Study of /Rubus/ spp. Var. Loch Ness transcriptome and gene expression changes in the flavonoid pathway along maturation. Biotechnological improvement of fruit yield and quality with bioefectors

Séminaire GENETROP par Daniel Garcia-Seco  (UMR IPME, daniel.garcia-seco@ird.fr).

Because of recent discoveries about the beneficial effects of polyphenols for human health there is an increasing interest in berries, especially blackberries, due to their high content of anthocyanins. We demonstrated the ability of P. fluorescens  N21.4 to improve both quality and production of blackberry in field conditions. The aim of the study was twofold, first to obtain a blackberry (Rubus sp. Var. Lochness) fruit transcriptome, and second, to study differential expression in the transcriptome caused by P. fluorescens  N21.4. De novo RNA-seq of ripe blackberries was performed. In total 34,552 annotated sequences were identified. Non redundant (NR), annotation showed that 25,418 genes has the highest similarity with/Fragaria vesca/  subspecies vesca. Reanalysis was undertaken by aligning the reads with this reference genome for a deeper analysis of the transcriptome.  We demonstrated that de novo assembly, using Trinity and later annotation with Blast using different databases, were complementary to alignment to the reference sequence using SOAPaligner/SOAP2. On the other hand, PGPR may trigger flavonoid biosynthesis as part of the induced systemic response (ISR)  given the important role of this pathway in plant defence, to cause increased levels of flavonoids in the fruit.  We have identified structural genes encoding enzymes of the phenylpropanoid and flavonoid biosynthetic pathways,  and regulatory genes likely involved in controlling the activity of pathway branches. We have also measured the major flavonols,  anthocyanins and catechins at three stages during ripening. Our results demonstrate the coordinated expression of flavonoid biosynthetic genes with the accumulation of these compounds in developing fruits of blackberry. Elicitation with/P. fluorescens/  N21.4 caused increased expression of flavonoid biosynthetic genes and an accompanying  increase in the concentration of selected flavonoids in fruits. This demonstrates the physiological mechanisms involved in the improvement of fruit quality by PGPR under field conditions, and highlights some of the genetic targets of elicitation  by beneficial bacteria.

*équipe d organisation :*
Laurence Albar (laurence.albar@ird.fr <mailto:laurence.albar@ird.fr>)
Valérie Poncet (valerie.poncet@ird.fr <mailto:valerie.poncet@ird.fr>)
Charlotte Tollenaere (charlotte.tollenaere@ird.fr <mailto:charlotte.tollenaere@ird.fr>)