Mapping QTLs for root traits in a recombinant inbred population from two indica ecotypes in rice

Evaluation of root traits in rainfed lowland rice is very difficult. Molecu lar genetic markers could be used as an alternative strategy to phenotypic selection for the improvement of rice root traits. This research was undert aken to map QTLs associated with five root traits using RFLP and AFLP marke rs. Recombinant inbred lines (RILs) were developed from two indica parents. IR58821-23-B-1-2-1 and IR52561-UBN-1-1-2, that were adapted to rainfed low land production systems. Using wax-petrolatum layers to simulate a hardpan in the soil, 166 RILs were evaluated for total root number (TRN), penetrate d root number (PRN), root penetration index (RPI, the ratio of PRN to TRN), penetrated root thickness (PRT) and penetrated root length (PRL) under gre enhouse conditions during the summer and the fall of 1997. A genetic linkag e map of 2022 cM length was constructed comprising 303 AFLP and 96 RFLP mar kers with an average marker space of 5.0 cM. QTL analysis via interval mapp ing detected 28 QTLs for these five root traits, which were located on chro mosomes 1, 2, 3, 4, 6, 7, 10 and 11. Individual QTLs accounted for between 6 and 27% of the phenotypic variation. Most of the favorable alleles were d erived from the parent IR58821-23-B-1-2-1, which was phenotypically superio r in root traits related to drought resistance. Three out of six QTLs for R PI were detected in both summer and fall experiments and they also were ass ociated with PRN in both experiments. Out of eight QTLs for RPT, five were common in both seasons. Two genomic regions on chromosome 2 were associated with three root traits (PRN, PRT and RPI), whereas three genomic regions o n chromosomes 2 and 3 were associated with two root traits (PRT and RPI). T wo QTLs affecting RPT and two QTLs affecting PRT were also found in similar genomic regions in other rice populations. The consistent QTLs across gene tic backgrounds and the common QTLs detected in both experiments should be good candidates for marker-assisted selection toward the incorporation of r oot traits in a drought resistance breeding program, especially for rainfed lowland rice.