Thatcher wheat line RL6149 carries Lr64 and a second leaf rust resistance gene on chromosome 1DS.

KEY MESSAGE: The leaf rust resistance gene Lr64 in the Thatcher wheat RL6149 was mapped to chromosome 6AL with SNP and KASP markers and a second leaf rust resistance gene was mapped to chromosome 1DS. RL6149, a near-isogenic line of Thatcher wheat, carries leaf rust resistance gene Lr64 on chromosome arm 6AL. The objective of this study was to develop molecular markers that can be easily used to select wheat lines with Lr64. RL6149 was crossed with Thatcher and F2 plants derived from a single F1 plant were advanced to F6 lines by single seed descent. The 100 F7 recombinant inbred lines (RIL) were inoculated with two races of P.triticina that differed widely for virulence in order to identify resistant and susceptible RIL. Thirty RIL that differed for resistance and the parental lines were genotyped with the 90 K Infinium iSelect single nucleotide polymorphism (SNP) array to find closely linked markers with Lr64. Seven linked SNPs on chromosome arm 6AL were converted into Kompetitive Allele Specific PCR (KASP) markers that were genotyped on the 100 RIL. A genetic linkage map for the seven KASP markers spanned 19.1 cM on chromosome arm 6AL. KASP marker K-IWB59855 was tightly linked to Lr64. A second unexpected gene for leaf rust resistance also segregated in the F7 lines. Four KASP markers that spanned 18.6 cM located the gene on chromosome 1DS. The KASP marker K-IWB38437 was tightly linked to the second leaf rust resistance gene.

Adult Plant Leaf Rust Resistance Derived from Toropi Wheat is Conditioned by Lr78 and Three Minor QTL.

Leaf rust caused by Puccinia triticina is an important disease of wheat in many regions worldwide. Durable or long-lasting leaf rust resistance has been difficult to achieve because populations of P. triticina are highly variable for virulence to race-specific resistance genes, and respond to selection by resistance genes in released wheat cultivars. The wheat cultivar Toropi, developed and grown in Brazil, was noted to have long-lasting leaf rust resistance that was effective only in adult plants. The objectives of this study were to determine the chromosome location of the leaf rust resistance genes derived from Toropi in two populations of recombinant inbred lines in a partial Thatcher wheat background. In the first population, a single gene with major effects on chromosome 5DS that mapped 2.2 centimorgans distal to IWA6289, strongly reduced leaf rust severity in all 3 years of field plot tests. This gene for adult plant leaf rust resistance was designated as Lr78. In the second population, quantitative trait loci (QTL) with small effects on chromosomes 1BL, 3BS, and 4BS were found. These QTL expressed inconsistently over 4 years of field plot tests. The adult plant leaf rust resistance derived from Toropi involved a complex combination of QTL with large and small effects.

Genetic Relationship of Stripe Rust Resistance Genes Yr34 and Yr48 in Wheat and Identification of Linked KASP Markers.

The Australian continent was free from wheat stripe rust caused by Puccinia striiformis f. sp. tritici until exotic incursions occurred in 1979 and 2002. The 2002 incursion enabled the identification of a new stripe rust resistance gene (Yr34) in the advanced breeding line WAWHT2046. In this study, we developed and validated markers closely linked with Yr34, which is located in the distal region in the long arm of chromosome 5A. Four kompetitive allele-specific polymerase chain reaction (KASP) and three sequence-tagged site (STS) markers derived from the International Wheat Genome Sequencing Consortium RefSeq v1.0 scaffold-77836 cosegregated with Yr34. Markers sun711, sun712, sun725, sunKASP_109, and sunKASP_112 were shown to be suitable for marker-assisted selection in a validation panel of 71 Australian spring wheat genotypes, with the exception of cultivar Orion that carried the Yr34-linked alleles for sunKASP_109 and sunKASP_112. Markers previously reported to be linked with adult plant stripe rust resistance gene Yr48 also cosegregated with Yr34. Wheat genotypes carrying Yr34 and Yr48 produced identical haplotypes for the Yr34-linked markers identified in this study and those previously reported to be linked with Yr48. Phenotypic testing of genotypes carrying Yr34 and Yr48 showed that both genes conferred similar seedling responses to pre-2002 and post-2002 P. striiformis f. sp. tritici pathotypes. Further testing of 600 F2 plants from a cross between WAWHT2046 and RIL143 (Yr48) with P. striiformis f. sp. tritici pathotype 134 E16A+Yr17+Yr27+ failed to reveal any susceptible segregants. Our results strongly suggest that Yr34 and Yr48 are the same gene, and that Yr48 should be considered a synonym of Yr34.

