Genetic mapping of loci affecting seedling and adult-plant resistance to powdery mildew derived from two CIMMYT wheat lines.

MAIN CONCLUSION: PM3 and PM8 alleles carried by two CIMMYT wheat lines confer powdery mildew resistance in seedlings and/or adult plants. A stage-specific epistatic interaction was observed between PM3 and PM8. Powdery mildew is an important foliar disease of wheat. Major genes for resistance, which have been widely used in wheat breeding programs, are typically effective against only limited numbers of virulence genes of the pathogen. The main aim of this study was to map resistance loci in wheat lines 7HRWSN58 and ZWW09-149 from the International Maize and Wheat Improvement Center (CIMMYT). Doubled haploid populations (Magenta/7HRWSN58 and Emu Rock/ZWW09-149) were developed and grown in controlled environment experiments and inoculated with a composite of Blumeria graminis f.sp. tritici isolates that had been collected at various locations in Western Australia. Plants were assessed for powdery mildew symptoms (percentage leaf area diseased) on seedlings and adult plants. Populations were subjected to genotyping-by-sequencing and assayed for known SNPs in the resistance gene PM3. Linkage maps were constructed, and markers were anchored to the wheat reference genome sequence. In both populations, there were asymptomatic lines that exhibited no symptoms. Among symptomatic lines, disease severity varied widely. In the Magenta/7HRWSN58 population, most of the observed variation was attributed to the PM3 region of chromosome 1A, with the allele from 7HRWSN58 conferring resistance in seedlings and adult plants. In the Emu Rock/ZWW09-149 population, two interacting quantitative trait loci were mapped: one at PM3 and the other on chromosome 1B. The Emu Rock/ZWW09-149 population was confirmed to segregate for a 1BL·1RS translocation that carries the PM8 powdery mildew resistance gene from rye. Consistent with previous reports that PM8-derived resistance can be suppressed by PM3 alleles, the observed interaction between the quantitative trait loci on chromosomes 1A and 1B indicated that the PM3 allele carried by ZWW09-149 suppresses PM8-derived resistance from ZWW09-149, but only at the seedling stage. In adult plants, the PM8 region conferred resistance regardless of the PM3 genotype. The resistance sources and molecular markers that were investigated here could be useful in wheat breeding.

Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset.

Enset (Ensete ventricosum (Welw.) Cheesman) is a drought tolerant, vegetatively propagated crop that was domesticated in Ethiopia. It is a staple food for more than 20 million people in Ethiopia. Despite its current importance and immense potential, enset is among the most genetically understudied and underexploited food crops. We collected 230 enset wild and cultivated accessions across the main enset producing regions in Ethiopia and applied amplified fragment length polymorphism (AFLP) and genotype by sequencing (GBS) analyses to these accessions. Wild and cultivated accessions were clearly separated from each other, with 89 genes found to harbour SNPs that separated wild from cultivated accessions. Among these, 17 genes are thought to be involved in flower initiation and seed development. Among cultivated accessions, differentiation was mostly associated with geographical location and with proximity to wild populations. Our results indicate that vegetative propagation of elite clones has favoured capacity for vegetative growth at the expense of capacity for sexual reproduction. This is consistent with previous reports that cultivated enset tends to produce non-viable seeds and flowers less frequently than wild enset.

QTL analysis and fine mapping of a QTL for yield-related traits in wheat grown in dry and hot environments.

Genetic control of grain yield and phenology was examined in the Excalibur/Kukri doubled haploid mapping population grown in 32 field experiments across the climatic zones of southern Australia, India and north-western Mexico where the wheat crop experiences drought and heat stress. A total of 128 QTL were identified for four traits: grain yield, thousand grain weight (TGW), days to heading and grain filling duration. These QTL included 24 QTL for yield and 27 for TGW, showing significant interactions with the environment (Q * E). We also identified 14 QTL with a significant, small main effects on yield across environments. The study focussed on a region of chromosome 1B where two main effect QTL were found for yield and TGW without the confounding effect of phenology. Excalibur was the source of favourable alleles: QYld.aww-1B.2 with a peak at 149.5-150.1 cM and QTgw.aww-1B at 168.5-171.4 cM. We developed near isogenic lines (NIL) for the interval including QYld.aww-1B.2 and QTgw.aww-1B and evaluated them under semi-controlled conditions. Significant differences in four pairs of NIL were observed for grain yield but not for TGW, confirming a positive effect of the Excalibur allele for QYld.aww-1B.2. The interval containing QYld.aww-1B.2 was narrowed down to 2.9 cM which corresponded to a 2.2 Mbp genomic region on the chromosome 1B genomic reference sequence of cv. Chinese Spring and contained 39 predicted genes.

