To investigate the genetic factors underlying constitutive and adaptive morphological traits of roots under different water-supply conditions, a recombinant inbred line (RIL) population derived from a cross between the lowland rice variety IR1552 and the upland rice variety Azucena with 249 molecular markers, was used in cylindrical-pot experiments. Eighteen QTLs were detected for seminal root length (SRL), adventitious root number (ARN), and lateral root length (LRL) and lateral root number (LRN) on the seminal root at a soil depth of from 3 to 6cm under flooding and upland conditions. One identical QTL was detected under both flooding and upland conditions. The relative parameters under the two water-supply conditions were also used for QTL analysis. Five QTLs for upland induced variations in the traits were detected with the positive alleles from Azucena. A comparative analysis was performed for the QTLs detected in this study and those reported from two other populations with Azucena as a parent. Several identical QTLs for root elongation were found across the three populations with positive alleles from Azucena. Candidate genes were screened from ESTs and cDNA-AFLP clones for comparative mapping with the detected QTLs. Two genes for cell expansion, OsEXP2 and endo-1,4-b-D-glucanase EGase, and four cDNA-AFLP clones from root tissues of Azucena, were mapped on the intervals carrying the QTLs for SRL and LRL under upland conditions, respectively.

A full-length coding domain sequence of a gene analogous to granule-bound starch synthase (GBSS; ADP-glucose-starch glucosyltransferase, EC 2.4.1.21) was cloned and defined as OsGBSSII based on a Nitrogen (N)-starvation-induced cDNA library constructed using the rapid subtraction hybridization method. The deduced amino acid sequence of OsGBSSII was 62–85% identical to those of GBSS proteins from other plant species. The exon/intron organization of OsGBSSII was similar to that of OsGBSSI. OsGBSSII was mainly expressed in leaves and its protein was exclusively bound to starch granules in rice leaves, which suggests that the amylose in rice leaves is synthesized by OsGBSSII. N-starvation-induced expression of OsGBSSII could be repressed by supplying nitrate, ammonia or amino acid (glutamic acid or glutamine), glucosamine (an inhibitor of hexokinase) or dark conditions. These results indicate that N-starvation induction was dependent on the photosynthetic product and hexokinase in rice leaves. Sugars induced the accumulation of OsGBSSII transcripts in excised leaves through glycolysis-dependent pathways. OsGBSSII gene expression is regulated by the circadian rhythm in rice leaves.

To investigate the genetic background for aluminum (Al) tolerance in rice, a recombinant inbred (RI) population, derived from a cross between an Al-sensitive lowland indica rice variety IR1552 and an Al-tolerant upland japonica rice variety Azucena, was used in culture solution. A molecular linkage map, together with 104 amplified fragment length polymorphism (AFLP) markers and 103 restriction fragment length polymorphism (RFLP) markers, was constructed to map quantitative trait loci (QTLs) and epistatic loci for Al tolerance based on the segregation for relative root length (RRL) in the population. RRL was measured after stress for 2 and 4 weeks at a concentration of 1mM of Al3+ and a control with a pH 4.0, respectively. Two QTLs were detected at both the 2nd and the 4th weeks on chromosomes 1 and 12 from unconditional mapping, while the QTL on chromosome 1 was only detected at the 2nd stress week from conditional mapping. The effect of the QTL on chromosome 12 was increased with an increase of the stress period from 2 to 4 weeks. The QTL on chromosome 1 was expressed only at the earlier stress, but its contribution to tolerance was prolonged during growth. At least one different QTL was detected at the different stress periods. Mean comparisons between marker genotypic classes indicated that the positive alleles at the QTLs were from the Al-tolerant upland rice Azucena. An important heterozygous non-allelic interaction on Al tolerance was found. The results indicated that tolerance in the younger seedlings was predominantly controlled by an additive effect, while an epistatic effect was more important to the tolerance in older seedlings; additionally the detected QTLs may be multiple allelic loci for Al tolerance and phosphorus-uptake efficiency, or for Al and Fe2+ tolerance.

We generated T-DNA insertions throughout the rice genome for saturation mutagenesis. More than 1000 flanking sequences were mapped on 12 rice chromosomes. Our results showed that T-DNA tags were not randomly spread on rice chromosomes and were preferentially inserted in gene-rich regions. Few insertions (2.4%) were found in repetitive regions. T-DNA insertions in genic (58.1%) and intergenic regions (41.9%) showed a good correlation with the predicted size distribution of these sequences in the rice genome. Whereas, obvious biases were found for the insertions in the 5'- and 3'-regulatory regions outside the coding regions both at 500-bp size and in introns rather than in exons. Such distribution patterns and biases for T-DNA integration in rice are similar to that of the previous report in Arabidopsis, which may result from T-DNA integration mechanism itself. Rice will require approximately the same number of T-DNA insertions for saturation mutagenesis as will Arabidopsis. A database of the T-DNA insertion sites in rice is publicly available at our web site

Aluminium (Al) toxicity is the major factor limiting crop productivity in acid soils. To investigate the molecular mechanisms of Al toxicity and Al tolerance of rice, cDNA-amplified fragment length polymorphism (cDNA-AFLP) was used for identifying Al-regulated genes in roots of an Al-tolerant tropical upland rice, Azucena, and an Al-sensitive lowland rice, IR1552. Nineteen function-known genes were found among 34 transcript-derived fragments (TDFs) regulated by Al stress. The results indicate that Al stress could induce the biosynthesis of lignin and other cell wall components in roots. Temporal expression patterns of 14 genes were identified between the two varieties. In silico mapping was performed for all the 33 unique genes. Two genes for a function-unknown protein and for a ubiquitin-like protein, respectively, were mapped on the interval with the common QTL (quantitative trait loci) for Al tolerance in rice on chromosome 1.