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The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 ( P -value) ≥ 3.0. The  PH  1.1  and  Zn  7.1  were consistently identified in all the four environments, ten QTLs  qDF  3.1 ,  qDF  6.2   qDF  9.1   qPH  5.1   qGL  3.1 ,  qGW  3.1 ,  qGW  11.1 , and  qZn  6.2  were detected in two environments, while two major loci  qBLB  11.1  and  qBLB  5.1  were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as  OsMADS50  for days to flowering,  osGA20ox2  for plant height, and  GS3  for grain length. Similarly,  Xa4  and  xa5  genes were identified for BLB resistance and  Pi5(t), Pi28(t) , and  Pi30(t)  genes were identified for Blast resistance. A number of metal homeostasis genes  OsMTP6 ,  OsNAS3 ,  OsMT2D ,  OsVIT1 , and  OsNRAMP7  were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification