Genome-wide identification of the LEA protein gene family in grapevine (Vitis vinifera L.)

Abstract

The Late Embryogenesis Abundant (LEA) protein gene family is associated with salt and drought stress tolerance in many plant species. However, the number of LEA-encoding genes in the grape (Vitis vinifera) genome has not been previously determined. Here, we conducted a phylogenetic analysis to identify individual members of the LEA gene family in V. vinifera. This analysis identified 60 members of this gene family classified into nine subfamilies (DHN, LEA1, LEA2, LEA3, LEA4, LEA5, LEA6, WHY and SMP) in the grape genome. With 35 members, the LEA2 subfamily constituted the largest subgroup. LEA-encoding genes are non-randomly distributed across most grape chromosomes, suggesting that, similarly to other species, a significant portion of VvLEAs was originated by segmental or tandem duplications. Bioinformatic analyses suggested that the majority of the grape LEA2 proteins is associated with plasma membrane whilst many members of other families are likely to be found in different subcellular locations such as cytoplasm, nucleus and mitochondria. The promoters of these genes contain cis-acting sequence elements associated with stress responses. Expression profiles of a subset of LEA-encoding genes from publically available Affymetrix Vitis vinifera (grape) Genome Array expression data showed that these genes are responsive to salt and dehydration. We also experimentally studied stress-responsive expression patterns of VvDHN1 encoding a dehydrin (DHN) and VvLEA D29L (VvLEA D29Like) encoding a LEA4 protein in the grape cultivar V. vinifera L. cvs. Cabernet Sauvignon (CS) and the rootstock Solonis X riparia 1616 C (1616 C) under salt- and PEG-induced drought stress by qRT-PCR. Both VvDHN1 and VvLEA D29L responded very strongly to these stresses in 1616 C whilst VvLEA D29L was induced only in CS. In response to PEG, VvLEA D29L was induced in both genotypes whilst VvDHN1 showed induction only in CS. Overall, our results suggest the LEA gene family is associated with stress tolerance and manipulation of these genes might provide increased stress tolerance in grapes.