Prioritization of candidate genes in QTL regions based on associations between traits and biological processes
Bargsten, J.W. ; Nap, J.P.H. ; Sanchez Perez, G.F. ; Dijk, A.D.J. van - \ 2014
BMC Plant Biology 14 (2014). - ISSN 1471-2229
genome-wide association - protein function prediction - arabidopsis-thaliana - nucleotide polymorphisms - enrichment analysis - flowering time - complex traits - oryza-sativa - rice - architecture
Background Elucidation of genotype-to-phenotype relationships is a major challenge in biology. In plants, it is the basis for molecular breeding. Quantitative Trait Locus (QTL) mapping enables to link variation at the trait level to variation at the genomic level. However, QTL regions typically contain tens to hundreds of genes. In order to prioritize such candidate genes, we show that we can identify potentially causal genes for a trait based on overrepresentation of biological processes (gene functions) for the candidate genes in the QTL regions of that trait. Results The prioritization method was applied to rice QTL data, using gene functions predicted on the basis of sequence- and expression-information. The average reduction of the number of genes was over ten-fold. Comparison with various types of experimental datasets (including QTL fine-mapping and Genome Wide Association Study results) indicated both statistical significance and biological relevance of the obtained connections between genes and traits. A detailed analysis of flowering time QTLs illustrates that genes with completely unknown function are likely to play a role in this important trait. Conclusions Our approach can guide further experimentation and validation of causal genes for quantitative traits. This way it capitalizes on QTL data to uncover how individual genes influence trait variation.
Mathematical Models Light Up Plant Signaling
Chew, Y.H. ; Smith, R.W. ; Jones, H.J. ; Seaton, D.D. ; Grima, R. ; Halliday, K.J. - \ 2014
The Plant Cell 26 (2014)1. - ISSN 1040-4651 - p. 5 - 20.
arabidopsis circadian clock - recombinant inbred lines - flowering-time - transcription factor - hypocotyl growth - floral induction - oryza-sativa - rice genome - cellular interactions - photoperiodic control
Plants respond to changes in the environment by triggering a suite of regulatory networks that control and synchronize molecular signaling in different tissues, organs, and the whole plant. Molecular studies through genetic and environmental perturbations, particularly in the model plant Arabidopsis thaliana, have revealed many of the mechanisms by which these responses are actuated. In recent years, mathematical modeling has become a complementary tool to the experimental approach that has furthered our understanding of biological mechanisms. In this review, we present modeling examples encompassing a range of different biological processes, in particular those regulated by light. Current issues and future directions in the modeling of plant systems are discussed.
Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs
Cardoso, C. ; Zhang, Y. ; Jamil, M. ; Hepworth, J. ; Charnikhova, T. ; Dimkpa, S.O.N. ; Reiff, C. ; Wright, M.H. ; Liu, J. ; Meng, X. ; Bouwmeester, H.J. ; Ruyter-Spira, C.P. - \ 2014
Proceedings of the National Academy of Sciences of the United States of America 111 (2014)6. - ISSN 0027-8424 - p. 2379 - 2384.
arbuscular mycorrhizal fungi - quantitative trait loci - tiller bud outgrowth - striga-hermonthica - oryza-sativa - phosphate deficiency - root morphology - arabidopsis - architecture - inhibition
Rice (Oryza sativa) cultivar Azucena—belonging to the Japonica subspecies—exudes high strigolactone (SL) levels and induces high germination of the root parasitic plant Striga hermonthica. Consistent with the fact that SLs also inhibit shoot branching, Azucena is a lowtillering variety. In contrast, Bala, an Indica cultivar, is a low-SL producer, stimulates less Striga germination, and is highly tillered. Using a Bala × Azucena F6 population, a major quantitative trait loci— qSLB1.1—for the exudation of SL, tillering, and induction of Striga germination was detected on chromosome 1. Sequence analysis of the corresponding locus revealed a rearrangement of a 51- to 59-kbp stretch between 28.9 and 29 Mbp in the Bala genome, resulting in the deletion of two cytochrome P450 genes—SLB1 and SLB2—with high homology to the Arabidopsis SL biosynthesis gene, MAX1. Both rice genes rescue the Arabidopsis max1-1 highly branched mutant phenotype and increase the production of the SL, ent-2'-epi-5-deoxystrigol, when overexpressed in Bala. Furthermore, analysis of this region in 367 cultivars of the publicly available Rice Diversity Panel population shows that the rearrangement at this locus is a recurrent natural trait associated with the Indica/Japonica divide in rice.