Accelerating wheat breeding for end-use quality with multi-trait genomic predictions incorporating near infrared and nuclear magnetic resonance-derived phenotypes.

KEY MESSAGE: Using NIR and NMR predictions of quality traits overcomes a major barrier for the application of genomic selection to accelerate improvement in grain end-use quality traits of wheat. Grain end-use quality traits are among the most important in wheat breeding. These traits are difficult to breed for, as their assays require flour quantities only obtainable late in the breeding cycle, and are expensive. These traits are therefore an ideal target for genomic selection. However, large reference populations are required for accurate genomic predictions, which are challenging to assemble for these traits for the same reasons they are challenging to breed for. Here, we use predictions of end-use quality derived from near infrared (NIR) or nuclear magnetic resonance (NMR), that require very small amounts of flour, as well as end-use quality measured by industry standard assay in a subset of accessions, in a multi-trait approach for genomic prediction. The NIR and NMR predictions were derived for 19 end-use quality traits in 398 accessions, and were then assayed in 2420 diverse wheat accessions. The accessions were grown out in multiple locations and multiple years, and were genotyped for 51208 SNP. Incorporating NIR and NMR phenotypes in the multi-trait approach increased the accuracy of genomic prediction for most quality traits. The accuracy ranged from 0 to 0.47 before the addition of the NIR/NMR data, while after these data were added, it ranged from 0 to 0.69. Genomic predictions were reasonably robust across locations and years for most traits. Using NIR and NMR predictions of quality traits overcomes a major barrier for the application of genomic selection for grain end-use quality traits in wheat breeding.

Analysis of leaf and stripe rust severities reveals pathotype changes and multiple minor QTLs associated with resistance in an Avocet × Pastor wheat population.

Leaf rust and stripe rust are important diseases of wheat world-wide and deployment of cultivars with genetic resistance is an effective and environmentally sound control method. The use of minor, additive genes conferring adult plant resistance (APR) has been shown to provide resistance that is durable. The wheat cultivar 'Pastor' originated from the CIMMYT breeding program that focuses on minor gene-based APR to both diseases by selecting and advancing generations alternately under leaf rust and stripe rust pressures. As a consequence, Pastor has good resistance to both rusts and was used as the resistant parent to develop a mapping population by crossing with the susceptible 'Avocet'. All 148 F(5) recombinant inbred lines were evaluated under artificially inoculated epidemic environments for leaf rust (3 environments) and stripe rust (4 environments, 2 of which represent two evaluation dates in final year due to the late build-up of a new race virulent to Yr31) in Mexico. Map construction and QTL analysis were completed with 223 polymorphic markers on 84 randomly selected lines in the population. Pastor contributed Yr31, a moderately effective race-specific gene for stripe rust resistance, which was overcome during this study, and this was clearly shown in the statistical analysis. Linked or pleiotropic chromosomal regions contributing to resistance against both pathogens included Lr46/Yr29 on 1BL, the Yr31 region on 2BS, and additional minor genes on 5A, 6B and 7BL. Other minor genes for leaf rust resistance were located on 1B, 2A and 2D and for stripe rust on 1AL, 1B, 3A, 3B, 4D, 6A, 7AS and 7AL. The 1AL, 1BS and 7AL QTLs are in regions that were not identified previously as having QTLs for stripe rust resistance. The development of uniform and severe epidemics facilitated excellent phenotyping, and when combined with multi-environment analysis, resulted in the relatively large number of QTLs identified in this study.

