Resistance to biotic and abiotic stress in the Triticeae

Poverty, hunger and malnutrition occur in many parts of the world despite the enormous progress that has taken place in agriculture and food production in the last century. It is estimated for wheat, that by 2020 the world will require a 60% increase in production to meet the projected requirement. Resistance to both biotic and abiotic stresses will be critical in reaching this goal. Distinct advantages accompany the use of genetic resistance to biotic and abiotic stresses. The most important advantage is the fact that response to the stress situation occurs independently of the managerial ability, skill and resource level of the producer. Anyone can use a stress resistant crop. Immense progress has been made in the field of functional genomics and molecular manipulation. It is clear that the restraining factor in future will not be the availability of scientific techniques and tools, or for that matter, genetic resources; but the human and financial capacity to achieve the goals on a world-wide scale so that they really do make a difference to the livelihood of the poor. Triticeae form a meaningful proportion of staple and non-staple food crops around the world. To achieve world-wide food security in the future, Triticeae with resistance to stresses will have to play a major role. The future demands crops with stable yield irrespective of environmental constraints, good quality and a high nutritional value; crops that are free of pesticide residues and other harmful substances.     

Use of polyethyleneimine polymer in cell culture as attachment factor and lipofection enhancer

Background  

Several cell lines and primary cultures benefit from the use of positively charged extracellular matrix proteins or polymers that enhance their ability to attach to culture plates. Polyethyleneimine is a positively charged polymer that has gained recent attention as a transfection reagent. A less known use of this cationic polymer as an attachment factor was explored with several cell lines.     

Comparison of chlorophyll and carotenoid concentrations among Russian wheat aphid (Homoptera: Aphididae)-infested wheat isolines

Russian wheat aphid, Diuraphis noxia (Mordvilko), feeding injury on 'Betta' wheat isolines with the Dn1 and Dn2 genes was compared by assessing chlorophyll and carotenoid concentrations, and aphid fecundity. The resistant Betta isolines (i.e., Betta-Dn1 and Betta-Dn2) supported similar numbers of aphids, but had significantly fewer than the susceptible Betta wheat, indicating these lines are resistant to aphid feeding. Diuraphis noxia feeding resulted in different responses in total chlorophyll and carotenoid concentrations among the Betta wheat isolines. The infested Betta-Dn2 plants had higher levels of chlorophylls and carotenoids in comparison with uninfested plants. In contrast, infested Betta-Dn1 plants had the same level of chlorophyll and carotenoid in comparison with uninfested plants. Our data provide essential information on the effect of D. noxia feeding on chlorophyll and carotenoid concentrations for Betta wheat and its isolines with D. noxia-resistant Dn1 and Dn2 genes.     

Relationship of aerobic and anaerobic parameters with 400 m front crawl swimming performance

The aims of the present study were to investigate the relationship of aerobic and anaerobic parameters with 400 m performance, and establish which variable better explains long distance performance in swimming. Twenty-two swimmers (19.1±1.5 years, height 173.9±10.0 cm, body mass 71.2±10.2 kg; 76.6±5.3% of 400 m world record) underwent a lactate minimum test to determine lactate minimum speed (LMS) (i.e., aerobic capacity index). Moreover, the swimmers performed a 400 m maximal effort to determine mean speed (S400m), peak oxygen uptake (V.O2PEAK) and total anaerobic contribution (C_ANA). The C_ANA was assumed as the sum of alactic and lactic contributions. Physiological parameters of 400 m were determined using the backward extrapolation technique (V.O2PEAK and alactic contributions of C_ANA) and blood lactate concentration analysis (lactic anaerobic contributions of C_ANA). The Pearson correlation test and backward multiple regression analysis were used to verify the possible correlations between the physiological indices (predictor factors) and S400m (independent variable) (p < 0.05). Values are presented as mean ± standard deviation. Significant correlations were observed between S400m (1.4±0.1 m·s^-1) and LMS (1.3±0.1 m·s^-1; r = 0.80), V.O2PEAK (4.5±3.9 L·min^-1; r = 0.72) and C_ANA (4.7±1.5 L·O₂; r= 0.44). The best model constructed using multiple regression analysis demonstrated that LMS and V.O2PEAK explained 85% of the 400 m performance variance. When backward multiple regression analysis was performed, C_ANA lost significance. Thus, the results demonstrated that both aerobic parameters (capacity and power) can be used to predict 400 m swimming performance.     

Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains

Background

Genetic markers and maps are instrumental in quantitative trait locus (QTL) mapping in segregating populations. The resolution of QTL localization depends on the number of informative recombinations in the population and how well they are tagged by markers. Larger populations and denser marker maps are better for detecting and locating QTLs. Marker maps that are initially too sparse can be saturated or derived de novo from high-throughput omics data, (e.g. gene expression, protein or metabolite abundance). If these molecular phenotypes are affected by genetic variation due to a major QTL they will show a clear multimodal distribution. Using this information, phenotypes can be converted into genetic markers.

Results

The Pheno2Geno tool uses mixture modeling to select phenotypes and transform them into genetic markers suitable for construction and/or saturation of a genetic map. Pheno2Geno excludes candidate genetic markers that show evidence for multiple possibly epistatically interacting QTL and/or interaction with the environment, in order to provide a set of robust markers for follow-up QTL mapping.We demonstrate the use of Pheno2Geno on gene expression data of 370,000 probes in 148 A. thaliana recombinant inbred lines. Pheno2Geno is able to saturate the existing genetic map, decreasing the average distance between markers from 7.1 cM to 0.89 cM, close to the theoretical limit of 0.68 cM (with 148 individuals we expect a recombination every 100/148=0.68 cM); this pinpointed almost all of the informative recombinations in the population.

Conclusion

The Pheno2Geno package makes use of genome-wide molecular profiling and provides a tool for high-throughput de novo map construction and saturation of existing genetic maps. Processing of the showcase dataset takes less than 30 minutes on an average desktop PC. Pheno2Geno improves QTL mapping results at no additional laboratory cost and with minimum computational effort. Its results are formatted for direct use in R/qtl, the leading R package for QTL studies. Pheno2Geno is freely available on CRAN under “GNU GPL v3”. The Pheno2Geno package as well as the tutorial can also be found at: http://pheno2geno.nl.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0475-6) contains supplementary material, which is available to authorized users.     

An AFLP-based genetic linkage map of Plasmodium chabaudi chabaudi

Background

Plasmodium chabaudi chabaudi can be considered as a rodent model of human malaria parasites in the genetic analysis of important characters such as drug resistance and immunity. Despite the availability of some genome sequence data, an extensive genetic linkage map is needed for mapping the genes involved in certain traits.

Methods

The inheritance of 672 Amplified Fragment Length Polymorphism (AFLP) markers from two parental clones (AS and AJ) of P. c. chabaudi was determined in 28 independent recombinant progeny clones. These, AFLP markers and 42 previously mapped Restriction Fragment Length Polymorphism (RFLP) markers (used as chromosomal anchors) were organized into linkage groups using Map Manager software.

Results

614 AFLP markers formed linkage groups assigned to 10 of 14 chromosomes, and 12 other linkage groups not assigned to known chromosomes. The genetic length of the genome was estimated to be about 1676 centiMorgans (cM). The mean map unit size was estimated to be 13.7 kb/cM. This was slightly less then previous estimates for the human malaria parasite, Plasmodium falciparum

Conclusion

The P. c. chabaudi genetic linkage map presented here is the most extensive and highly resolved so far available for this species. It can be used in conjunction with the genome databases of P. c chabaudi, P. falciparum and Plasmodium yoelii to identify genes underlying important phenotypes such as drug resistance and strain-specific immunity.     

Stress protein of cyanobacteria CP36: interaction with photoactive complexes and formation of supramolecular structures

Cyanobacterium Anacystis nidulans R2, Synechocystis sp. PCC 6803 (wild-type strain and mutants Delta2 and Delta3 lacking PSII and PSI, respectively), and Synechocystis sp. BO 9201 synthesize the pigment--protein complex CP36 (CPIV-4, CP43') under iron deficiency in the medium. Accumulation of CP36 is accompanied by structural reorganizations in the photosynthetic membranes. Integrating mean times of excitation relaxation (quenching) are 2.2 nsec (CP36), 1 nsec (PSI), and 420 psec (PSII in Fm state). The energy migration between CP36 and the photosystems can be described by a model of a one-layer ring of CP36 around core-complexes. The excitation from CP36 to PSI is transferred within <10 psec. The energy transfer from CP36 to PSII occurs during 170 psec. Cells with low content of CP36 probably contain only a latent fraction of unbound to phycobilisomes PSII which is the analog of PSIIbeta of higher plants. In PSI there are four binding sites for CP36 monomers per RC. PSII can bind up to 32 molecules of CP36 per RC. Cells with a large amount of CP36 contain monomer form of PSII core-complex which can bind eight tetramers of CP36 (8 binding sites). In conditions of iron deficiency only one monomer of a dimer PSII core-complex is destroyed and released chlorophyll is accumulated in CP36. Accumulation of CP36 in A. nidulans cells can be accompanied by membrane stacking which is similar to the stacking in chlorophyll b-containing organisms. The stacking can occur in the region of localization of PSII latent fraction bound to CP36. The membrane stacking shields PSII stromal surfaces from the aqueous phase for activation of electron transfer on the acceptor side of PSII.     