Loss of Function in Mlo Orthologs Reduces Susceptibility of Pepper and Tomato to Powdery Mildew Disease Caused by Leveillula taurica
Zheng, Z. ; Nonomura, T. ; Appiano, M. ; Pavan, S.N.C. ; Matsuda, Y. ; Toyoda, H. ; Wolters, A.M.A. ; Visser, R.G.F. ; Bai, Y. - \ 2013
PLoS ONE 8 (2013)7. - ISSN 1932-6203 - 14 p.
real-time pcr - capsicum-annuum - subcellular-localization - nonhost resistance - gene-expression - oryza-sativa - cell-death - barley - family - identification
Powdery mildew disease caused by Leveillula taurica is a serious fungal threat to greenhouse tomato and pepper production. In contrast to most powdery mildew species which are epiphytic, L. taurica is an endophytic fungus colonizing the mesophyll tissues of the leaf. In barley, Arabidopsis, tomato and pea, the correct functioning of specific homologues of the plant Mlo gene family has been found to be required for pathogenesis of epiphytic powdery mildew fungi. The aim of this study was to investigate the involvement of the Mlo genes in susceptibility to the endophytic fungus L. taurica. In tomato (Solanum lycopersicum), a loss-of-function mutation in the SlMlo1 gene results in resistance to powdery mildew disease caused by Oidium neolycopersici. When the tomato Slmlo1 mutant was inoculated with L. taurica in this study, it proved to be less susceptible compared to the control, S. lycopersicum cv. Moneymaker. Further, overexpression of SlMlo1 in the tomato Slmlo1 mutant enhanced susceptibility to L. taurica. In pepper, the CaMlo2 gene was isolated by applying a homology-based cloning approach. Compared to the previously identified CaMlo1 gene, the CaMlo2 gene is more similar to SlMlo1 as shown by phylogenetic analysis, and the expression of CaMlo2 is up-regulated at an earlier time point upon L. taurica infection. However, results of virus-induced gene silencing suggest that both CaMlo1 and CaMlo2 may be involved in the susceptibility of pepper to L. taurica. The fact that overexpression of CaMlo2 restored the susceptibility of the tomato Slmlo1 mutant to O. neolycopersici and increased its susceptibility to L. taurica confirmed the role of CaMlo2 acting as a susceptibility factor to different powdery mildews, though the role of CaMlo1 as a co-factor for susceptibility cannot be excluded.
Analysis of genetic diversity in farmers' rice varieties in Sierra Leone using morphological and AFLP markers
Chakanda, R.T.M. ; Treuren, R. van; Visser, L. ; Berg, R.G. van den - \ 2013
Genetic Resources and Crop Evolution 60 (2013)4. - ISSN 0925-9864 - p. 1237 - 1250.
millet pennisetum-glaucum - oryza-sativa - west-africa - dna - polymorphism - cultivation - glaberrima - management - origin - gambia
The objective of the current research was to investigate the status of rice genetic resources in post-war Sierra Leone using both morphological and amplified fragment length polymorphism (AFLP) data. Specifically, we aimed at investigating farmers’ rice genetic resources for homogeneity and differentiation, and at examining the genetic identity of similarly named varieties, including varieties within Sierra Leone, and between Sierra Leone and Guinea. This research was also motivated by the assumption that genetic erosion might have occurred as a result of the civil war. To determine the level of diversity and genetic relationships among farmers’ varieties of rice recently collected in Sierra Leone, two methods were used using subsets of the collected samples: (1) Using morphological data, 74 samples of 29 different varieties were analysed to investigate the relationship between (a) varieties grown in two districts in Sierra Leone, and (b) the two main cultivated species, Oryza sativa and Oryza glaberrima. A dendrogram largely clustered the varieties according to region and to the species to which the varieties belonged. (2) Using AFLP data, three separate investigations were conducted: (a) 33 samples of 10 varieties were investigated to evaluate diversity within and between varieties. The results indicated that the rice varieties possess different levels of intra-variety variation, whereas inter-variety diversity was high enough to distinguish one variety from the other. In particular, an AMOVA analysis revealed that 38 % of the total variation occurred within varieties, and 62 % between varieties. (b) 37 samples of 18 different varieties were investigated to determine the consistency of naming of varieties by farmers. The results showed that there was consistency in the naming by farmers of traditional varieties, but inconsistency in the naming of newly acquired varieties and cultivars. (c) 12 samples were investigated to check the identity of varieties carrying identical names collected in two separate regions, Sierra Leone and the neighbouring country of Guinea. The results indicated no close genetic relationships between the varieties found in Sierra Leone and Guinea despite similarities in the names given to these varieties by farmers, indicating the influence of different cultivation practices in the two countries.