Inheritance and molecular mapping of a gene conferring seedling resistance against Puccinia hordei in the barley cultivar Ricardo.

Genetic studies were undertaken to determine the inheritance and genomic location of uncharacterised seedling resistance to leaf rust, caused by Puccinia hordei, in the barley cultivar Ricardo. The resistance was shown to be conferred by a single dominant gene, which was tentatively designated RphRic. Bulk segregant analysis (BSA) and genetic mapping of an F(3) mapping population using multiplex-ready SSR genotyping and Illumina GoldenGate SNP assay located RphRic in chromosome 4H. Given that this is the first gene for leaf rust resistance mapped on chromosome 4H, it was designated Rph21. The presence of an additional gene, Rph2, in Ricardo, was confirmed by the test of allelism. The seedling gene Rph21 has shown effectiveness against all Australian pathotypes of P. hordei tested since at least 1992 and hence represents a new and useful source of resistance to this pathogen.

Characterisation of a new stripe rust resistance gene Yr47 and its genetic association with the leaf rust resistance gene Lr52.

Two Iranian common wheat landraces AUS28183 and AUS28187 from the Watkins collection showed high levels of seedling resistance against Australian pathotypes of leaf rust and stripe rust pathogens. Chi-squared analyses of rust response segregation among F(3) populations derived from crosses of AUS28183 and AUS28187 with a susceptible genotype AUS27229 revealed monogenic inheritance of leaf rust and stripe rust resistance. As both genotypes produced similar leaf rust and stripe rust infection types, they were assumed to carry the same genes. The genes were temporarily named as LrW1 and YrW1. Molecular mapping placed LrW1 and YrW1 in the short arm of chromosome 5B, about 10 and 15 cM proximal to the SSR marker gwm234, respectively, and the marker cfb309 mapped 8-12 cM proximal to YrW1. LrW1 mapped 3-6 cM distal to YrW1 in two F(3) populations. AUS28183 corresponded to the accession V336 of the Watkins collection which was the original source of Lr52. Based on the genomic location and accession records, LrW1 was concluded to be Lr52. Because no other seedling stripe rust resistance gene has previously been mapped in chromosome 5BS, YrW1 was permanently named as Yr47. A combination of flanking markers gwm234 and cfb309 with phenotypic assays could be used to ascertain the presence of Lr52 and Yr47 in segregating populations. This investigation characterised a valuable source of dual leaf rust and stripe rust resistance for deployment in new wheat cultivars. Transfer of Lr52 and Yr47 into current Australian wheat backgrounds is in progress.

Saturation and mapping of a major Fusarium head blight resistance QTL on chromosome 3BS of Sumai 3 wheat.

Fusarium head blight (FHB) is a destructive disease in wheat. The major quantitative trait locus (QTL) on 3BS from Sumai 3 and its derivatives has been used as a major source of the resistance to FHB worldwide, but the discrepancy in reported location of the major QTL could block its using in map based cloning and marker assisted selection. In this study, Chinese Spring-Sumai 3 chromosome 3B substitution line was used as resistant parent of the mapping population to reduce the confounded effect of genetic background in Sumai 3. The major QTL region was saturated with the Sequence Tagged Microsatellite (STM) and Sequence Tagged Site (STS) markers. A linkage map of chromosome 3B with 36 markers covering a genetic distance of 112.4 cM was constructed. Twelve new markers were inserted into the chromosome region where the major QTL was located. The average interval distance between markers was 1.5 cM. Multiple QTL Models (MQM) mapping indicated that the major QTL was located in the interval of Xgwm533-Xsts9-1, and explained 45.6% of phenotypic variation of the resistance to FHB. The SSR (simple sequence repeat) marker Xgwm533 and STM marker Xstm748tcac are closely linked to the major QTL.

Genetic Diversity in Australian Populations of Puccinia graminis f. sp. avenae.

