Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection

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 dou bled-haploid (DH) population of rice derived from the cross IR64/Azucena, w e started a marker-assisted backcross program to transfer the Azucena allel e at four QTLs for deeper roots (on chromosomes 1, 2, 7 and 9) from selecte d DH lines into IR64. We selected the backcross progenies strictly on the b asis of their genotypes at the marker loci in the target regions up to the BC3F2. We assessed the proportion of alleles remaining from Azucena in the non-target areas of the BC3F2, plants, which was in the range expected for the backcross stage reached. Twenty nine selected BC3F3 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 carrying target 1, one had significantly improved root traits over IR64. T hree of the seven NILs carrying target 7 alone, as well as three of the eig th NILs carrying both targets I and 7, showed significantly improved root m ass at depth. Four of the six NILs carrying target 9 had significantly impr oved maximum root length. Five NILs carrying target 2 were phenotyped, but none had a root phenotype significantly different from that of IR64. A re-a nalysis of the initial data with the composite interval mapping technique r evealed two linked QTLs with opposite 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 ar e discussed. The NILs with an improved root system will permit testing the importance of root depth for water-limited environments.