Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis

Background  

Cell responses to environmental stimuli are usually organized as relatively separate responsive gene modules at the molecular level. Identification of responsive gene modules rather than individual differentially expressed (DE) genes will provide important information about the underlying molecular mechanisms. Most of current methods formulate module identification as an optimization problem: find the active sub-networks in the genome-wide gene network by maximizing the objective function considering the gene differential expression and/or the gene-gene co-expression information. Here we presented a new formulation of this task: a group of closely-connected and co-expressed DE genes in the gene network are regarded as the signatures of the underlying responsive gene modules; the modules can be identified by finding the signatures and then recovering the "missing parts" by adding the intermediate genes that connect the DE genes in the gene network.     

Mapping QTLs associated with drought avoidance in upland rice

The identification of molecular markers linked to genes controlling drought resistance factors in rice is a necessary step to improve breeding efficiency for this complex trait. QTLs controlling drought avoidance mechanisms were analyzed in a doubled-haploid population of rice. Three trials with different drought stress intensities were carried out in two sites. Leaf rolling, leaf drying, relative water content of leaves and relative growth rate under water stress were measured on 105 doubled haploid lines in two trials and on a sub-sample of 85 lines in the third one. Using composite interval mapping with a LOD threshold of 2.5, the total number of QTLs detected in all trials combined was 11 for leaf rolling, 10 for leaf drying, 11 for relative water content and 10 for relative growth rate under stress. Some of these QTLs were common across traits. Among the eleven possible QTLs for leaf rolling, three QTLs (on chromosomes 1, 5 and 9) were common across the three trials and four additional QTLs (on chromosomes 3, 4 and 9) were common across two trials. One QTL on chromosome 4 for leaf drying and one QTL on chromosome 1 for relative water content were common across two trials while no common QTL was identified for relative growth rate under stress. Some of the QTLs detected for leaf rolling, leaf drying and relative water content mapped in the same places as QTLs controlling root morphology, which were identified in a previous study involving the same population. Some QTL identified here were also located similarly with other QTLs for leaf rolling as reported from other populations. This study may help to chose the best segments for introgression into rice varieties and improvement of their drought resistance.     

Identification of drought tolerance determinants by genetic analysis of root response to drought stress and abscisic Acid

Drought stress is a common adverse environmental condition that seriously affects crop productivity worldwide. Due to the complexity of drought as a stress signal, deciphering drought tolerance mechanisms has remained a major challenge to plant biologists. To develop new approaches to study plant drought tolerance, we searched for phenotypes conferred by drought stress and identified the inhibition of lateral root development by drought stress as an adaptive response to the stress. This drought response is partly mediated by the phytohormone abscisic acid. Genetic screens using Arabidopsis (Arabidopsis thaliana) were devised, and drought inhibition of lateral root growth (dig) mutants with altered responses to drought or abscisic acid in lateral root development were isolated. Characterization of these dig mutants revealed that they also exhibit altered drought stress tolerance, indicating that this root response to drought stress is intimately linked to drought adaptation of the entire plant and can be used as a trait to access the elusive drought tolerance machinery. Our study also revealed that multiple mechanisms coexist and together contribute to whole-plant drought tolerance.     

Fractal analysis on root systems of rice plants in response to drought stress

A fractal analytical method was used to examine the developmental responses of root systems in upland rice genotype CT9993-5-10-1-M (japonica) and lowland genotype IR62266-42-6-2 (indica) (abbreviated as CT9993 and IR62266, respectively) to soil water stress. The root systems were grown for one month in root boxes with 25 cm in length, 2 cm in width and 40 cm in depth, which were filled with soil. The root systems were sampled by following the needle-pinboard method, and then spread on the transparent plastic films with nets after carefully washing out the soils. The two-dimensional images of root systems were digitized by using a scanner. The digitized images were used for analysis based on fractal geometry with the box-counting method. The reductions in shoot dry weight, photosynthesis rate and transpiration rate of IR62266 by soil drought were greater than those of CT9993. The change of fractal parameters in response to soil moisture conditions differed between the two rice genotypes. The values of fractal abundance (FA) and fractal dimension (FD) in well-watered IR62266 plants were larger than in CT9993. The value of FA of IR62266 was decreased more by drought stress than that of CT9993, indicating that the volume of soils explored by the whole root systems of CT9993 was maintained or less decreased under drought stress in comparison to IR62266. Moreover, the values of FD tended to increase in CT9993 while it tended to decrease in IR62266 in response to drought. These root responses detected by the fractal analysis in CT9993 may be advantageous for its extracting more water from drying soils, which explains its better growth under drought-stressed condition.     