Optimal neoadjuvant chemotherapy duration in Wilms tumour with intravascular thrombus: A literature review and evidence from SIOP WT 2001 trial.

INTRODUCTION: Preoperative chemotherapy is recommended for children with Wilms tumour with intravascular extension. Extended chemotherapy may improve resectability, but increase tumour adherence to vascular endothelium, precluding complete resection. To evaluate the optimal length of preoperative treatment, we report a two-part review comprising systematic review of the literature and investigation of patients treated in the International Society of Paediatric Oncology (SIOP) WT 2001 trial. METHODS: Studies were identified using Medline and Embase databases from 1996 to present. English language titles reporting management of intravascular Wilms tumour were analysed. Patients with Wilms tumour and thrombus were identified from the SIOP WT 2001 trial. Overall survival (OS) and event-free survival (EFS), tumour regression, completeness of resection and cavectomy were investigated. RESULTS: The search retrieved 43 articles documenting 498 children. Note that 72% of the patients received neoadjuvant chemotherapy: 101 received standard course (4-6 weeks, standard course neoadjuvant chemotherapy [StC]) and 62 extended course (> 6 weeks, extended course neoadjuvant chemotherapy [EC]). There was no significant difference between the groups in terms of thrombus regression or completeness of resection. EFS was greater in the StC group (78 vs 54%; P = .04). Of 4511 patients registered in the SIOP WT 2001 trial, 166 had thrombus. Note that 97% of the patients received neoadjuvant chemotherapy: 63 StC and 67 EC. There was no significant difference between the groups with regard to tumour regression, complete resection, or cavectomy. Survival was significantly higher in those receiving StC than EC (OS: 95% vs 82%, P = .025; EFS: 88% vs 72%, P = .047). CONCLUSION: There is no evidence that prolonged courses of neoadjuvant chemotherapy beyond the recommended protocols confer any additional benefit in treating intravascular extension of Wilms tumour.

Genome-wide association mapping of grain yield in a diverse collection of spring wheat (Triticum aestivum L.) evaluated in southern Australia.

Wheat landraces, wild relatives and other 'exotic' accessions are important sources of new favorable alleles. The use of those exotic alleles is facilitated by having access to information on the association of specific genomic regions with desirable traits. Here, we conducted a genome-wide association study (GWAS) using a wheat panel that includes landraces, synthetic hexaploids and other exotic wheat accessions to identify loci that contribute to increases in grain yield in southern Australia. The 568 accessions were grown in the field during the 2014 and 2015 seasons and measured for plant height, maturity, spike length, spike number, grain yield, plant biomass, HI and TGW. We used the 90K SNP array and two GWAS approaches (GAPIT and QTCAT) to identify loci associated with the different traits. We identified 17 loci with GAPIT and 25 with QTCAT. Ten of these loci were associated with known genes that are routinely employed in marker assisted selection such as Ppd-D1 for maturity and Rht-D1 for plant height and seven of those were detected with both methods. We identified one locus for yield per se in 2014 on chromosome 6B with QTCAT and three in 2015, on chromosomes 4B and 5A with GAPIT and 6B with QTCAT. The 6B loci corresponded to the same region in both years. The favorable haplotypes for yield at the 5A and 6B loci are widespread in Australian accessions with 112 out of 153 carrying the favorable haplotype at the 5A locus and 136 out of 146 carrying the favorable haplotype at the 6A locus, while the favorable haplotype at 4B is only present in 65 out of 149 Australian accessions. The low number of yield QTL in our study corroborate with other GWAS for yield in wheat, where most of the identified loci have very small effects.

A locus on barley chromosome 5H affects adult plant resistance to powdery mildew.

Adult plant resistance against plant pathogens is of interest as a means to achieve durable resistance. Prior to this research, the barley lines CLE210 (from Uruguay) and Denar (from the Czech Republic) had been reported to exhibit adult-plant resistance against powdery mildew. Here, populations of doubled haploid lines from crosses of these lines with the susceptible cultivar Baudin were evaluated for powdery mildew resistance in field experiments. Using linkage maps constructed from genotyping-by-sequencing (GBS) data, it was determined that differences in resistance were largely attributable to a region on the long arm of chromosome 5H (5HL). Therefore, KASP™ assays were developed based on GBS tag sequences mapped on that chromosome, providing more reliable genetic maps. In each population, a large-effect QTL was mapped on 5HL. As no sequence variation was detected between CLE210 and Denar in this region of 5HL, the two sources of resistance may be identical by descent in the QTL region and carry the same resistance gene. Marker assays from the QTL region were evaluated on a panel of barley lines, providing information that breeders could use to select assays for use in marker-assisted selection.

Genetic Basis for Variation in Wheat Grain Yield in Response to Varying Nitrogen Application.

Nitrogen (N) is a major nutrient needed to attain optimal grain yield (GY) in all environments. Nitrogen fertilisers represent a significant production cost, in both monetary and environmental terms. Developing genotypes capable of taking up N early during development while limiting biomass production after establishment and showing high N-use efficiency (NUE) would be economically beneficial. Genetic variation in NUE has been shown previously. Here we describe the genetic characterisation of NUE and identify genetic loci underlying N response under different N fertiliser regimes in a bread wheat population of doubled-haploid lines derived from a cross between two Australian genotypes (RAC875 × Kukri) bred for a similar production environment. NUE field trials were carried out at four sites in South Australia and two in Western Australia across three seasons. There was genotype-by-environment-by-treatment interaction across the sites and also good transgressive segregation for yield under different N supply in the population. We detected some significant Quantitative Trait Loci (QTL) associated with NUE and N response at different rates of N application across the sites and years. It was also possible to identify lines showing positive N response based on the rankings of their Best Linear Unbiased Predictions (BLUPs) within a trial. Dissecting the complexity of the N effect on yield through QTL analysis is a key step towards elucidating the molecular and physiological basis of NUE in wheat.

Genetic association of stomatal traits and yield in wheat grown in low rainfall environments.

BACKGROUND: In wheat, grain filling is closely related to flag leaf characteristics and function. Stomata are specialized leaf epidermal cells which regulate photosynthetic CO2 uptake and water loss by transpiration. Understanding the mechanisms controlling stomatal size, and their opening under drought, is critical to reduce plant water loss and maintain a high photosynthetic rate which ultimately leads to elevated yield. We applied a leaf imprinting method for rapid and non-destructive phenotyping to explore genetic variation and identify quantitative traits loci (QTL) for stomatal traits in wheat grown under greenhouse and field conditions. RESULTS: The genetics of stomatal traits on the adaxial surface of the flag leaf was investigated using 146 double haploid lines derived from a cross between two Australian lines of Triticum aestivum, RAC875 and Kukri. The drought tolerant line RAC875 showed numerous small stomata in contrast to Kukri. Significant differences between the lines were observed for stomatal densitity and size related traits. A negative correlation was found between stomatal size and density, reflecting a compensatory relationship between these traits to maintain total pore area per unit leaf surface area. QTL were identified for stomatal traits on chromosomes 1A, 1B, 2B, and 7A under field and controlled conditions. Most importantly some of these loci overlap with QTL on chromosome 7A that control kernel number per spike, normalized difference vegetation index, harvest index and yield in the same population. CONCLUSIONS: In this first study to decifer genetic relationships between wheat stomatal traits and yield in response to water deficit, no significant correlations were observed among yield and stomatal traits under field conditions. However we found some overlaps between QTL for stomatal traits and yield across environments. This suggested that stomatal traits could be an underlying mechanism increasing yield at specific loci and used as a proxy to track a target QTL in recombinant lines. This finding is a step-forward in understanding the function of these loci and identifying candidate genes to accelerate positional cloning of yield QTL in wheat under drought.

A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family.

