Nandudu Leah, Sheat Samar, Winter Stephan, Ogbonna Alex, Kawuki Robert, Jannink Jean-Luc
School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States.
Root Crops Department, National Crops Resources Research Institute (NaCRRI), Kampala, Uganda.
Front Plant Sci. 2024 Mar 13;15:1365132. doi: 10.3389/fpls.2024.1365132. eCollection 2024.
Cassava, a vital global food source, faces a threat from Cassava Brown Streak Disease (CBSD). CBSD results from two viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). These viruses frequently pose challenges to the traditional symptom-based 1-5 phenotyping method due to its limitations in terms of accuracy and objectivity. Quantitative polymerase chain reaction (qPCR) offers precise virus quantification, although high costs hinder its widespread adoption. In this research, we utilized qPCR to measure the viral titer/load of CBSV and UCBSV. The objectives were to evaluate titer variability within the Cycle 2 (C2) population in two different environments, establish connections between viral titers and CBSD severity scores from the 1-5 scoring method, perform Genome-Wide Association Studies (GWAS) to identify genomic regions associated with CBSV and UCBSV titers, and investigate the functional annotated genes. The results demonstrated a significantly higher prevalence of CBSV (50.2%) in clones compared to UCBSV (12.9%) with mixed infections in some cases. Genotypic effects, particularly concerning UCBSV, were significant, with genotype-by-environment effects primarily influencing CBSV titer. GWAS Studies identified genomic regions associated with CBSV and UCBSV titers. Twenty-one SNP markers on chromosomes 10, 13, 17, and 18 exhibited significant associations with CBSV titer, collectively explaining 43.14% of the phenotypic variation. Additionally, 25 SNP markers on chromosomes 1, 2, 4, 5, 8, 11, 12, 13, 16, and 18 were associated with UCBSV titer, and explained 70.71% of the phenotypic variation. No shared genomic regions were identified between CBSV and UCBSV viral titers. Gene ontology analysis also revealed diverse gene functions, especially in transport and catalytic activities. These findings enhance our understanding of virus prevalence, genetics, and molecular functions in cassava plants, offering valuable insights for targeted breeding strategies.
木薯是一种重要的全球粮食来源，正面临木薯褐色条纹病（CBSD）的威胁。CBSD由两种病毒引起：木薯褐色条纹病毒（CBSV）和乌干达木薯褐色条纹病毒（UCBSV）。由于传统的基于症状的1 - 5表型分析方法在准确性和客观性方面存在局限性，这些病毒经常给该方法带来挑战。定量聚合酶链反应（qPCR）可提供精确的病毒定量，尽管成本高昂阻碍了其广泛应用。在本研究中，我们利用qPCR来测量CBSV和UCBSV的病毒滴度/载量。目标是评估在两种不同环境下第二代（C2）群体中的滴度变异性，建立病毒滴度与1 - 5评分法的CBSD严重程度评分之间的联系，进行全基因组关联研究（GWAS）以识别与CBSV和UCBSV滴度相关的基因组区域，并研究功能注释基因。结果表明，与UCBSV（12.9%）相比，CBSV在克隆中的流行率显著更高（50.2%），在某些情况下存在混合感染。基因型效应，特别是关于UCBSV的效应显著，基因型与环境的交互效应主要影响CBSV滴度。GWAS研究确定了与CBSV和UCBSV滴度相关的基因组区域。10号、13号、17号和18号染色体上的21个单核苷酸多态性（SNP）标记与CBSV滴度表现出显著关联，共同解释了43.14%的表型变异。此外，1号、2号、4号、5号、8号、11号、12号、13号、16号和18号染色体上的25个SNP标记与UCBSV滴度相关，并解释了70.71%的表型变异。在CBSV和UCBSV病毒滴度之间未发现共享的基因组区域。基因本体分析还揭示了多种基因功能，特别是在运输和催化活性方面。这些发现加深了我们对木薯植株中病毒流行率、遗传学和分子功能的理解，为定向育种策略提供了有价值的见解。
