背景:面对当代气候脆弱性和全球气温不断上升,maydis叶枯病(MLB)的流行对玉米生产构成潜在威胁。这项研究通过采用包含336个品系的多样化小组,努力辨别标记-性状关联并阐明玉米对MLB抗性的候选基因。该小组正在四个环境中筛选MLB,采用标准的人工接种技术。利用从基因分型测序(GBS)获得的总共128,490个SNP进行全基因组关联研究(GWAS)和单倍型分析。
结果:GWAS鉴定出26个与MLB耐药相关的高度显著的SNP,在检查的标记中。其中7个SNP,在新的染色体组(9.06、5.01、9.01、7.04、4.06、1.04和6.05)中报道的与以下基因相关:bzip23,NAGS1,CDPK7,天冬氨酸蛋白酶NEP-2,VQ4和Wun1,其特征在于它们在减少真菌活性中的作用,加强对坏死病原体的防御机制,调节植物激素信号,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,因为它们与抗坏死病原体的功能相关。值得注意的是,本8.06,拥有五个SNP,显示与针对MLB的防御调节基因有关,表明潜在的功能基因簇的形成,触发针对MLB的级联反应。计算机研究显示,大多数基因的基因表达水平超过每千碱基百万(FPKM)十个片段,并证明了共表达网络中所有候选基因之间的共表达。单倍型回归分析显示Bonferroni≤0.05时13种常见显著单倍型之间存在关联。由这些显著的单倍型解释的表型变异范围从低到中等,提出了一种结合多个抗性等位基因以增强对MLB的抗性的育种策略。此外,发现一个特定的单倍型区块(Hap_8.3)由两个SNP(S8_152715134,S8_152460815)组成,在GWAS中识别出,解释了9.45%的变异(PVE)。
结论:鉴定的与目的性状相关的SNP/单倍型有助于等位基因多样性的富集,并在基因组学辅助育种中直接适用于增强玉米MLB抗性。
BACKGROUND: 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).
RESULTS: 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).
CONCLUSIONS: 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.