Molecular Plant Breeding 2024, Vol.15, No.6, 340-350 http://genbreedpublisher.com/index.php/mpb 343 in identifying QTL associated with traits such as resistance to Fusarium and Gibberella ear rots, which are critical for improving maize resilience and yield (Giomi et al., 2021; Akohoue and Miedaner, 2022). 4.3 Development and identification of SNP markers linked to resistance traits The development and identification of SNP markers linked to resistance traits in maize involve several steps. QTL mapping studies have identified numerous SNPs associated with resistance to ear rots. For instance, a study identified 14 resistant QTLs for Gibberella ear rot (GER) using a combination of QTL mapping and GradedPool-Seq (GPS) (Yuan et al., 2022). GWAS have been used to detect alleles associated with increased resistance to Fusarium ear rot (FER). One study identified 45 SNPs and 15 haplotypes significantly associated with FER resistance (Chen et al., 2016). Meta-analysis of multiple studies has refined the identification of stable QTL and candidate genes. For example, a meta-analysis re-analyzed 224 QTL and identified 40 meta-QTL (MQTL) associated with resistance to Fusarium and Gibberella ear rots. Identified SNP markers and candidate genes are validated through cross-validation with transcriptomic data and other genetic studies. This ensures the reliability of the markers for use in breeding programs (Zhou et al., 2021; Akohoue and Miedaner, 2022). These SNP markers and associated QTL provide valuable resources for breeding programs aimed at improving maize resistance to ear rots and other diseases, ultimately enhancing yield and grain quality. 5 QTL Mapping of Resistance to Ear Rot in Maize 5.1 Identification of QTLs associated with ear rot resistance Quantitative trait loci (QTL) mapping has been extensively used to identify genomic regions associated with resistance to ear rot in maize (Chen et al., 2017). Several studies have identified multiple QTLs that contribute to resistance against Fusarium ear rot (FER) and Gibberella ear rot (GER). For instance, a meta-analysis re-analyzed 224 QTLs from 15 studies and identified 40 meta-QTLs (MQTLs) associated with resistance traits such as fumonisin and deoxynivalenol accumulation, silk and kernel resistances, kernel dry-down rate, and husk coverage (Akohoue and Miedaner, 2022). Another study using a multiparent advanced-generation intercross (MAGIC) population identified 13 minor QTLs across various chromosomes, highlighting the quantitative nature of ear rot resistance (Figure 2) (Butrón et al., 2019). Additionally, a study using a recombinant inbred line (RIL) population identified 11 QTLs for GER resistance, with six additive and six epistatic QTLs contributing to the genetic architecture of resistance (Zhou et al., 2021). 5.2 Integration of SNP markers with QTL mapping for better resolution The integration of single nucleotide polymorphism (SNP) markers with QTL mapping has significantly improved the resolution and accuracy of identifying resistance loci. For example, a study combining QTL mapping with GradedPool-Seq (GPS) identified 14 resistant QTLs and five significant SNPs associated with GER resistance, with a peak SNP on chromosome 4 overlapping with a QTL, suggesting a potential target region for resistance (Yuan et al., 2022). Another study employed a high-density SNP array to genotype a RIL population, leading to the identification of 11 QTLs for GER resistance, including five stable QTLs (Zhou et al., 2021). Furthermore, a genome-wide association study (GWAS) in tropical maize germplasm identified 45 SNPs and 15 haplotypes associated with FER resistance, with eight loci colocated with QTLs identified through linkage mapping (Chen et al., 2016). 5.3 Key regions of the maize genome involved in ear rot resistance Several key regions of the maize genome have been consistently identified as being involved in ear rot resistance. For instance, the meta-analysis identified 14 refined MQTLs on chromosomes 1, 2, 3, 4, 7, and 9, with some regions harboring promising candidate genes such as terpene synthase21 (tps21) and flavonoid O-methyltransferase2 (fomt2) (Akohoue and Miedaner, 2022). Another study highlighted the importance of regions on chromosomes 3 and 7, specifically 210~220 Mb on chromosome 3 and 166~173 Mb on chromosome 7, which contain QTLs for FER resistance and fumonisin content (Butrón et al., 2019). Additionally, a study mapping QTLs for disease resistance and associated traits identified significant QTLs in bins 1.06, 2.03, 3.06, 5.04, 5.07, and 6.05, with the most important QTLs overlapping in bin 2.03 (Giomi et al., 2021). These key genomic regions provide valuable targets for breeding programs aimed at improving ear rot resistance in maize.
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