Microsatellite markers linked to six Russian wheat aphid resistance genes in wheat

The Russian wheat aphid (RWA), Diuraphis noxia Mordvilko, is a serious economic pest of wheat and barley in North America, South America, and South Africa. Using aphid-resistant cultivars has proven to be a viable tactic for RWA management. Several dominant resistance genes have been identified in wheat, Triticum aestivum, including Dn1 in PI 137739, Dn2 in PI 262660, and at least three resistance genes (Dn5+) in PI 294994. The identification of RWA-resistant genes and the development of resistant cultivars may be accelerated through the use of molecular markers. DNA of wheat from near-isogenic lines and segregating F₂ populations was amplified with microsatellite primers via PCR. Results revealed that the locus for wheat microsatellite GWM111 (Xgwm111), located on wheat chromosome 7DS (short arm), is tightly linked to Dn1, Dn2 and Dn5, as well as Dnx in PI 220127. Segregation data indicate RWA resistance in wheat PI 220127 is also conferred by a single dominant resistance gene (Dnx). These results confirm that Dn1, Dn2 and Dn5 are tightly linked to each other, and provide new information about their location, being 7DS, near the centromere, instead of as previously reported on 7DL. Xgwm635 (near the distal end of 7DS) clearly marked the location of the previously suggested resistance gene in PI 294994, here designated as Dn8. Xgwm642 (located on 1DL) marked and identified another new gene Dn9, which is located in a defense gene-rich region of wheat chromosome 1DL. The locations of markers and the linked genes were confirmed by di-telosomic and nulli-tetrasomic analyses. Genetic linkage maps of the above RWA resistance genes and markers have been constructed for wheat chromosomes 1D and 7D. These markers will be useful in marker-assisted breeding for RWA-resistant wheat. Received: 17 May 2000 / Accepted: 13 June 2000     

Aphid (Hemiptera: Aphididae) resistance in wheat near-isogenic lines

Plant and aphid biomass, photosynthetic pigment (chlorophylls a and b and carotenoids) concentrations, and chlorophyll a/b and chlorophyll/carotenoid ratios were quantified in aphid-infested 'Tugela' near-isogenic lines (Tugela, Tugela-Dn1, Tugela-Dn2, and Tugela-Dn5). The objectives were to quantify changes of photosynthetic pigments (chlorophylls a and b, and carotenoids) caused by aphid feeding and assess resistance of wheat isolines through aphid and plant biomass analysis. Biomass of bird cherry-oat aphid, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)-infested plants was lower than Russian wheat aphid, Diuraphis noxia (Mordvilko) (Hemiptera: Aphididae),- infested plants. When infested by D. noxia, all lines showed increased biomass over time, except Tugela where biomass decreased on day 12. No difference in plant biomass was detected among R. padi-infested and uninfested wheat lines. Biomass of D. noxia from Tugela (D. noxia-susceptible) was significantly higher than from plants with Diuraphis noxia-resistant Dn genes. Diuraphis noxia biomass from Tugela-Dn1 and Dn2 lines was not different from each other, but they were lower than from Tugela-Dn5. In contrast, there was no difference in R. padi biomass among wheat lines. Concentrations of chlorophylls a and b and carotenoids were significantly lower in D. noxia-infested plants compared with R. padi-infested and uninfested plants. When infested by D. noxia, chlorophyll a and b concentrations were not different among wheat lines on day 3, but they were lower in Tugela and Tugela-Dn1 than in Tugela-Dn2 and -Dn5 plants on days 6 and 12. However, no difference was detected in chlorophyll a/b or chlorophyll/carotenoid ratio among Tugela lines. The study demonstrated that Dn genes in the Tugela isolines conferred resistance to D. noxia but not to R. padi. Tugela-Dn1 was antibiotic, Tugela-Dn2 was tolerant and antibiotic, and Tugela-Dn5 was moderately antibiotic.