Table_10_Comprehensive meta-analysis of QTL and gene expression studies identify candidate genes associated with Aspergillus flavus resistance in maize.xlsx

Aflatoxin (AF) contamination, caused by Aspergillus flavus, compromises the food safety and marketability of commodities, such as maize, cotton, peanuts, and tree nuts. Multigenic inheritance of AF resistance impedes conventional introgression of resistance traits into high-yielding commercial maize varieties. Several AF resistance-associated quantitative trait loci (QTLs) and markers have been reported from multiple biparental mapping and genome-wide association studies (GWAS) in maize. However, QTLs with large confidence intervals (CI) explaining inconsistent phenotypic variance limit their use in marker-assisted selection. Meta-analysis of published QTLs can identify significant meta-QTLs (MQTLs) with a narrower CI for reliable identification of genes and linked markers for AF resistance. Using 276 out of 356 reported QTLs controlling resistance to A. flavus infection and AF contamination in maize, we identified 58 MQTLs on all 10 chromosomes with a 66.5% reduction in the average CI. Similarly, a meta-analysis of maize genes differentially expressed in response to (a)biotic stresses from the to-date published literature identified 591 genes putatively responding to only A. flavus infection, of which 14 were significantly differentially expressed (−1.0 ≤ Log2Fc ≥ 1.0; p ≤ 0.05). Eight MQTLs were validated by their colocalization with 14 A. flavus resistance-associated SNPs identified from GWAS in maize. A total of 15 genes were physically close between the MQTL intervals and SNPs. Assessment of 12 MQTL-linked SSR markers identified three markers that could discriminate 14 and eight cultivars with resistance and susceptible responses, respectively. A comprehensive meta-analysis of QTLs and differentially expressed genes led to the identification of genes and makers for their potential application in marker-assisted breeding of A. flavus-resistant maize varieties.

黄曲霉毒素（AF）污染，由黄曲霉引起，严重损害了诸如玉米、棉花、花生和坚果等商品的食品安全及市场可接受度。黄曲霉毒素抗性的多基因遗传特性阻碍了传统抗性性状导入高产商业玉米品种。在玉米中，已从多对亲本作图和全基因组关联研究（GWAS）中报道了多个黄曲霉毒素抗性相关的数量性状位点（QTL）和标记。然而，解释不一致表型变异性且置信区间（CI）较大的QTL限制了其在标记辅助选择中的应用。对已发表QTL的元分析可以识别出具有更窄CI的显著元-QTL（MQTL），以可靠地识别与黄曲霉毒素抗性相关的基因和连锁标记。利用356个报道的QTL中的276个，控制玉米对黄曲霉感染和黄曲霉毒素污染的抗性，我们鉴定了10个染色体上共58个MQTL，平均置信区间缩小了66.5%。同样，对至今已发表的文献中玉米在（非）生物胁迫下差异表达基因的元分析，鉴定出591个仅对黄曲霉感染有反应的推测基因，其中14个基因的表达差异显著（|Log2Fc| ≥ 1.0；p ≤ 0.05）。通过GWAS在玉米中鉴定出的14个黄曲霉抗性相关单核苷酸多态性（SNPs）与其共定位，验证了8个MQTL。在MQTL区间和SNPs之间物理邻近的基因总数为15个。评估12个MQTL连锁简单重复序列（SSR）标记，鉴定出三个标记可以区分对黄曲霉有抗性和易感反应的14个和8个品种。对QTL和差异表达基因的全面元分析导致了与黄曲霉抗性玉米品种标记辅助育种潜在应用的基因和标记的鉴定。