Abstract: The Arabidopsis thaliana sterol carrier protein-2 (AtSCP2) is a small, basic and peroxisomal protein that in vitro enhances the transfer of lipids between membranes. AtSCP2 and all other plant SCP-2 that have been identified are single-domain polypeptides, whereas in many other eukaryotes SCP-2 domains are expressed in the terminus of multidomain polypeptides. The AtSCP2 transcript is expressed in all analysed tissues and developmental stages, with the highest levels in floral tissues and in maturing seeds. The expression of AtSCP2 is highly correlated with the multifunctional protein-2 (MFP2) involved in beta-oxidation. A. thaliana Atscp2-1 plants deficient in AtSCP2 show altered seed morphology, a delayed germination, and are dependent on an exogenous carbon source to avoid a delayed seedling establishment. Metabolomic investigations revealed 110 variables (putative metabolites) that differed in relative concentration between Atscp2-1 and normal A. thaliana wild-type seedlings. Microarray analysis revealed that many genes whose expression is altered in mutants with a deficiency in the glyoxylate pathway, also have a changed expression level in Atscp2-1.

Abstract: Plant seedling morphological characteristics are known to be important in drought resistance of rice (Oryza sativa L.) varieties. Ninety six recombinant inbred-line (RIL) rice lines of an indica and japonica cross were grown in both flooding condition and upland condition and QTLs for seedling morphology traits were examined using 256 markers. A total of 33 putative QTLs were associated with the four seedling traits: shoot height (SH), root biomass (RW), shoot biomass (SW) and root to shoot dry weight ratio (RSR). Four QTLs detected were the same under control and upland conditions. The ratio between the mean value of the seedling trait under upland and flooding conditions was used for assessing drought tolerance. A total of 7 QTLs for drought tolerance were detected with contribution rates varying from 10.0 to 27.0%. Comparative analysis was performed for the QTLs detected in this case and those reported from two other populations with the same upland rice variety Azucena as parent. Several identical QTLs for plant mass and seedling length across the three populations with the positive alleles from the upland rice Azucena were found, which suggests that these alleles of Azucena may be involved in water stress-accelerated plant mass and elongation of rice under different genetic backgrounds. Four cell wall-related candidate genes for OsEXP2, OsEXP4, EXT and XET were mapped on the intervals carrying the QTLs for seedling traits. These identified QTLs for seedling traits might be useful for improving drought resistance of rice by MAS.

Abstract: To investigate the genetic factors underlying constitutive and adaptive root growth under different water-supply conditions, a double haploid (DH) population, derived from a cross between lowland rice variety IR64 and upland rice variety Azucena, with 284 molecular markers was used in cylindrical pot experiments. Several QTLs for seminal root length (SRL), adventitious root number (ARN) and total root dry weight (RW) respectively, under both flooding and upland conditions were detected. Two identical QTLs for SRL and RW were found under flooding and upland conditions. The relative parameters defined as the ratio of parameters under the two water-supply conditions were also used for QTL analysis. A comparative analysis among different genetic populations was performed for the QTLs for root traits and several consistent QTLs for root traits across genetic backgrounds were detected. Candidate genes for cell expansion and elongation were used for comparative mapping with the detected QTLs. Four cell wall-related expressed sequence tags (ESTs) for OsEXP2, OsEXP4, EXT and Xet were mapped on the intervals carrying the QTLs for root traits.

Abstract: 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.

