Abstract：
Rice yellow mottle virus disease, caused by Rice yellow mottle virus (RYMV), is the most important disease of lowland rice in Uganda. However, little is known about its genetic diversity in Uganda and relationships with other strains elsewhere across Africa. A new degenerate primer pair that targets amplification of the entire RYMV coat protein gene (circa 738 bp) was designed to aid virus variability analysis using RT-PCR and Sanger sequencing. A total of 112 rice leaf samples from plants with RYMV mottling symptoms were collected during the year 2022 in 35 lowland rice fields within Uganda. The RYMV RT-PCR results were 100% positive, and all 112 PCR products were sequenced. BLASTn analysis revealed that all isolates were closely related (93 to 98%) to those previously studied originating from Kenya, Tanzania, and Madagascar. Despite high purifying selection pressure, diversity analysis on 81 out of 112 RYMV CP sequences revealed a very low diversity index of 3 and 1.0% at the nucleotide and amino acid levels, respectively. Except for glutamine, amino acid profile analysis revealed that all 81 Ugandan isolates shared the primary 19 amino acids based on the RYMV coat protein region examined. Except for one isolate (UG68) from eastern Uganda that clustered alone, phylogeny analysis revealed two major clades. The Ugandan RYMV isolates were phylogenetically related to those from the Democratic Republic of Congo, Madagascar, and Malawi but not to RYMV isolates in West Africa. Thus, the RYMV isolates in this study are related to serotype 4, a strain common in eastern and southern Africa. RYMV serotype 4 originated in Tanzania, where evolutionary forces of mutation have resulted in the emergence and spread of new variants. Furthermore, mutations are evident within the coat protein gene of the Ugandan isolates, which may be attributed to changing RYMV pathosystems as a result of rice production intensification in Uganda. Overall, the diversity of RYMV was limited and most noticeably in eastern Uganda.
摘要：
水稻黄斑驳病毒病,由水稻黄斑驳病毒（RYMV）引起，是乌干达低地水稻最主要的病害。然而,鲜为人知，关于其在乌干达的遗传多样性以及与非洲其他地方的其他菌株的关系。一种新的简并引物对，靶向整个RYMV外壳蛋白基因的扩增（约738bp）被设计用于使用RT-PCR和Sanger测序来辅助病毒变异性分析。在2022年期间，在乌干达的35个低地稻田中收集了来自具有RYMV斑点症状的植物的112个水稻叶片样品。RYMVRT-PCR结果为100%阳性,并对所有112个PCR产物进行测序。BLASTN分析显示，所有分离株与先前研究的来自肯尼亚的分离株密切相关（93-98％），坦桑尼亚,马达加斯加。尽管净化选择压力很高，对112个RYMVCP序列中的81个进行的多样性分析显示，在核苷酸和氨基酸水平上的多样性指数非常低，分别为3％和1.0％，分别。除了谷氨酰胺,氨基酸谱分析显示，根据所检查的RYMV外壳蛋白区域，所有81个乌干达分离株共享19个主要氨基酸。除了一个来自乌干达东部的分离株(UG68)单独聚集，系统发育分析揭示了两个主要分支。乌干达RYMV分离株与刚果民主共和国分离株的系统发育相关，马达加斯加，马拉维,但不是西非的RYMV分离株。因此，本研究中的RYMV分离株与血清型4有关，这是一种在东部和南部非洲常见的菌株。RYMV血清型4起源于坦桑尼亚，变异的进化力量导致了新变异的出现和传播。此外，乌干达分离株的外壳蛋白基因中有明显的突变，这可能归因于乌干达水稻生产集约化导致RYMV病理系统的变化。总的来说,RYMV的多样性是有限的，最明显的是乌干达东部。
