Ault Noah, Ren Shuchao, Payne David, Li Yongfang, Srinivasan Asha, Zheng Yun, Sunkar Ramanjulu, Naidu Rayapati A
Department of Plant Pathology, Washington State University - Irrigated Agriculture Research and Extension Center, Prosser, WA, 99350, USA.
College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China.
BMC Genomics. 2025 Apr 29;26(1):417. doi: 10.1186/s12864-025-11539-4.
Red blotch disease, caused by Grapevine red blotch virus (GRBV, genus Grablovirus, family Geminiviridae), negatively impacts vine health, fruit yield, and quality, leading to substantial economic losses to growers. While recent studies have enhanced our understanding of the epidemiology of GRBV and its effects, little is known about the molecular basis of the host-virus interactions. Since small RNAs (sRNAs) are known to play a central role in host-virus interactions, this study was undertaken to investigate sRNA dynamics in leaves and berries at two phenological stages (asymptomatic pre- and symptomatic post-véraison) of GRBV-infected grapevines (Vitis vinifera cv. Merlot).
Among the 140 microRNAs (miRNAs) detected, 41 isoforms belonging to 18 miRNA families exhibited significant differential expression in response to GRBV infection. Furthermore, 50 miRNAs showed differential expression in samples from pre- and post-véraison stages. A total of 58 conserved and 41 novel targets for known V. vinifera miRNAs were validated using degradome sequencing data from leaf samples of pre- and post-véraison stages. Additionally, virus-derived siRNAs (vsiRNAs) specific to GRBV were present only in GRBV-positive samples. The vsiRNAs predominantly ranged from 19 to 24 nucleotides (nt), with the 21nt size being the most abundant. Mapping vsiRNAs across the GRBV genome revealed an uneven distribution, with vsiRNA-generating hotspots predominantly located in the V3 ORF. Of the 83 most abundant vsiRNAs, grapevine target transcripts were identified for eight of them.
Identification of differentially expressed miRNAs and vsiRNAs, as well as their targets, offered important insights into various pathways and mechanisms that were affected in grapevine infected with GRBV and in modulating different host responses in leaves and berries. This research serves as a foundation for a better understanding of the molecular interactions in this plant-geminivirus pathosystem.
葡萄红斑点病由葡萄红斑点病毒（GRBV，Grablovirus属，双生病毒科）引起，对葡萄藤健康、果实产量和品质产生负面影响，给种植者造成重大经济损失。尽管最近的研究增进了我们对GRBV流行病学及其影响的理解，但对于宿主 - 病毒相互作用的分子基础知之甚少。由于已知小RNA（sRNA）在宿主 - 病毒相互作用中起核心作用，本研究旨在调查GRBV感染的葡萄（葡萄品种梅洛）在两个物候阶段（无症状的转色前和有症状的转色后）叶片和浆果中的sRNA动态变化。
在检测到的140种 microRNA（miRNA）中，属于18个miRNA家族的41种异构体在响应GRBV感染时表现出显著差异表达。此外，50种miRNA在转色前和转色后阶段的样品中表现出差异表达。利用转色前和转色后阶段叶片样品的降解组测序数据，验证了已知葡萄miRNA的总共58个保守靶标和41个新靶标。此外，GRBV特异性的病毒衍生siRNA（vsiRNA）仅存在于GRBV阳性样品中。vsiRNA主要长度范围为19至24个核苷酸（nt），其中21nt大小最为丰富。将vsiRNA定位到GRBV基因组上显示分布不均匀，vsiRNA产生热点主要位于V3 ORF。在83种最丰富的vsiRNA中，鉴定出其中8种的葡萄靶转录本。
差异表达的miRNA和vsiRNA及其靶标的鉴定，为GRBV感染的葡萄中受影响的各种途径和机制以及调节叶片和浆果中不同宿主反应提供了重要见解。本研究为更好地理解这种植物 - 双生病毒病理系统中的分子相互作用奠定了基础。
