The aim of this work was to improve early season drought tolerance in the upland rice variety Kalinga III, a variety that was not used for mapping drought-related traits. It was used as a recurrent parent in backcrossing with marker-assisted selection (MAS) with the Philippines variety Azucena as the donor parent of five carrier chromosomes for introgression. Four target segments carried a QTL for root traits and the fifth carried a recessive gene for aroma. We summarise the marker-assisted selection in three backcross (BC) generations and further pyramid crosses to stack multiple target segments from Azucena. We combined MAS with client-oriented breeding in bulk populations selected for QTLs from the BC2 generation. Phenotypic evaluation of the resultant bulks and near-isogenic lines was carried out. Screens for root traits were conducted in soil-filled pipes under field conditions in Bangalore, India. Over three years, six bulks and four advanced BC3 lines (known as PY lines) were evaluated by farmers in their own fields in eastern India. In addition replicated drought trials were carried out under upland conditions in three locations (two in eastern India and one in western India). The results demonstrate the complexities of selecting for root traits with low heritability and the effect of the evaluation environment. None-the-less, some of the products of this programme were shown to outperform Kalinga III and were acceptable to upland farmers in eastern India.