Elucidating the transcriptomic bases of floral alterations hindering fruit set rate in Malbec clones

Abstract

Fruit set is the transformation of flowers into berries, a major component of yield in grapevines. The efficiency of this process dependson multiple factors, including plants’ reproductive performance. In Malbec, it has been shown that fruit set rate is highly variable and clone dependent. Furthermore, extremely low fruit set rates were associated with morphological and functional floral alterations. Here, we aimed to elucidate the transcriptomic bases of such flower alterations by analyzing three Malbec clones. Clones Mb510 and Mb515 wereselected for exhibiting consistently low fruit set rates, and clone Mb508 was selected as a high fruit set rate control. Total RNAwasextracted from flowers sampled before anthesis (stage EL-14), and each clone was represented by three biological replicates. RNA-seqwas performed with Illumina technology to obtain stranded short-reads (average coverage 20x). Differential gene expression analyses were performed using a pipeline based on the R package DESeq2. Two pairwise analyses were performed to identify differentiallyexpressed genes (DEGs): Mb508 vs Mb510 and Mb508 vs Mb515. In both comparisons several statistically significant DEGs were detected (p < 0.05), some of them relevant for flower development and functionality. In clone Mb510 low fruit set rate was linked to anthers indehiscence and low pollen viability. This phenotype was explained by the downregulated genes DEHYDRATION INDUCED PROTEIN (Vitvi10g00491) and EXPANSIN-A10 (Vitvi17g01251), involved in anthers’ cell wall dehydration, loosening and opening. Furthermore, flavonoids are needed for the correct pollen maturation and a key enzyme for flavonoid biosynthesis was downregulated in Mb510: FLAVONOID 3’5′ HYDROXYLASE (Vitvi06g01890). In regard to clone Mb515, low fruit set was associated withmalformations such as stamen-pistil fusions, as well as decumbent/crinkled stamens. Two transcription factors associated with the described phenotypes were significantly downregulated in Mb515: CYCLOIDEA(Vitvi17g00374) involved in flower symmetry determination, and bHLH021 (Vitvi18g04102) involved in masculine organogenesis and gametogenesis. Overall, downregulation ofkey genes involved in floral development and functionality provided insight into the molecular mechanisms impairing fruit set rate and yield in specific Malbec clones.