ABSTRACT Sequence-tagged microsatellite profiling was used to develop 110 microsatellites for Puccinia graminis f. sp. tritici (causal agent of wheat stem rust). Low microsatellite polymorphism was exhibited among 10 pathogenically diverse P. graminis f. sp. tritici isolates collected from Australian cereal growing regions over a period of at least 70 years, with two polymorphic loci detected, each revealing two alleles. Limited cross-species amplification was observed for the wheat rust pathogens, P. triticina (leaf rust) and P. striiformis f. sp. tritici (stripe rust). However, very high transferability was revealed with P. graminis f. sp. avenae (causal agent of oat stem rust) isolates. A genetic diversity study of 47 P. graminis f. sp. avenae isolates collected from an Australia-wide survey in 1999, and a historical group of 16 isolates collected from Australian cereal growing regions from 1971 to 1996, revealed six polymorphic microsatellite loci with a total of 15 alleles. Genetic analysis revealed the presence of several clonal lineages and subpopulations in the pathogen population, and wide dispersal of identical races and genotypes throughout Australian cereal-growing regions. These findings demonstrated the dynamic population structure of this pathogen in Australia and concur with the patterns of diversity observed in pathogenicity studies.

Sequence-tagged microsatellite profiling (STMP): a rapid technique for developing SSR markers.

We describe a technique, sequence-tagged microsatellite profiling (STMP), to rapidly generate large numbers of simple sequence repeat (SSR) markers from genomic or cDNA. This technique eliminates the need for library screening to identify SSR-containing clones and provides an approximately 25-fold increase in sequencing throughput compared to traditional methods. STMP generates short but characteristic nucleotide sequence tags for fragments that are present within a pool of SSR amplicons. These tags are then ligated together to form concatemers for cloning and sequencing. The analysis of thousands of tags gives rise to a representational profile of the abundance and frequency of SSRs within the DNA pool, from which low copy sequences can be identified. As each tag contains sufficient nucleotide sequence for primer design, their conversion into PCR primers allows the amplification of corresponding full-length fragments from the pool of SSR amplicons. These fragments permit the full characterisation of a SSR locus and provide flanking sequence for the development of a microsatellite marker. Alternatively, sequence tag primers can be used to directly amplify corresponding SSR loci from genomic DNA, thereby reducing the cost of developing a microsatellite marker to the synthesis of just one sequence-specific primer. We demonstrate the utility of STMP by the development of SSR markers in bread wheat.

Targeted development of informative microsatellite (SSR) markers.

We describe a novel approach, selectively amplified microsatellite (SAM) analysis, for the targeted development of informative simple sequence repeat (SSR) markers. A modified selectively amplified microsatellite polymorphic loci assay is used to generate multi-locus SSR fingerprints that provide a source of polymorphic DNA markers (SAMs) for use in genetic studies. These polymorphisms capture the repeat length variation associated with SSRs and allow their chromosomal location to be determined prior to the expense of isolating and characterising individual loci. SAMs can then be converted to locus-specific SSR markers with the design and synthesis of a single primer specific to the conserved region flanking the repeat. This approach offers a cost-efficient and rapid method for developing SSR markers for predetermined chromosomal locations and of potential informativeness. The high recovery rate of useful SSR markers makes this strategy a valuable tool for population and genetic mapping studies. The utility of SAM analysis was demonstrated by the development of SSR markers in bread wheat.

Sequence tagged microsatellite profiling (STMP): improved isolation of DNA sequence flanking target SSRs.

Sequence tagged microsatellite profiling (STMP) enables the rapid development of large numbers of co-dominant DNA markers, known as sequence tagged microsatellites (STMs). Each STM is amplified by PCR using a single primer specific to the conserved DNA sequence flanking the microsatellite repeat in combination with a universal primer that anchors to the 5'-ends of the microsatellites. It is also possible to convert STMs into conventional microsatellite, or simple sequence repeat (SSR), markers that are amplified using a pair of primers flanking the repeat sequence. Here, we describe a modification of the STMP procedure to significantly improve the capacity to convert STMs into conventional SSRs and, therefore, facilitate the development of highly specific DNA markers for purposes such as marker-assisted breeding. The usefulness of this technique was demonstrated in bread wheat.

