Bread wheat (Triticum aestivum L., 2n = 6x = 42) is one of the most important staple food and also the world’s highest-grown and traded cereal. It provides about 21% of calories and 19% of day-to-day protein to approximately 4.5 billion global population. The annual gain in wheat yield should be increased from the current level of around 1% to 1.6% to meet the food demand of the estimated global population of 9 billion by the year 2050.

Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 29 Bonferroni-corrected marker-trait associations (MTAs) in 15 chromosomes representing all the three wheat subgenomes. The GFD showed the highest MTAs (9), followed by GWPS (7), GY (4), GNPS (4), PH (3), and DH (2). Furthermore, 22 MTAs were identified with more than 10% phenotypic variation. A total of 5 stable MTAs i.e. AX-95210025, AX-95024590, AX-94978133, AX-94539354, and AX-94425015 were identified in more than one environment and associated with the expression of GFD, DH, GY, GWPS, and GFD, respectively. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTL governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as Lipase_3 domain, Serpin-N3.2, PIG-H domain, Proteasome subunit alpha type, C2H2-type domain, NAC domain, 3-ketoacyl-CoA synthase, PMEI domain, DUF1618 domain, involved in the regulation of tillering, plant height, spikelet fertility, insect resistance against seed damage, growth and development, and fitness. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).