Identification of candidate markers associated with agronomic traits in rice using discriminant analysis

Plant genetic mapping strategies routinely utilize marker genotype frequencies obtained from progeny of controlled crosses to declare presence of a quantitative trait locus (QTL) on previously constructed linkage maps. We have evaluated the potential of discriminant analysis (DA), a multivariate statistical procedure, to detect candidate markers associated with agronomic traits among inbred lines of rice (Oryza sativa L.). A total of 218 lines originating from the US and Asia were planted in field plots near Alvin, Texas, in 1996 and 1997. Agronomic data were collected for 12 economically important traits, and DNA profiles of each inbred line were produced using 60 SSR and 114 RFLP markers. Model-based methods revealed population structure among the lines. Marker alleles associated with all traits were identified by DA at high levels of correct percent classification within subpopulations and across all lines. Associated marker alleles pointed to the same and different regions on the rice genetic map when compared to previous QTL mapping experiments. Results from this study suggest that candidate markers associated with agronomic traits can be readily detected among inbred lines of rice using DA combined with other methods described in this report.N. Zhang and Y. Xu contributed equally to work and considered as first authors.Approved for publication by the Director of the Louisiana Agricultural Experiment Station as paper no. 04-14-0335.     

Quantitative trait loci associated with drought tolerance at reproductive stage in rice

Drought is a major constraint to rice (Oryza sativa) yield and its stability in rainfed and poorly irrigated environments. Identifying genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and development of more drought tolerant cultivars. Quantitative trait loci (QTL) for grain yield and its components and other agronomic traits were identified using a subset of 154 doubled haploid lines derived from a cross between two rice cultivars, CT9993-510 to 1-M and IR62266-42 to 6-2. Drought stress treatments were managed by use of a line source sprinkler irrigation system, which provided a linearly decreasing level of irrigation coinciding with the sensitive reproductive growth stages. The research was conducted at the Ubon Rice Research Center, Ubon, Thailand. A total of 77 QTL were identified for grain yield and its components under varying levels of water stress. Out of the total of 77 QTL, the number of QTL per trait were: 7-grain yield (GY); 8-biological yield (BY); 6-harvest index (HI); 5-d to flowering after initiation of irrigation gradient (DFAIG); 10-total spikelet number (TSN); 7-percent spikelet sterility (PSS); 23-panicle number (PN); and 11-plant height (PH). The phenotypic variation explained by individual QTL ranged from 7.5% to 55.7%. Under well-watered conditions, we observed a high genetic association for BY, HI, DFAIG, PSS, TSN, PH, and GY. However, only BY and HI were found to be significantly associated with GY under drought treatments. QTL flanked by markers RG104 to RM231, EMP2_2 to RM127, and G2132 to RZ598 on chromosomes 3, 4, and 8 were associated with GY, HI, DFAIG, BY, PSS, and PN under drought treatments. The aggregate effects of these QTL on chromosomes 3, 4, and 8 resulted in higher grain yield. These QTL will be useful for rainfed rice improvement, and will also contribute to our understanding of the genetic control of GY under drought conditions at the sensitive reproductive stage. Close linkage or pleiotropy may be responsible for the coincidence of QTL detected in this experiment. Digenic interactions between QTL main effects for GY, BY, HI, and PSS were observed under irrigation treatments. Most (but not all) DH lines have the same response in measure of productivity when the intensity of water deficit was increased, but no QTL by irrigation treatment interaction was detected. The identification of genomic regions associated with GY and its components under drought stress will be useful for marker-based approaches to improve GY and its stability for farmers in drought-prone rice environments.     

Identification of functional candidate genes for drought tolerance in rice

Drought tolerance (DT) in rice is known to be controlled by many quantitative trait loci (QTLs) and involved differential expression of large numbers of genes, but linking QTLs with their underlying genes remains the most challenging issue in plant molecular biology. To shed some light on this issue, differential gene expression in response to PEG simulated drought in 3 unique genetic materials (a lowland rice, IR64 and its derived line, PD86 which has 11 introgressed DT QTLs, and a upland rice IRAT109) was investigated using a PCR-based subtractive hybridization strategy. More than 300 unique subtracted cDNA sequences, covering genes of diverse cellular activities and functions, were identified and confirmed by semi-quantitative and quantitative RT-PCR. Detailed bioinformatics analyses of the data revealed two interesting results. First, the levels and mechanisms of DT of the three rice lines were associated with the number and types of differentially expressed genes, suggesting different DT mechanisms in rice are controlled by different sets of genes and different metabolic pathways, and most differentially expressed genes under drought were able to contribute to DT. Second, there appeared a high correspondence in genomic location between DT QTLs and clusters of differentially expressed genes in rice, suggesting some DT QTLs may represent clusters of co-regulated and functionally related genes. Thus, differential gene expression analyses using genetically characterized materials can provide additional insights into the molecular basis of QTLs and convergent evidence to shortlist the candidate genes for target QTLs. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Bin-Ying Fu and Jian-Hua Xiong are contributed to this work equally.     

