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Identification and expression analyses of new potential regulators of xylem development and cambium activity in cassava (Manihot esculenta)

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Abstract

Main conclusions

We have identified new potential regulators of xylem cell-type determination and cellular proliferation in cassava and studied their expression in roots. Results are highly relevant for cassava biotechnology.

Cassava’s root system is composed of two types of root that coexist in every individual: the fibrous and the storage roots. Whether a root becomes fibrous or storage depends on the xylem cell types that it develops: fibrous roots develop xylem fibres and vessels while storage roots develop parenchyma xylem, the starch-storing tissue. A crucial question in cassava root development is how the specific xylem cell types differentiate and proliferate in the fibrous and storage roots. Using phylogenetic, protein sequence and synteny analyses we identified (1) MeVND6, MeVND7.1, MeVND7.2, MeNST3.1 and MeNST3.2 as the potential cassava orthologues of the Arabidopsis regulators of xylem cell type determination AtVND6, AtVND7 and AtNST3; and (2) MeWOX4.1 and MeWOX4.2 as the potential cassava orthologues of the Arabidopsis cambium regulator AtWOX4. Fibrous and storage roots were anatomically characterised and tested for the expression of the identified genes. Results revealed that (1) MeVND7.1 and MeVND7.2 are expressed in the fibrous but not in the storage roots; (2) MeVND6 shows low expression in both root types; (3) MeNST3.1 is not expressed in the fibrous or storage roots, while MeNST3.2 is highly expressed in both root-types and (4) MeWOX4.1 and, to a higher level, MeWOX4.2 are expressed in both the fibrous and storage roots. Results open new avenues for research in cassava root development and for food security-oriented biotechnology programmes.

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Acknowledgements

We acknowledge John Beeching (University of Bath) for providing plants, David Alabadí (IBMCP-CSIC-UPV, Valencia), Miguel Blazquez (IBMCP-CSIC-UPV, Valencia), Liam Dolan (University of Oxford) and Ana Milhinhos (University of Oxford) for critical review of the manuscript and/or scientific discussions. This work was partially supported by The Royal Society—UK (RG15032).

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Author notes

  1. Javier Agusti

    Present address: Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), C/Ingeniero Fausto Elio s/n, 46011, Valencia, Spain

Authors and Affiliations

  1. Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK

    Tyche Siebers, Bruno Catarino & Javier Agusti

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  1. Tyche Siebers
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Corresponding author

Correspondence to Javier Agusti.

Electronic supplementary material

Below is the link to the electronic supplementary material.

425_2016_2623_MOESM1_ESM.pdf

Suppl. Fig. S1 MEME alignments of AtNST3, MeNST3.1, MeNST3.2 identify the NAC domain in all three sequences and a domain present in cassava but not-conserved in Arabidopsis (PDF 200 kb)

425_2016_2623_MOESM2_ESM.pdf

Suppl. Fig. S2 MEME alignments of AtWOX4, MeWOX4.1, MeWOX4.2 identify the homeobox domain and the WUS-Box motif in all three sequences (PDF 204 kb)

425_2016_2623_MOESM3_ESM.pdf

Suppl. Fig. S3 Synteny between the genomic region containing VND6 putative orthologues in Manihot esculenta, Linum usitatissimum, Populus trichocarpa, Salix purpurea, Gossypium raimondii, Theobroma cacao and Arabidopsis thaliana. Each box represents a gene. Boxes point to the gene orientation. Lines connect genes encoding the same putative orthologue across species. Dark grey central boxes represent the VND6 orthologue in each species. White boxes represent unknown proteins or proteins with no function assigned (PDF 78 kb)

425_2016_2623_MOESM4_ESM.pdf

Suppl. Fig. S4 Synteny between the genomic region containing VND7 putative orthologues in Manihot esculenta, Linum usitatissimum, Populus trichocarpa, Salix purpurea, Gossypium raimondii, Theobroma cacao and Arabidopsis thaliana. Each box represents a gene. Boxes point to the gene orientation. Lines connect genes encoding the same putative orthologue across species. Dark grey central boxes represent the VND7 orthologue in each species. White boxes represent unknown proteins or proteins with no function assigned (PDF 78 kb)

425_2016_2623_MOESM5_ESM.pdf

Suppl. Fig. S5 Synteny between the genomic region containing NST3 putative orthologues in Manihot esculenta, Linum usitatissimum, Populus trichocarpa, Gossypium raimondii, Theobroma cacao and Arabidopsis thaliana. Each box represents a gene. Boxes point to the gene orientation. Lines connect genes encoding the same putative orthologue across species. Dark grey central boxes represent the NST3 orthologue in each accession. White boxes represent unknown proteins or proteins with no function assigned (PDF 85 kb)

425_2016_2623_MOESM6_ESM.pdf

Suppl. Fig. S6 Synteny between the genomic region containing WOX4 putative orthologues in Manihot esculenta, Linum usitatissimum, Populus trichocarpa, Salix purpurea, Gossypium raimondii, Theobroma cacao and Arabidopsis thaliana. Each box represents a gene. Boxes point to the gene orientation. Lines connect genes encoding the same putative orthologue across species. Dark grey central boxes represent the WOX4 orthologue in each species. White boxes represent unknown proteins or proteins with no function assigned (PDF 82 kb)

Suppl. File S1 Trimmed alignments for NAC phylogeny analyses (TXT 4 kb)

Suppl. File S2 Trimmed alignments for WOX phylogeny analyses (TXT 1 kb)

Suppl. File S3 Genes used for synteny analyses (PDF 87 kb)

Suppl. Table S1 Primers used for gene expression analyses (PDF 16 kb)

Suppl. Table S2 Accession numbers of proteins used for phylogeny (PDF 17 kb)

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Siebers, T., Catarino, B. & Agusti, J. Identification and expression analyses of new potential regulators of xylem development and cambium activity in cassava (Manihot esculenta). Planta 245, 539–548 (2017). https://doi.org/10.1007/s00425-016-2623-2

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