Mapping quantitative trait loci for root traits related to drought resistance in rice (Oryza sativa L.) using AFLP markers

About one quarter of the global rice area belongs to rainfed lowland ecosystem where drought has been a major limiting factor to the productivity. Due to presence of compact sub-soil layer in rainfed lowlands rice roots hardly can grow deeper to extract water from lower soil horizons to offset the effects of drought. Because of absence of reliable and efficient screening techniques under field conditions, little progress has been made to breed varieties with increased root penetration ability through compact soil and other root traits associated with drought resistance. To overcome the screening problems, molecular genetic markers could be used to identify genotypes possessing the genes affecting the root traits that impart resistance against drought.;The present study was undertaken to map quantitative trait loci controlling five root parameters including penetration ability using amplified fragment length polymorphism (AFLP) markers. A population of 166 recombinant inbred lines developed from two indica parents, IR58821-23-B-2-1 with high root penetration ability and IR52561-UBN-1-12 with low root penetration ability, was evaluated using wax-petrolatum layers which simulate compact soil in the greenhouse during summer and fall, 1997. Root penetration ability was determined as the ratio of penetrated root number to the total number of roots for each genotype. A linkage map was constructed comprising 383 AFLP and 106 RFLP markers. Single marker analysis identified 33 AFLP markers linked with QTLs for five root traits while interval mapping detected 28 QTLs, each accounting for 5.8 to 27.2 percent of the phenotypic variation. At most of the QTLs favorable alleles were donated from the parent IR58821-23-1-2-1.;Three out of six QTLs controlling root penetration index were expressed in both summer and fall experiments with large phenotypic effects and these three QTLs were also found to control penetrated root number in both experiments. Out of eight, five QTLs affecting penetrated root thickness were expressed in both seasons. Two QTLs were common to control three traits, penetrated root number, root penetration index and penetrated root thickness while three QTLs were common for penetrated root thickness and root penetration index. Most of the QTLs were located within 4 cM from the nearest flanking markers. These tightly linked markers could be used in the introgression of QTLs to elite rainfed lowland cultivars to equip them with drought resistance mechanisms.