To gather more information regarding salt-tolerance in rice (Oryza sativa L.), we identified gene loci controlling growth in paddy fields flooded with salt water. We analyzed the quantitative trait loci (QTL) using 98 backcross-inbred lines (BIL) derived from the backcross between Nipponbare (moderately salt-tolerant rice, as recurrent parent) and Kasalath (salt susceptible rice) in the four cropping seasons from 1999 to 2002. Shoot length, tiller number and shoot fresh weight were determined in the plants grown in a paddy field flooded with fresh water (NaCl; less than 10 mM, control group) and in the plants grown in a paddy field flooded with salt water (NaCl; 50-120 mM, saline group). A total of 27 QTLs for these traits were detected in the saline and control groups. Among them in the saline group, QTLs detected all four seasons were located on four regions on chromosomes 1, 2, 3 and 7. QTLs located on the long-arm of chromosome 2 regulated tiller number, and QTLs located on the long-arms of chromosomes 1 and 3, and the short-arms of chromosome 7 regulated shoot length. QTLs for shoot length located on the long-arms of chromosome 1 were detected in the control and saline paddy fields. QTLs in the other three regions were detected only in the saline group. The Nipponbare alleles of the two QTLs on chromosomes 3 and 7 contributed to the increase in shoot length, while the Kasalath allele of QTL on chromosome 2 contributed to the increase in tiller number. Therefore, these results suggest that three QTLs on chromosomes 2, 3 and 7 play essential roles in the growth of rice in the paddy field flooded with salt water.
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