, 13_OL: outer layers at 13 DAF, 30_OL: outer layers at 30 DAF. Data are the mean ± Standard deviation of three biological replicates
Fig. 2
Fig. 2
Principal component analysis (PCA) of transcriptomic data from endosperm (End) and outer layers (OL) of sorghum grains at different developmental stages (7, 13 and 30 Days After Flowering (DAF)). A, B, C: representation of samples as functions of components 1 to 4. D: Number of transcripts explaining 50% and 90% of the different components. 7_End: endosperm at 7 DAF; 13End: endosperm at 13 DAF; 30_End: endosperm at 30 DAF; 7_OL: outer layers at 7 DAF, 13_OL: outer layers at 13 DAF, 30_OL: outer layers at 30 DAF
See this image and copyright information in PMC

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