Cellulose is a fundamentally important component of cell walls of higher plants. It provides a scaffold that allows the development and growth of the plant to occur in an ordered fashion. Cellulose also provides mechanical strength, which is crucial for both normal development and to enable the plant to withstand both abiotic and biotic stresses. We quantified the cellulose concentration in the culm of 288 two--rowed and 288 six--rowed spring type barley accessions that were part of the USDA funded barley Coordinated Agricultural Project (CAP) program in the USA. When the population structure of these accessions was analysed we identified six distinct populations, four of which we considered to be comprised of a sufficient number of accessions to be suitable for genome-wide association studies (GWAS). These lines had been genotyped with 3072 SNPs so we combined the trait and genetic data to carry out GWAS. The analysis allowed us to identify regions of the genome containing significant associations between molecular markers and cellulose concentration data, including one region cross-validated in multiple populations. To identify candidate genes we assembled the gene content of these regions and used these to query a comprehensive RNA-seq based gene expression atlas. This provided us with gene annotations and associated expression data across multiple tissues, which allowed us to formulate a supported list of candidate genes that regulate cellulose biosynthesis. Several regions identified by our analysis contain genes that are co-expressed with cellulose synthase A (HvCesA) across a range of tissues and developmental stages. These genes are involved in both primary and secondary cell wall development. In addition, genes that have been previously linked with cellulose synthesis by biochemical methods, such as HvCOBRA, a gene of unknown function, were also associated with cellulose levels in the association panel. Our analyses provide new insights into the genes that contribute to cellulose content in cereal culms and to a greater understanding of the interactions between them.

Nephron sparing surgery (NSS) for unilateral wilms tumor (UWT): the SIOP 2001 experience.

BACKGROUND: Total nephrectomy (TN) remains the standard treatment of unilateral Wilms tumors (uWT). The SIOP WT-2001 protocol allowed Nephron Sparing Surgery (NSS) for polar or peripherally non-infiltrating tumors. AIM: Inventory of the current SIOP NSS-experience. PROCEDURES: 2,800 patients with a unilateral, localized or metastatic and an unequivocal surgical technique recorded were included. All had neo-adjuvant chemotherapy and delayed surgery. In 91 (3%) NSS was performed and in 2709 TN. Data was retrieved from the SIOP WT 2001 database. RESULTS: NSS group contained 65% stage I tumours and the TN group 48%. Tumor volume (at diagnosis and surgery) was significantly smaller in the NSS group. Within stage III, after NSS, 7/12 (58%) had positive margins (M +), 5 with tumor negative lymph nodes (LN-). After TN, 355/712 (55%) had M + , 182 were LN-. Treatment of M+ in the NSS group resulted in two conversions to TN (one combined with radiotherapy), three patients had radiotherapy only and in two patients local therapy, if given, was not recorded. After NSS, four recurrences occurred. For localized disease the 5-year overall (OS) and event free survival (EFS) in NSS group was 100 and 94.8 (95% CI:89.9-99.9), respectively, while OS and EFS in the TN group were 94.4 (95% CI: 93.2-95.5, log-rank test P = 0.06) and 86.5 (95% CI:85.0-88.1, log-rank test P = 0.06), respectively. CONCLUSIONS: NSS was only performed in 3% of patients with uWT. Despite excellent survival with few relapses, the gain of nephrons needs to be weighed against the risk to induce stage III with intensified therapy.

Response of predatory mites to a herbivore-induced plant volatile: genetic variation for context-dependent behaviour.

Plants infested with herbivores release specific volatile compounds that are known to recruit natural enemies. The response of natural enemies to these volatiles may be either learned or genetically determined. We asked whether there is genetic variation in the response of the predatory mite Phytoseiulus persimilis to methyl salicylate (MeSa). MeSa is a volatile compound consistently produced by plants being attacked by the two-spotted spider mite, the prey of P. persimilis. We predicted that predators express genetically determined responses during long-distance migration where previously learned associations may have less value. Additionally, we asked whether these responses depend on odors from uninfested plants as a background to MeSa. To infer a genetic basis, we analyzed the variation in response to MeSa among iso-female lines of P. persimilis by using choice-tests that involved either (1) MeSa presented as a single compound or (2) MeSa with background-odor from uninfested lima bean plants. These tests were conducted for starved and satiated predators, i.e., two physiological states, one that approximates migration and another that mimics local patch exploration. We found variation among iso-female lines in the responses to MeSa, thus showing genetic variation for this behavior. The variation was more pronounced in the starved predators, thus indicating that P. persimilis relies on innate preferences when migrating. Background volatiles of uninfested plants changed the predators' responses to MeSa in a manner that depended on physiological state and iso-female line. Thus, it is possible to select for context-dependent behavioral responses of natural enemies to plant volatiles.