Campos, N.

Carpentier, Sebastien C.

Hueber, Y.

Kissel, E.

Swennen, Rony L.

Wesemael, J. van

CGSpace

Quantification and identification of allele specific proteins for polyploid non-model crops: Proof of principle for 3 banana genotypes/phenotypes.Jelle van Wesemael1, Yann Hueber2, Ewaut Kissel1, Nadia Campos1, Rony Swennen1,3,4, Sebastien Carpentier1,5260 amino acid polymorphisms (SAAP) are identified by alignment of thepeptide sequences to every cultivar specific database130 additional allele specific genes are selected through combination ofunivariate and multivariate statistics based on the peptide abundance.Some polymorphisms in the droughttolerant phenotype (ABB) displayhomeolog expression biasMultivariate: Sparse Partial Least Squares (sPLS-DA, mixomics, R)Univariate: Kruskal-Wallis (p<0.05, BH corrected)Cultivar specific genes are involved ingeneral osmotic stress responses.The variant specific read count (mRNA) was calculated forthe ABB cultivar, a triploid hybrid cross:1 Musa acuminata (A)2 Musa balbisiana (B) genomes.Thus we expect:33% of reads A-isoform66% of reads B-isoform27 genes have 100 % B reads (expression level dominance)Phenotype of preference (ABB) invests in root growthwith minimal setback under osmotic stressMining the Musa genome by integration of transcriptomics withproteomics identifies 390 genes with allele specificity linked to thedifferential phenotypeThe phenotype is controlled by different protein isoform(s) / transcript(s) / gene copy(s).This integrative workflow allows to unravel genetic diversity in polyploid (non-) modelcrops at the gene variant level.We identified 2754 proteins260 identified SAAP130 with differential peptide abundanceSome of the allele specific transcript levels show deviations from what is expected basedon the genomic constitution27 identified polymorphisms show 100% biased expression levels.Specific alleles are enriched in genes related to general osmotic stress responses,respiration, ROS scavenging, and HSP.Banana (Musa spp.) is the most important fruit crop in the world.Cultivars are triploid, hybrid crosses of M. acuminata (A) and M. balbisiana (B)Vulnerable to droughtPolyploidy results in a plethora of genomic, transcriptomic, and proteomic productscontrolling the phenotype.Allelic variants are of interest for climate smart agriculture : flexibility towards theenvironmentOur goal: Mining the Musa biodiversity for drought tolerance:Select allele specific proteins linked to the observed phenotypic differences amongthree contrasting genotypes by integration of transcriptomics and proteomics.The ABB genotype shows more rootgrowth under control and mild osmoticstress conditions.GO-term Description p (Fisher)GO:0006096 Glycolytic process 0.003GO:0006457 Protein folding 0.015GO:0006950 Response to stress 0.018The functions of identified alleles are enriched ingeneral osmotic stress responsesIdentified specific lociAuthor Affiliations: 1Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KULeuven, B-3001 Leuven. 2Bioversity International, Parc Scientifique AgropolisII, 34397 Montpellier Cedex5, France. 3Bioversity International, Willem De Croylaan 42, B-3001 Leuven, Belgium. 4InternationalInstitute of Tropical Agriculture (iita.org). C/0 The Nelson Mandela African Institution of Science andTechnology, P.O. Box 44, Arusha, Tanzania. 5Facility for Systems Biology based Mass Spectrometry(SYBIOMA), KU Leuven, B-3001 Leuven.Contact: jelle.vanwesemael@kuleuven.beAcknowledgements: Edwige André, Lut Ooms, Els Thiry, Saskia Windelinckx, and Kusay Arat aregratefully acknowledged for their technical assistance. Financial support for JvW by the PhD fellowshipfrom Bioversity international, financed by the Belgian Directorate General for Developmental Cooperation(DGDC) is gratefully acknowledgedCultivarsAlignment of peptide query to amino acid (RNA based) database(BLAST)Example of Ma02_t23730 (Sucrose Synthase 2)Variant analysis (RNA)

Quantification and identification of allele specific proteins for polyploidnon-model crops: Proof of principle for 3 banana genotypes/phenotypes

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Quantification and identification of allele specific proteins for polyploidnon-model crops: Proof of principle for 3 banana genotypes/phenotypes

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