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. 2021 Nov 4;21(1):514.
doi: 10.1186/s12870-021-03276-z.

Comparative transcriptome analysis of coleorhiza development in japonica and Indica rice

Tao Song #  1   2 , Debatosh Das #  2 , Neng-Hui Ye  3 , Guan-Qun Wang  4 , Fu-Yuan Zhu  1 , Mo-Xian Chen  1   5 , Feng Yang  6 , Jian-Hua Zhang  7   8   9
Affiliations

Comparative transcriptome analysis of coleorhiza development in japonica and Indica rice

Tao Song et al. BMC Plant Biol. .

Abstract

Background: Coleorhiza hairs, are sheath-like outgrowth organs in the seeds of Poaceae family that look like root hair but develop from the coleorhiza epidermal cells during seed imbibition. The major role of coleorhiza hair in seed germination involves facilitating water uptake and nutrient supply for seed germination. However, molecular basis of coleorhiza hair development and underlying genes and metabolic pathways during seed germination are largely unknown and need to be established.

Results: In this study, a comparative transcriptome analysis of coleorhiza hairs from japonica and indica rice suggested that DEGs in embryo samples from seeds with embryo in air (EIA) as compared to embryo from seeds completely covered by water (CBW) were enriched in water deprivation, abscisic acid (ABA) and auxin metabolism, carbohydrate catabolism and phosphorus metabolism in coleorhiza hairs in both cultivars. Up-regulation of key metabolic genes in ABA, auxin and dehydrin and aquaporin genes may help maintain the basic development of coleorhiza hair in japonica and indica in EIA samples during both early and late stages. Additionally, DEGs involved in glutathione metabolism and carbon metabolism are upregulated while DEGs involved in amino acid and nucleotide sugar metabolism are downregulated in EIA suggesting induction of oxidative stress-alleviating genes and less priority to primary metabolism.

Conclusions: Taken together, results in this study could provide novel aspects about the molecular signaling that could be involved in coleorhiza hair development in different types of rice cultivars during seed germination and may give some hints for breeders to improve seed germination efficiency under moderate drought conditions.

Keywords: Abscisic acid; Auxin; Coleorhiza hair; Indica; Japonica; Transcriptomics; Water.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Phenotypic comparison of coleorhiza hair development in japonica (NIP) and indica (9311) cultivars. A and E, coleorhiza hair development in japonica under CBW at T1 and T2stages. B and F, coleorhiza hair development in indica under CBW at T1 and T2 stages. C and G, coleorhiza hair development in japonica under EIA conditions at T1 and T2 stages. D and H, coleorhiza hair development in indica under EIA conditions at T1 and T2 stages
Fig. 2
Fig. 2
Overview of RNA-seq in coleorhiza hair development of japonica and indica cultivars. A, PCA variation analysis of samples in japonica and indica. B, Total DEGs in japonica and indica at T1 and T2 stages. C, Venn diagram of DEGs shared by japonica and indica at T1 and T2 stages
Fig. 3
Fig. 3
Biological process (BP) in GO enrichments analysis of DEGs in japonica and indica. A, Up-regulated DEGs at T1 and T2 enriched in BP in both cultivars. B, Down-regulated DEGs at T1 and T2 enriched in BP in both cultivars. C, DEGs up-regulated at T1 and down-regulated at T2 enriched in BP in both cultivars. D, Common DEGs down-regulated at T1 and up-regulated at T2 stage in both cultivars
Fig. 4
Fig. 4
KEGG analysis of DEGs accumulated pathways shared in japonica and indica. A, DEGs that were up-regulated at T1 and T2 stages in accumulated pathways. B, DEGs that were down-regulated at T1 and T2 stages in accumulated pathways. C, DEGs that were up-regulated at T1 stages and down-regulated at T2 stages in accumulated pathways
Fig. 5
Fig. 5
DEGs involved in GO enriched biological processes. A, DEGs enriched in “responses to water deprivation” BP categories. B, DEGs enriched in “carbohydrate catabolic process” BP categories
Fig. 6
Fig. 6
DEGs enriched in “phosphorus catabolic process and xylan catabolic process” BP categories of GO enrichments
Fig. 7
Fig. 7
KEGG analysis of DEGs related to ABA biosynthetic pathways in coleorhiza hair development in japonica and indica
Fig. 8
Fig. 8
KEGG analysis of DEGs related to auxin biosynthetic pathways in coleorhiza hair development in japonica and indica
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References

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