Dept. of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
International Maize and Wheat Improvement Centre (CIMMYT), Hyderabad, India.
BMC Genomics. 2024 Aug 5;25(1):760. doi: 10.1186/s12864-024-10655-x.
In the face of contemporary climatic vulnerabilities and escalating global temperatures, the prevalence of maydis leaf blight (MLB) poses a potential threat to maize production. This study endeavours to discern marker-trait associations and elucidate the candidate genes that underlie resistance to MLB in maize by employing a diverse panel comprising 336 lines. The panel was screening for MLB across four environments, employing standard artificial inoculation techniques. Genome-wide association studies (GWAS) and haplotype analysis were conducted utilizing a total of 128,490 SNPs obtained from genotyping-by-sequencing (GBS).
GWAS identified 26 highly significant SNPs associated with MLB resistance, among the markers examined. Seven of these SNPs, reported in novel chromosomal bins (9.06, 5.01, 9.01, 7.04, 4.06, 1.04, and 6.05) were associated with genes: bzip23, NAGS1, CDPK7, aspartic proteinase NEP-2, VQ4, and Wun1, which were characterized for their roles in diminishing fungal activity, fortifying defence mechanisms against necrotrophic pathogens, modulating phyto-hormone signalling, and orchestrating oxidative burst responses. Gene mining approach identified 22 potential candidate genes associated with SNPs due to their functional relevance to resistance against necrotrophic pathogens. Notably, bin 8.06, which hosts five SNPs, showed a connection to defense-regulating genes against MLB, indicating the potential formation of a functional gene cluster that triggers a cascade of reactions against MLB. In silico studies revealed gene expression levels exceeding ten fragments per kilobase million (FPKM) for most genes and demonstrated coexpression among all candidate genes in the coexpression network. Haplotype regression analysis revealed the association of 13 common significant haplotypes at Bonferroni ≤ 0.05. The phenotypic variance explained by these significant haplotypes ranged from low to moderate, suggesting a breeding strategy that combines multiple resistance alleles to enhance resistance to MLB. Additionally, one particular haplotype block (Hap_8.3) was found to consist of two SNPs (S8_152715134, S8_152460815) identified in GWAS with 9.45% variation explained (PVE).
The identified SNPs/ haplotypes associated with the trait of interest contribute to the enrichment of allelic diversity and hold direct applicability in Genomics Assisted Breeding for enhancing MLB resistance in maize.
面对当代气候脆弱性和不断上升的全球气温，玉米叶斑病（MLB）的流行对玉米生产构成了潜在威胁。本研究通过使用包含 336 条线的多样化面板，旨在通过标记-性状关联来识别和阐明与玉米对 MLB 抗性相关的候选基因。该面板在四个环境中对 MLB 进行了筛选，使用标准人工接种技术。利用从基因分型测序（GBS）获得的总共 128490 个 SNP 进行全基因组关联研究（GWAS）和单倍型分析。
GWAS 在检测到的标记中鉴定出与 MLB 抗性相关的 26 个高度显著的 SNP。其中 7 个 SNP 报告在新的染色体 bin（9.06、5.01、9.01、7.04、4.06、1.04 和 6.05）中与基因相关：bzip23、NAGS1、CDPK7、天冬氨酸蛋白酶 NEP-2、VQ4 和 Wun1，它们的作用是减弱真菌活性、增强对坏死性病原体的防御机制、调节植物激素信号转导和协调氧化爆发反应。基因挖掘方法确定了 22 个与 SNP 相关的潜在候选基因，因为它们与抵抗坏死性病原体的功能相关。值得注意的是，包含 5 个 SNP 的 bin 8.06 与针对 MLB 的防御调节基因有关，表明形成了一个功能性基因簇，触发了针对 MLB 的级联反应。在计算机模拟研究中，大多数基因的每千碱基百万片段（FPKM）超过十个片段，并且在共表达网络中所有候选基因之间显示出共表达。单倍型回归分析显示，在 Bonferroni ≤ 0.05 时，有 13 个常见显著单倍型存在关联。这些显著单倍型解释的表型方差范围从低到中等，表明一种结合多个抗性等位基因以增强对 MLB 抗性的育种策略。此外，发现一个特定的单倍型块（Hap_8.3）由 GWAS 中鉴定出的两个 SNP（S8_152715134、S8_152460815）组成，具有 9.45%的变异解释（PVE）。
与性状相关的鉴定 SNP/单倍型有助于丰富等位基因多样性，并且在基因组辅助育种中直接适用于提高玉米对 MLB 的抗性。
