Sandhu, SurinderWajhat-Un-Nisa2024-03-042024-03-042023Wajhat-Un-Nisa (2023). Genome wide association studies and genomic prediction for maydis leaf blight resistance in tropical maize (Zea mays L.) (Unpublished Ph.D. Dissertation). Punjab Agricultural University, Ludhiana, Punjab, India.https://krishikosh.egranth.ac.in/handle/1/5810207342The present study was undertaken to identify marker-trait associations (MTA) and candidate genes associated with maydis leaf blight (MLB) in maize (Zea mays L.). A diverse panel of 359 genotypes, known as the CIMMYT Asia Associated Mapping Panel (CAAM), was used in this study. The evaluation of MLB resistance was conducted through artificial inoculation across four different environments (two years and two locations). Disease severity was measured on the scale of 1-9. Significant variation was observed for genotypes. Heritability was high (>70%) for the trait. GGE-biplot depicted the stability and performance with lower disease score. A set of 10 genotypes was reported as resistant across environments with average disease score of 3.0. Best linear unbiased predictor (BLUPs) values were used for GWAS with 128,490 SNPs. Linkage disequilibrium (LD) decay in panel was estimated to be ~ 0.9 kb at r2 =0.1. Based on cumulative analysis of data, a total of 26 significant SNPs, distributed across all ten chromosomes were associated with MLB resistance. Notably, the highest number (6) of SNPs was reported on chromosome 8, 5 SNPs within bin 8.06 and 1 SNP in bin 8.01. This suggests that chromosome 8 plays a crucial role in MLB resistance. Seven novel SNPs were reported from chromosomal bins viz., 9.06, 6.05, 5.01, 1.04, 7.04, 9.01, and 4.06. Gene mining and in silico expression analysis led to the identification of 22 putative candidate genes (on the basis of significant SNPs) with the functional relevance for resistance against necrotrophic pathogen. The expression values were above 2 fragments per kilobase of transcript per million mapped reads (FPKM). The important candidate genes were protein suppressor of PHYA-105 1/SPA, ATP-dependent helicase, MYB DNA-Binding domain, PR5-like receptor kinase, bZIP transcription factor 23, Aspartic proteinase nepenthesin-2, Cdpk7, acetyltransferase NAGS1, Ubiquitin protein ligase binding, B3 domain containing protein, and ABC transporter B family member 4. These genes play pivotal roles in promoting basal defence and effector-triggered immunity (ETI) within the plant through phyto-hormone signaling, oxidative burst, hypersensitivity cell death response, transport of secondary metabolites, mitogen activated protein kinase (MAPK) mechanism, and serine/threonine protein kinase activity against necrotrophic fungi. The co-expression and physical interaction among candidate genes were 88.70%, and 8.98%, respectively. All the candidate genes were co-expressing, indicating potential functional relationships. However, physical interaction was observed between the genes SPA1/ GRMZM2G061602 and ABI3/GRMZM2G313737, associated with single SNP (S8_155841067). The sub-cellular localization predicted signals in nucleus, chloroplast, vacuole, extracellular space, and cell membrane for candidate genes. Genomic Prediction (GP) was performed using a subset of 9223 SNPs including the significant markers with genomic-BLUP model, as five-fold cross-validation. Prediction accuracy of 0.35 was observed across four environments with the training and testing set from the CAAM panel in the ratio of 90:10. The accuracy depicted higher genetic diversity in association mapping panel and potential use of GP strategies to enhance selection efficiency. The study enriched allelic diversity, along with the understanding of underlying resistance mechanism against MLB in maize.EnglishThesis