Characterization of a rice gene showing organ-specific expression in response to salt stress and drought.

Protein changes induced by salinity stress were investigated in the roots of the salt-sensitive rice cultivar Taichung native 1. We found eight proteins to be induced and obtained partial sequences of one with a molecular mass of 15 kilodaltons and an isoelectric point of 5.5. Using an oligonucleotide probe based on this information, a cDNA clone, salT, was selected and found to contain an open reading frame coding for a protein of 145 amino acid residues. salT mRNA accumulates very rapidly in sheaths and roots from mature plants and seedlings upon treatment with Murashige and Skoog salts (1%), air drying, abscisic acid (20 microM), polyethylene glycol (5%), sodium chloride (1%), and potassium chloride (1%). Generally, no induction was seen in the leaf lamina even when the stress should affect all parts of the plant uniformly. The organ-specific response of salT is correlatable with the pattern of Na+ accumulation during salt stress.     

Mapping QTLs associated with drought resistance in rice: Progress, problems and prospects

The use of molecular markers in the mapping of traits of agronomic importance holds great promise for speeding the development of improved plant varieties and increasing our understanding of the physiological or molecular mechanisms behind biological phenomena. The technique is now being applied to drought resistance in rice (Oryza sativa L.). Drought is important because a considerable proportion of the world rice area is not irrigated and can be prone to water deficit. A large number of people, particular some of the poorest rice farmers, stand to gain if new varieties which combine high yield and drought resistance can be developed. Rice should be particularly useful for the molecular genetic analysis of drought resistance because of its growing role as a model monocot species and the diversity of drought resistance mechanisms which are found in the germplasm. We briefly review the traits which might be considered important in improving drought resistance in rice, before explaining the molecular mapping approach. We review progress at locating quantitative trait loci (QTLs) for individual mechanisms of drought resistance in controlled environment conditions. This includes a detailed comparison of reported QTLs related to root morphological characters. The search for QTLs associated with field performance under drought stress is analysed and the problems associated with understanding the genetic control of a complex physical and physiological phenomenon under conditions of substantial environmental variation are highlighted. We emphasise that the use of near isogenic lines in overcoming some of the problems offers considerable promise for the future.(seconded from CIRAD-CA, France)     

Identification of QTLs associated with physiological nitrogen use efficiency in rice

Demand for low-input sustainable crop cultivation is increasing to meet the need for environment-friendly agriculture. Consequently, developing genotypes with high nutrient use efficiency is one of the major objectives of crop breeding programs. This study was conducted to identify QTLs for traits associated with physiological nitrogen use efficiency (PNUE). A recombinant inbred population (DT-RILs) between Dasanbyeo (a tongil type rice, derived from an indica x japonica cross and similar to indica in its genetic make-up) and TR22183 (a Chinese japonica variety) consisting of 166 F8 lines was developed and used for mapping. A frame map of 1,409 cM containing 113 SSR and 103 STS markers with an average interval of 6.5 cM between adjacent marker loci was constructed using the DT-RILs. The RILs were cultivated in ordinary-N (N-P2O5-K2O = 100-80-80 kg/ha) and low-N (N-P2O5-K2O= 50-80-80 kg/ha) (100 kg/ha) conditions. PNUE was positively correlated with the harvest index and grain yield in both conditions. Twenty single QTLs (S-QTLs) and 58 pairs of epistatic loci (E-QTLs) were identified for the nitrogen concentration of grain, nitrogen concentration of straw, nitrogen content of shoot, harvest index, grain yield, straw yield and PNUE in both conditions. The phenotypic variance explained by these S-QTLs and E-QTLs ranged from 11.1 to 44.3% and from 16.0% to 63.6% , respectively. The total phenotypic variance explained by all the QTLs for each trait ranged from 35.8% to 71.3%, showing that the expression of PNUE and related characters depends significantly upon genetic factors. Both S-QTLs and E-QTLs may be useful for marker-assisted selection (MAS) to develop higher PNUE genotypes.