Attentional biases for food cues in overweight and individuals with obesity: a systematic review of the literature.

Obesity rates have increased dramatically in recent decades, and it has proven difficult to treat. An attentional bias towards food cues may be implicated in the aetiology of obesity and influence cravings and food consumption. This review systematically investigated whether attentional biases to food cues exist in overweight/obese compared with healthy weight individuals. Electronic database were searched for relevant papers from inception to October 2014. Only studies reporting food-related attentional bias between either overweight (body mass index [BMI] 25.0-29.9 kg m(-2)) or obese (BMI ≥ 30) participants and healthy weight participants (BMI 18.5-24.9) were included. The findings of 19 studies were reported in this review. Results of the literature are suggestive of differences in attentional bias, with all but four studies supporting the notion of enhanced reactivity to food stimuli in overweight individuals and individuals with obesity. This support for attentional bias was observed primarily in studies that employed psychophysiological techniques (i.e. electroencephalogram, eye-tracking and functional magnetic resonance imaging). Despite the heterogeneous methodology within the featured studies, all measures of attentional bias demonstrated altered cue-reactivity in individuals with obesity. Considering the theorized implications of attentional biases on obesity pathology, researchers are encouraged to replicate flagship studies to strengthen these inferences.

Salbutamol delivery from a hydrofluoroalkane pressurized metered-dose inhaler in pediatric ventilator circuits: an in vitro study.

STUDY OBJECTIVES: The aim of our study was to determine the in vitro delivery of salbutamol from a pressurized metered-dose inhaler (pMDI) containing hydrofluoroalkane (HFA) propellant through various delivery devices to four models of a pediatric lung. DESIGN: To determine the effect of electrostatic charge, delivery of salbutamol was initially assessed with a multistage liquid impinger (MSLI) through an inline nonchamber device (Baxter MDI Adapter) and a small (Aerochamber MV) and a large (Nebuhaler) inline chamber device. Following this, the delivery was assessed to four lung models appropriate for a child of 70 kg, 50 kg, 15 kg, and 4 kg, with the same three reduced static devices inserted directly into a pediatric ventilator circuit. MEASUREMENTS AND RESULTS: Reduction of electrostatic charge improved small particle delivery through holding chambers to the MSLI by 12 to 14%. In the ventilator model, the mean delivery was between 1.9% and 5.4% for the nonchamber device, between 14.3% and 27.2% for the small holding chamber, and between 7.2% and 25.7% for the large holding chamber. Delivery was the least efficient in the 4-kg model compared to the 70-kg, 50-kg, and 15-kg models. CONCLUSIONS: Salbutamol from an HFA pMDI is delivered efficiently through inline holding chambers with reduced static in pediatric ventilator settings. A large holding chamber has no advantage over a small holding chamber. In addition, salbutamol delivery is more efficient through a holding chamber than through a nonchamber device.

Parental attitudes toward infant pulmonary function testing.

Infant pulmonary function tests (PFTs) have proven increasingly popular and useful for clinical and research purposes. Informed consent requires accurate information on side effects. Our aim was to quantify minor side effects from a parental point of view by means of a questionnaire. The parents of 97 infants attending for PFTs were asked to complete a simple questionnaire. Eighty-one parents (84%) returned the questionnaire. Forty-one percent felt that their infants were not troubled by the process of administering the sedative chloral hydrate, whereas 55% suffered mild to moderate distress. In contrast, 94% of infants were not distressed by the actual PFTs. Similarly, 46% of parents were not distressed by the administration of sedative to their infant, with 49% expressing distress to a mild or moderate degree. Although 73% of parents were not distressed by watching their infants undergo the PFTs, 27% were to a mild to moderate degree. Seventy-three percent of infants were untroubled on waking. Seventy percent of infants had a good nights sleep after the PFTs. The vast majority of parents (94%) were happy to recommend that others allow their infants to undergo similar testing. We noted that most problems caused by infant PFTs relate to the administration of the sedative. Most infants awake from the tests not distressed and sleep normally the following night.

