Genome-Wide Identification and Expression Analysis of Senescence-Associated Genes in Grapevine (Vitis vinifera L.) Reveal Their Potential Functions in Leaf Senescence Order

Abstract

Natural leaf senescence is an acclimation strategy that enables plants to reallocate nutrients. In the present study, interestingly, we found that the basal mature leaves of grapevine primary shoots (P) exhibited the earliest senescence, followed by the apical young leaves of secondary shoots (ST), and then the basal mature leaves of secondary shoots (S). The Chl level decreased with the extent of leaf senescence. According to the genome-wide identification and expression analysis, sixteen senescence-associated genes (SAGs) involved in Chl breakdown were identified in the grapevine genome. Their expression patterns showed that the transcript changes in VvSGR, VvPPH2, and VvFtsH6-2 corresponded to the changes in Chl content among P, S, and ST. The changes in the transcription of VvNYC1, VvSGR, VvPAO1, VvPAO2, VvPAO4, VvPPH1, VvPPH3, and VvFtsH6-1 only contributed to low Chl levels in P. The cis-element analysis indicated that these SAGs possessed several light- and hormone-responsive elements in their promoters. Among them, ABA-responsive elements were found in twelve of the sixteen promoters of SAGs. Correspondingly, ABA-signaling components presented various changes in transcription among P, S, and ST. The transcription changes in VvbZIP45 and VvSnRK2.1 were similar to those in VvSGR, VvPPH2, and VvFtsH6-2. The other nine ABA-signaling components, which included VvRCAR2, VvRCAR4, VvRCAR6, VvRCAR7, VvRCAR2, VvPP2C4, VvPP2C9, VvbZIP25, and VvSnRK2.3, were highly expressed in P but there was no difference between S and ST, with similar expression patterns for VvNYC1, VvSGR, VvPAO1, VvPAO2, VvPAO4, VvPPH1, VvPPH3, and VvFtsH6-1. These results suggested that the senescence of P and ST could be regulated by different members of Chl breakdown-related SAGs and ABA-signaling components. These findings provide us with important candidate genes to further study the regulation mechanism of leaf senescence order in grapevine.

Keywords: ABA; chlorophyll; gene expression; grapevine; leaf order; senescence.

Figure 1

Leaf senescence depends on the leaf’s position in the grapevine. (A–C) Photographs of grapevine leaves with different extents of leaf senescence; (D,E) the content of chlorophyll a (Ca) and chlorophyll b (Cb). Values represent the means ± SD of 3 biological replicates. Different lowercase letters represent significant differences at p-value < 0.05.

Figure 2

Phylogenetic analysis of Chl degradation-related SAGs. (A) Phylogenetic analysis of NYC/NOL from grapevine, Arabidopsis (Arabidopsis thaliana), tobacco (Nicotiana tabacum), and sweet orange (Citrus sinensis). (B) Phylogenetic analysis of SGR/SGRL from Arabidopsis (Arabidopsis thaliana), cabbage (Brassica campestris), soybean (Glycine max), rice (Oryza sativa), maize (Zea mays), and bamboo (Neosinocalamus affinis). (C) Phylogenetic analysis of RCCR from grapevine, Arabidopsis (Arabidopsis thaliana), cabbage (Brassica rapa var. parachinensis), and sweet orange (Citrus sinensis). (D) Phylogenetic analysis of HCAR from grapevine, Arabidopsis (Arabidopsis thaliana), sweet orange (Citrus sinensis), tobacco (Nicotiana tabacum), and rice (Oryza sativa). (E) Phylogenetic analysis of PAO from grapevine, Arabidopsis (Arabidopsis thaliana), sweet orange (Citrus sinensis), tobacco (Nicotiana tabacum), cabbage (Brassica rapa var. parachinensis), and pepper (Capsicum annuum). (F) Phylogenetic analysis of PPH from grapevine, Arabidopsis (Arabidopsis thaliana), tobacco (Nicotiana tabacum), sweet orange (Citrus sinensis), cabbage (Brassica rapa var. Parachinensis), and perennial ryegrass (Lolium perenne). (G) Phylogenetic analysis of FtsH from grapevine and Arabidopsis (Arabidopsis thaliana).

Figure 3

The expression patterns of Chl degradation-related SAGs in grapevine leaves with different extents of leaf senescence. Values represent the means ± SD of three biological replicates. Different lowercase letters represent significant differences at p-value < 0.05.

Figure 4

The expression patterns of ABA-signaling components in grapevine leaves with different extents of leaf senescence. Values represent the means ± SD of 3 biological replicates. Different lowercase letters represent significant differences at p-value < 0.05.