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



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Texas Tech University


Rice is the primary food source for more than one-third of the world's population and is grown in diverse agro-ecological conditions. 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 the presence of compact sub-soil layers in rainfed lowlands, rice roots hardly can grow deeper to extract water from lower soil horizons to offset the effects of drought during water-deficit periods. Because of an absence of easy, 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 identify and map quantitative trait loci (QTLs) controlling five root parameters including penetration ability using Amplified Fragment Length Polymorphism (AFLP) markers. A population of 166 recombinant inbred lines (RILs) developed from two indica parents, IR58821-23-B-2-1 with high root penetration ability and thicker roots and IR52561-UBN-1-12 with low root penetration ability and thinner roots, was evaluated using wax-petrolatum layers which simulate compact soil. Plants were grown in a randomized complete block design with five replications in the greenhouse during the summer and fall of 1997 Data were recorded for total root number, penetrated root number, root penetration index, penetrated root thickness and penetrated root length. All the traits showed normal frequency distribution and transgressive segregation. Root penetration ability was determined as root penetration index which was calculated as the ratio of penetrated root number to the total number of roots for each genotype. A linkage map was constructed comprising 383 AFLP markers and 106 RFLP markers as anchors encompassing the 12 rice chromosomes with an average marker spacing of 5.0 cM. QTLs analysis was performed using single-marker and interval mapping methods. Single marker analysis identified 33 AFLP markers on chromosomes 2, 3, 4, 6, 7 and 11 significantly associated with the five root traits while interval mapping detected 28 QTLs, each accounting for 5.8 to 27.2 percent of the phenotypic variation for these traits. Out of 28 QTLs, 12 were linked with AFLP markers only and 9 with RFLP markers only while the rest were linked with both AFLP and RFLP markers. Most of the favorable alleles were donated from the parent IR58821-23-1-2-1 which was phenotypically superior in root traits related to drought resistance.

Despite some differences in temperature, day length and light intensity, 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 the penetrated root number in both experiments. Out of eight QTLs affecting penetrated root thickness, five were expressed in both seasons indicating its low sensitivity to environments. This is in good agreement with the high positive correlation between the experiments for this trait. None of the five QTLs for penetrated root length was commonly detected in both experiments, suggesting its high sensitivity to environmental changes. 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 indicating their pleiotropic gene action or close linkage of the concerned QTLs. Three QTLs affecting root penetrafion index and two QTLs affecting penetrated root thickness were also found to be located on the similar genomic regions in earlier studied populations influencing the same root traits. Most of the detected QTLs were located within 4 cM from the nearest flanking markers. These tightly linked markers could be used in the introgression of these QTLs to elite rainfed lowland cultivars in order to equip them with drought resistance mechanisms.



Rice -- Roots -- Growth, Rice -- Genetic engineering, Rice -- Breeding, Rice -- Drought tolerance