Bronchodilator responsiveness testing using raised volume forced expiration in recurrently wheezing infants.

We hypothesized that a new test of infant lung function, less affected by shifts in lung volume, might better detect bronchodilator effects. Using the raised volume forced expiration technique (RVFET), the effect of a bronchodilator on lung function was studied in 22 infants with a history of recurrent wheeze and five healthy infants. Forced expiratory volume in 0.75 s (FEV0.75), forced expiratory vital capacity (FVC), and forced expiratory flow at 75% of FVC (FEF75%) were measured by forcing expiration, using an inflatable jacket from a lung volume set by an inspiratory pressure of 20 cm H2O. A minimum of five measurements were made at baseline and following the administration of 500 microg of salbutamol from a metered dose inhaler via a small volume metal spacer. Changes in lung function in the group of 25 infants who received salbutamol were compared to seven infants who received placebo aerosol. No significant changes occurred in measures of lung function following salbutamol administration when compared to baseline or placebo despite a significant increase in heart rate. A shift in lung volume is unlikely the reason why infants do not demonstrate a change in forced expiration following bronchodilator administration.

Aerosol delivery to wheezy infants: a comparison between a nebulizer and two small volume spacers.

Inhalation therapy for wheezy infants with either a nebulizer or a pressurized metered-dose inhaler (pMDI) through a spacer is common practice. The aim of our study was to compare aerosol delivery to wheezy infants from a nebulizer and from a pMDI via two small volume spacers. Twenty wheezy infants (aged 4-12 months) were recruited. They inhaled salbutamol from a Pari-Baby nebulizer, from a detergent-coated Babyhaler, and from a Nebuchamber in random order. A filter was placed between the inhalation systems and the patients. The amount of salbutamol deposited on the filter was measured using an ultraviolet spectrophotometer and was expressed as a percentage of the total nebulized or actuated doses. The mean total nebulized dose for the Pari-Baby (1030 micrograms) was higher (P < 0.001) than the mean actuated dose from a pMDI for the Babyhaler (374 micrograms) and for the Nebuchamber (378 micrograms). Mean drug deposition on the filter was 40.2% (150 micrograms) of the total actuated dose for the detergent-coated Babyhaler and 40.7% (154 micrograms) of the total actuated dose for the Nebuchamber. There was no significant difference in drug deposition on the filter between the two spacers. Mean drug deposition on the filter was 25.3% (260 micrograms) of the total nebulized dose for the Pari-Baby nebulizer. There was no weight dependence in drug deposition on the filter for the two spacers, but, drug deposition increased with the subject's weight for the nebulizer. We have shown that aerosol delivery to wheezy infants from a pMDI through small volume spacers is effective and that a higher percentage of the total amount of salbutamol is delivered than from a nebulizer. The weight dependence in drug deposition for the nebulizer can be of clinical relevance.

Axis I disorders in adjustable gastric band patients: the relationship between psychopathology and weight loss.

BACKGROUND: Bariatric surgery candidates have higher rates of co-morbid psychological illnesses than those in the general population. The effect of weight loss on these illnesses is unclear. METHODS: This prospective observational study explored psychiatric co-morbidities and weight loss outcomes in 204 gastric banding surgery candidates. Psychiatric co-morbidities were assessed prior to surgery and 2 years post-surgery. One hundred and fifty patients (74%) completed assessments at both time points. RESULTS: At baseline, 39.7% of the patients met the criteria for a current axis I disorder as defined by the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM-IV). Mood disorders were the most frequent (26.5%), followed by anxiety disorders (15.2%) and binge eating disorder (13.2%). Preoperative psychopathology predicted clinical psychopathology at 2 years. No preoperative or post-operative axis I disorder was significantly related to weight loss at 2 years. The frequency of current axis I disorders decreased significantly from 39.7% preoperatively to 20% 2 years post-surgery. CONCLUSIONS: The point prevalence of psychopathology in this sample of Australian bariatric candidates is high. Psychopathology, preoperatively and at 2 years of follow-up, was not associated with weight loss at 2 years.