Quantification of the relationship between strigolactones and Striga hermonthica infection in rice under varying levels of nirtrogen and phosphorus
Jamil, M. ; Charnikhova, T. ; Cardoso, C. ; Jamil, T. ; Ueno, K. ; Verstappen, F.W.A. ; Asami, T. ; Bouwmeester, H.J. - \ 2011
Weed Research 51 (2011)4. - ISSN 0043-1737 - p. 373 - 385.
arbuscular mycorrhizal fungi - asiatica l kuntze - germination stimulants - upland rice - seed-germination - parasitic weeds - root parasites - soil fertility - oryza-sativa - sorghum
Strigolactone exudation, as well as Striga hermonthica germination and attachment, was studied under different levels of nitrogen (N) and phosphorus (P) in two cultivars of rice (IAC 165 and TN 1). Exudation of strigolactones by rice was the highest under mineral-deficient conditions, whereas increasing N and P dose reduced the amount of strigolactones in the exudates. Deficiency of P led to the highest strigolactone exudation, when compared with N or NP deficiency. Production of strigolactones differed strongly between the two cultivars. IAC 165 produced about 100-fold higher amounts than TN 1 of 2'-epi-5-deoxystrigol, orobanchol and three new strigolactones. Across all N and P treatments, a positive relationship was found between the amount of strigolactones in the exudates of both cultivars and in vitro S. hermonthica germination. These results show that the positive effect of fertiliser application in S. hermonthica control is, at least partly, because of the suppression of strigolactone production and hence of S. hermonthica germination and subsequent attachment. This warrants further research into practical application. Maintaining suitable N and P nutrient status of soil through fertiliser use might be a promising strategy to reduce damage in cereals by this notorious weed.
Challenges for weed management in African rice systems in a changing climate
Rodenburg, J. ; Meinke, H.B. ; Johnson, D.E. - \ 2011
The Journal of Agricultural Science 149 (2011). - ISSN 0021-8596 - p. 427 - 435.
atmospheric carbon-dioxide - elevated co2 - west-africa - intensification sri - germination ecology - lowland conditions - striga-asiatica - oryza-sativa - upland rice - plants
Global changes including increases in temperature, atmospheric greenhouse gases, soil degradation and competition for land and water resources, will have multiple impacts on rice production systems in Africa. These changes will affect weed communities, and management approaches must be adapted to take this into account. Higher temperatures and limited water availability will generally advantage C4 over C3 plants (e.g. rice). Conversely, elevated carbon dioxide (CO2) levels will improve the competitiveness of rice relative to C4 weeds, which comprise many of the problem weeds of rice. Increased atmospheric CO2 levels may also improve tolerance of rice against parasitic weeds, while prevalence of parasitic species may be amplified by soil degradation and more frequent droughts or floods. Elevated CO2 levels tend to promote growth below-ground relative to above-ground, particularly in perennial (C3) species. This may render mechanical control of weeds within a cropping season less effective or even counterproductive. Increased CO2 levels, rainfall and temperature may also reduce the effectiveness of chemical control, while the implementation of adaptation technologies, such as water-saving irrigation regimes, will have negative consequences for rice–weed competition. Rain-fed production systems are prevalent throughout Africa and these are likely to be most vulnerable to direct effects of climate change (e.g. higher temperatures and changes in rainfall patterns). Effective weed management strategies in these environments could encompass off-season tillage, the use of well-adapted cultivars (i.e. those with drought and heat tolerance, high weed competitiveness and parasitic weed resistance or tolerance) and rotations, intercropping or short, off-season fallows with weed-suppressive legumes including those that suppress parasitic weeds. In irrigated, non-flooded rice systems, weeds are expected to become more serious. Specifically, perennial rhizomatous C3 weeds and species adapted to hydromorphic conditions are expected to increase in prevalence. By implementing an integrated weed management strategy primarily targeted at weed prevention, dependency on flood water, herbicides and mechanical control can be lessened. Off-season deep tillage, stale seed bed techniques, use of clean seeds and irrigation water, competitive cultivars, timely transplanting at optimum spacing and judicious fertilizer timings are suitable candidate components for such a strategy. Integrated, novel approaches must be developed to assist farmers in coping with the challenges of weed control in the future
Soil carbon balance of rice-based cropping systems of the Indo-Gangetic Plains
Shibu, M.E. ; Keulen, H. van; Leffelaar, P.A. ; Aggarwal, P.K. - \ 2010
Geoderma 160 (2010)2. - ISSN 0016-7061 - p. 143 - 154.
