Brown rust (caused by Puccinia melanocephala H. & P. Sydow) is one of the most devastating diseases in commercial sugarcane production. It could reduce sugarcane yield by up to 50% depending on the susceptibility levels of cultivars. Breeding disease-resistant cultivars is the most effective, economical, and environmentally friendly option to control brown rust. A genome-wide association study was conducted on a field trial using 432 sugarcane clones following an augmented design with two replications. Brown rust was screened using the whorl inoculation method over two crop cycles. The genotype data were obtained through target enrichment sequencing technologies. The gene actions considering six different models and marker dosage effects were included during the marker-trait analysis. A total of seven, nine, and seven nonredundant marker-trait associations were identified for plant cane, first ratoon, and across two crop cycles, respectively. The most significant (p-value 6.17E⁻²⁰) marker (chr01p59833543) has the additive effect of −0.63 for the diplo-additive model and reduced disease severity the most (41.35%) due to heterozygote (AG) over homozygote allele (AA) combination in the tested clones. Gene annotation of the monoploid sugarcane genome R570 suggested that six putative candidate genes were co-located with significant markers associated with brown rust resistance in sugarcane. The putative candidate genes regulated the formation of a cell wall barrier that plays a crucial role in controlling brown rust pathogen infection. The results of this study will open the path to exploiting new resistance sources for brown rust resistance in commercial sugarcane.

中文翻译：

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甘蔗褐锈病的标志性状关联及候选基因鉴定


褐锈病（由Puccinia melanocephala H. & P. Sydow引起）是商业甘蔗生产中最具破坏性的疾病之一。它可以使甘蔗产量降低多达 50%，具体取决于品种的易感性水平。培育抗病品种是控制褐锈病最有效、最经济、最环保的选择。在田间试验中使用 432 个甘蔗克隆进行了全基因组关联研究，遵循具有两个重复的增强设计。使用轮生接种法在两个作物周期中筛选褐锈病。基因型数据是通过靶标富集测序技术获得的。在标记-性状分析过程中，考虑了 6 种不同模型和标记剂量效应的基因作用。共鉴定出 7 、 9 和 7 个非冗余标记性状关联，分别用于植物甘蔗、第一根和两个作物周期。最显著 （p 值 6.17E-20） 标记 （chr01p59833543） 对于二倍体加性模型具有 -0.63 的加法效应，并且由于杂合子 （AG） 优于纯合子等位基因 （AA） 组合，疾病严重程度降低最 （41.35%）在测试克隆中。单倍体甘蔗基因组 R570 的基因注释表明，六个推定的候选基因与甘蔗中与褐锈病抗性相关的重要标记位于同一位置。推定的候选基因调节细胞壁屏障的形成，该屏障在控制褐锈病病原体感染中起着至关重要的作用。这项研究的结果将为开发商业甘蔗抗褐锈病的新抗性来源开辟道路。