Table_11_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（Aspergillus flavus）引起，损害了诸如玉米、棉花、花生和坚果等商品的安全性及市场可接受度。AF抗性的多基因遗传特性阻碍了抗性性状的传统导入至高产量商业玉米品种中。在玉米中，已从多个双亲本定位和全基因组关联研究（GWAS）中报道了与AF抗性相关的多个数量性状基因座（QTL）和标记。然而，解释表型变异不一致的大置信区间（CI）的QTL限制了其在标记辅助选择中的应用。对已发表QTL的元分析能够识别出具有更窄置信区间（CI）的显著元-QTL（MQTL），以可靠地鉴定与AF抗性相关的基因和连锁标记。利用356个报道的QTL中控制对黄曲霉感染和AF污染的抗性的276个QTL，我们在所有10条染色体上确定了58个MQTL，平均置信区间缩小了66.5%。类似地，对至今已发表的文献中关于玉米基因在（非）生物胁迫下的差异表达进行元分析，确定了591个仅对黄曲霉感染作出反应的假设性基因，其中14个基因的表达存在显著差异（|Log2Fc| ≥ 1.0；p ≤ 0.05）。通过GWAS在玉米中识别的14个与黄曲霉抗性相关的单核苷酸多态性（SNPs）的共定位验证了8个MQTL。在MQTL区间和SNPs之间，有15个基因在物理上靠近。对12个MQTL关联的简单序列重复（SSR）标记进行评估，确定了3个标记可以区分14个对黄曲霉感染具有抗性的品种和8个易感品种。对QTL和差异表达基因的综合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相关的基因和标记的鉴定。