organic-matter - climate-change - nitrogen mineralization - cycle feedbacks - jute corchorus - yield declines - oryza-sativa - dynamics - wheat - management
An agricultural land use system centred on rice-based cropping systems as common in the Indo-Gangetic Plains (IGP), with its annual cycles of wet and dry, puddling and ploughing, is unique and exerts a specific influence on soil organic matter (SOM) dynamics. Reports of yield ‘stagnation’ in some parts of the IGP with a decline in SOM quantity and quality raises concerns about the sustainability of the rice–wheat system in the region. Proper understanding of the soil carbon balance and of measures required to build up or maintain the soil carbon status of such a production system is therefore important for its sustainable production. Long-term experiments conducted in this region are especially useful in gaining understanding of soil carbon dynamics, since the processes affecting carbon dynamics are slow in nature. We used a simple analytical model—Yang's model—to calculate carbon balances in the rice-based cropping systems of the IGP in India. We used eight data sets from rice-based cropping systems from different sub-regions in the IGP, with different crop managements applied to rice, wheat or a third crop. Carbon input into the soil from crop biomass was calculated using data on crop yield and Harvest Index (HI). The values of soil organic carbon content predicted by the model were comparable to the observed values (r = 0.91). The model performs well in situations with porous soils (low clay content), with a pH values in the neutral range (7–7.5) and low annual rainfall as in the situation of Ludhiana-1 and 2. However, it underperforms in situations with heavy clay soils with high rainfall, causing severe anaerobic conditions. The model projections for the long-term (by 2080) show a decline in SOC at all sites in the IGP. Hence, the yield stagnation in the IGP, which has been attributed to a decline in SOC and the associated reduction in nutrient supply, could lead to further decreases in SOC levels, aggravated by climate change-induced higher temperatures.
Developing selection protocols for weed competitiveness in aerobic rice
Zhao, D.L. ; Atlin, G.N. ; Bastiaans, L. ; Spiertz, J.H.J. - \ 2006
Field Crops Research 97 (2006)2-3. - ISSN 0378-4290 - p. 272 - 285.
oryza-sativa - seeded rice - brachiaria-brizantha - suppressive ability - wheat-varieties - lolium-rigidum - cultivars - traits - interference - tolerance
Aerobic rice production systems, wherein rice is dry-sown in non-puddled soil and grown as an upland crop, offer large water savings but are subject to severe weed infestation. Weed-competitive cultivars will be critical to the adoption of aerobic rice production by farmers. Breeding weed-competitive cultivars requires an easily used selection protocol, preferably based on traits that can be measured under weed-free conditions. To develop such an indirect selection index for weed competitiveness, 40 rice cultivars were evaluated in aerobic soil conditions in a weed-free environment in 2003 and in weedy environments over 3 years (2001¿2003). Broad-sense heritabilities (H) of vegetative and harvest traits and their genetic correlation with weed biomass and yield under weed competition were estimated. All the traits measured under weed-free conditions were closely correlated with the same traits measured under weedy conditions. Crop vigor ratings at 2, 4, and 6 weeks after sowing (WAS), canopy ground cover at 6 WAS, height at 3 and 4 WAS, tillers per plant at 4 and 8 WAS, vegetative crop biomass at 4 and 9 WAS and plant erectness at 3 WAS under weed-free conditions in 2003 were all positively correlated with means for yield under weed competition and negatively with means for weed biomass across three years. In general, traits associated with rapid seedling biomass accumulation were also strongly associated with weed suppression and yield under weed competition. Regression analysis revealed that yield and early vigor under weed-free conditions in a single three-replicate trial could be used together in an indirect selection index, explaining 89% and 48% of variation for yield under weed competition and weed biomass, respectively. The predicted indirect selection efficiencies of weed-free yield and vigor ratings as selection criteria for yield under weed competition and weed biomass were high. Visual vigor rating at 4 WAS is the best vegetative trait as an indirect selection criterion for use together with weed-free yield, but it could be replaced by plant height at 4 WAS without loss in selection effectiveness