Abstract: Short periods of water deprivation can stimulate the growth of seminal and lateral roots in rice, and inhibit the emergence of adventitious roots. Identification of genes in the different tissues that respond to a water deficit may help us to understand the mechanism underlying root growth under conditions when water is scarce. cDNA-amplified fragment length polymorphism (AFLP) analysis was used to profile gene expression upon imposition of water deficit in three types of root tissue from the upland rice variety Azucena: seminal root tips, lateral root zones and adventitious root primordial zones. In all, 121 unique transcript-derived fragments (TDFs) were cloned, and Northern analysis was carried out for 30 TDFs to confirm their expression patterns. Sixty-six TDFs were differentially expressed in all three root samples. Four (AC2, D6, L22 and T23) were up-regulated by water deficit in seminal root tips and lateral root zones, and down-regulated in adventitious root primordial zones, an expression pattern which reflects the phenotypic changes observed in the different root sectors. In contrast, T17 and T37 showed the opposite expression pattern in Azucena: up-regulation in adventitious roots and repression in the other two zones. Functions could be assigned to five of these six TDFs on the basis of homology: they encode an expansin (T37), a fruit-ripening protein similar to ASR (T23), submergence-induced protein 2A (T17), a dehydrin (D6) and a 9- cis -epoxycarotenoid dioxygenase1 (L22), respectively. AC2 did not show a significant match to any known gene. Northern analysis showed that these six clones exhibited expression patterns that differed between the two cultivars tested (Azucena and the lowland variety IR1552) with respect to regulation by water limitation. Furthermore, T17, T37, D6 and T23 mapped within intervals known to contain QTLs (quantitative trait loci) for root growth in rice under water deficit. These genes may regulate or co-regulate the growth and development of the three root zones in a tissue-specific manner, and may play a role in the processes that underlie the early changes in root architecture under conditions of water deprivation.

Abstract: Aluminum (Al) toxicity is the major factor limiting crop productivity in acid soils. In this study, a recombinant inbreed line (RIL) 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 for mapping quantitative trait loci (QTLs) for Al tolerance. Three QTLs for relative root length (RRL) were detected on chromosome 1, 9, 12, respectively, and 1 QTL for root length under Al stress is identical on chromosome 1 after one week and two weeks stress. Comparison of QTLs on chromosome 1 from different studies indicated an identical interval between C86 and RZ801 with gene(s) for Al tolerance. This interval provides an important start point for isolating genes responsible for Al tolerance and understanding the genetic nature of Al tolerance in rice. Four Al induced ESTs located in this interval were screened by reverse Northern analysis and confirmed by Northern analysis. They would be candidate genes for the QTL.

Abstract: 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 6 cm 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-beta-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.

Abstract: The seminal roots of an upland rice variety, Azucena, showed accelerated elongation in response to a water deficit. The elongation of cortical cells in the elongation zone is rapidly stimulated within 16 h by the water deficit. cDNA-AFLP analysis was used to examine gene expression in seminal root tips at four time points (4, 16, 48 and 72 h) during the water deficit. One hundred and six unique genes induced by the water deficit were obtained. The expression patterns of these genes were confirmed by Northern blot analysis based on 21 selected genes representing different patterns. The 106 upregulated genes were composed of 60 genes of known function, 28 genes of unknown function and 18 novel genes. Sixty genes of known functions were involved in transport facilitation, metabolism and energy, stress- and defense-related proteins, cellular organization and cell-wall biogenesis, signal transduction, expression regulator and transposable element, suggesting that seminal root tips undergo a complex adaptive process in response to the water deficit. Expression of 22 genes reached a maximum within 16 h of water deficit treatment. These included aquaporin (PIP2a), 9-cis-epoxycarotenoid dioxygenase (NCED1) and a negative regulator of gibberellin signal transduction (SPY); eight other genes participated in cell wall loosening or vesicle traffic.

Abstract: Understanding the growth and physiological responses of rice to upland conditions would be helpful for designing treatments to improve the tolerance of rice under a rainfed system. The objective of this study was to investigate the initiation,elongation and membrane stability of seminal, lateral and adventitious roots of upland rice after 9-d upland condition treatment. Compared with control roots under waterlogged conditions, upland water deficiency conditions favor seminal and lateral root growth over adventitious root growth by accelerating seminal root elongation, promoting lateral root initiation and elongation, and reducing the elongation and number of adventitious roots. Enhanced total root number and length resulted in increase of total root dry weight and thereby increasing the root-to-shoot ratio. Organic compound leakage from seminal root tips and adventitious roots increased progressively to some extent with upland culture duration, while significant increases in seminal root tips were the consequence of loss of membrane integrity caused by the upland-condition enhanced growth.