Abstract Drought is one of the main abiotic constraints in rice. A deep root system contributes efficiently to maintaining the water status of the crop through a stress period. After identifying QTLs affecting root parameters in a doubled-haploid (DH) population of rice derived from the cross IR64/Azucena, we started a marker-assist- ed backcross program to transfer the Azucena allele at four QTLs for deeper roots (on chromosomes 1, 2, 7 and 9) from selected DH lines into IR64. We selected the backcross progenies strictly on the basis of their geno- types at the marker loci in the target regions up to the BC 3 F 2 . We assessed the proportion of alleles remaining from Azucena in the non-target areas of the BC 3 F 2 plants, which was in the range expected for the back- cross stage reached. Twenty nine selected BC 3 F 3 near- isogenic lines (NILs) were developed and compared to IR64 for the target root traits and three non-target traits in replicated experiments. Of the three tested NILs carry- ing target 1, one had significantly improved root traits over IR64. Three of the seven NILs carrying target 7 alone, as well as three of the eigth NILs carrying both targets 1 and 7, showed significantly improved root mass at depth. Four of the six NILs carrying target 9 had sig- nificantly improved maximum root length. Five NILs carrying target 2 were phenotyped, but none had a root phenotype significantly different from that of IR64. A re-analysis of the initial data with the composite interval mapping technique revealed two linked QTLs with op- posite effects in this area. Some NILs were taller than IR64 and all had a decreased tiller number because of a likely co-introgression of linked QTLs. The usefulness of NILs, the efficiency of marker-aided selection for QTLs and the relationship between root traits are dis- cussed. The NILs with an improved root system will per- mit testing the importance of root depth for water-limited environments. Keywords Drought tolerance · Oryza sativa · Root depth · Near-isogenic lines · Marker-aided selection · Introgression · QTLs Introduction Rice is the main food crop of the world with 85% of its production devoted to human consumption (IRRI 1997). Rice is a heavy consumer of water, needing some 5,000 liters of water to produce 1 kg of rice, and is less effi- cient in the way it uses water than eihter wheat or maize. Drought is an increasingly important problem limiting rice production in many areas of Asia. Drought naturally affects the rainfed rice ecosystems because the crop re- lies strictly on rainfall for its water supply. It also in- creasingly affects the irrigated rice ecosystem because of undependable irrigation water (IRRI 1995). Drought is the source of huge yield losses. For example, Widawsky and O’Toole (1990) evaluated at 3.0 million tons the an- nual drought losses from the 24 millions hectares of rice of Eastern India, which represented 22% of all losses from technical constraints. A deep and thick root system is generally considered as a favorable element allowing the crop to maintain its water status under stress condi- tions (Nguyen et al. 1997) when there is water at depth. However, little effort has gone into improving the genet- ic potential of rice for root traits because of the difficul- ties in measuring and manipulating them. Communicated by H.C. Becker L. Shen · B. Courtois ( ✉ ) · K.L. McNally · S. Robin · Z. Li International Rice Research Institute, MCPO Box 3127, 1271 Makati City, The Philippines Fax: 33 4 67 61 56 05; e-mail: brigitte.courtois@cirad.fr Present addresses: L. Shen, Plant Molecular Genetics Laboratory, Texas Tech University, TX79409-2122, USA B. Courtois, CIRAD-AMIS, TA40/03, Avenue Agropolis, 34398 Montpellier Cedex 5, France S. Robin, Deptartment of Crop Improvement, Agricultural College and Research Institute, Navalur Kuttapattu, Trichy 9, Tamil Nadu, India Theor Appl Genet (2001) 103:75–83 © Springer-Verlag 2001 ORIGINAL PAPER L. Shen · B. Courtois · K.L. McNally · S. Robin · Z. Li Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection Received: 17 July 2000 / Accepted: 20 October 2000