Abstract: We describe the DNA replication timing programs of fourteen yeast mutants with an extended S phase identified by a novel genome-wide screen. These mutants are associated with the DNA replication machinery, cell-cycle control and dNTP synthesis and affect different parts of S phase. In thirteen of the mutants, origin activation time scales with the duration of S phase. A limited number of origins becomes inactive in these strains, with inactive origins characterized by small replicons and are distributed throughout S phase. In sharp contrast, cells deleted of MRC1, a gene implicated in replication fork stabilization and in the replication checkpoint pathway, maintained wild-type firing times despite over two-fold lengthening of S phase. Numerous dormant origins were activated in this mutant. Our data suggests that most perturbations that lengthen S phase affect the entire program of replication timing, rather than a specific subset of origins, maintaining the relative order of origin firing time and delaying firing with relative proportions. Mrc1 emerges as a regulator of this robustness of the replication program.