Differences on the transcriptomic profiles explain clonal phenotypic variation in Vitis vinifera L. ‘Malbec’

CALDERÓN LUCIANO; CARBONELL-BEJERANO, PABLO; CLAUDIO MUÑOZ; BREE, LAURA; BERGAMIN, DANIEL; CRISTOBAL SOLA; IBÁÑEZ, JAVIER; JOSÉ MIGUEL MARTÍNEZ-ZAPATER; DETLEF WEIGEL; LIJAVETZKY, DIEGO

Quedlinburg

Simposio; XIII. International Symposium on Grapevine Breeding and Genetics; 2022

Julius Kühn-Institut

Cultivated grapevines are clonally propagated, mainly to maintain phenotypic traits of productiveinterest; this practice turns particularly relevant in the wine industry to preserve the varietal typicity.Nonetheless, a wide clonal phenotypic diversity has been reported for several cultivars. Malbec isappreciated for producing high-quality red wines and recognized world-wide as the flag cultivar ofthe Argentine viticulture. Previous analyses demonstrated a notorious clonal phenotypic diversity forMalbec, in technologically relevant traits. On the other hand, clonal genetic diversity was shown tobe scarce, affecting mostly the intergenic regions. Aiming to dissect the molecular bases of thereported phenotypic diversity, we studied 27 clonal accessions grown under the same environmentaland cultural conditions at Vivero Mercier Argentina experimental vineyard. Phenotypic analyses wereperformed on berries at technological maturity (∼23º Brix), during two consecutive seasons (2017-2019). More precisely, we meassured: i) phenolic composition, ii) analytical profile and iii) skinweight. Afterwards, we chose the six accessions exhibiting extreme contrasting values for theevaluated features. Whole RNA extractions were performed from veraison berries (75% colored),from the six selected clones. Illumina stranded paired-end reads (150 bp in length) were obtained,totaling ∼122 Gb of transcriptomic data for 18 samples (6 clones x 3 biological replicates). In order toperform differential gene expression (DEG) and gene ontology (GO) enrichment analyses, theobtained transcriptomic data was aligned to a Malbec reference genome, assembled de novo in atruly-phased fashion and annotated by our group. After performing a discriminant analysis includingall RNA-seq data, clone Cot-595 exhibited a highly differentiated transcriptomic profile. Moreover,this clone showed the highest total polyphenols and anthocyanins concentration, while clones Mb-506 and Cot-596 showed the lowest concentrations. Therefore, we focused the fore coming DEG andGO analyses to pairwise comparisons among the three mentioned accessions. Consistently, Cot-595exhibited GO enrichment for genes involved in the anthocyanins biosynthesis pathways, while Mb-506 and Cot-596 showed enrichment for genes involved in metabolic pathways that regulatevegetative growth. These results suggest that phenotypic diversity observed among Malbec clones,might have solid ground on the described differences at the transcriptomic level.