A major root architecture QTL responding to water limitation in durum wheat

The optimal root system architecture (RSA) of a crop is context dependent and critical for efficient resource capture in the soil. Narrow root growth angle promoting deeper root growth is often associated with improved access to water and nutrients in deep soils during terminal drought. RSA, therefore is a drought-adaptive trait that could minimize yield losses in regions with limited rainfall. Here, GWAS for seminal root angle (SRA) identified seven marker-trait associations clustered on chromosome 6A, representing a major quantitative trait locus (qSRA-6A) which also displayed high levels of pairwise LD (r2 = 0.67). Subsequent haplotype analysis revealed significant differences between major groups. Candidate gene analysis revealed loci related to gravitropism, polar growth and hormonal signaling. No differences were observed for root biomass between lines carrying hap1 and hap2 for qSRA-6A, highlighting the opportunity to perform marker-assisted selection for the qSRA-6A locus and directly select for wide or narrow RSA, without influencing root biomass. Our study revealed that the genetic predisposition for deep rooting was best expressed under water-limitation, yet the root system displayed plasticity producing root growth in response to water availability in upper soil layers. We discuss the potential to deploy root architectural traits in cultivars to enhance yield stability in environments that experience limited rainfall

Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust

Multi-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci

Impact of malaria diagnostic choice on monitoring of Plasmodium falciparum prevalence estimates in the Democratic Republic of the Congo and relevance to control programs in high-burden countries

Malaria programs rely upon a variety of diagnostic assays, including rapid diagnostic tests (RDTs), microscopy, polymerase chain reaction (PCR), and bead-based immunoassays (BBA), to monitor malaria prevalence and support control and elimination efforts. Data comparing these assays are limited, especially from high-burden countries like the Democratic Republic of the Congo (DRC). Using cross-sectional and routine data, we compared diagnostic performance and Plasmodium falciparum prevalence estimates across health areas of varying transmission intensity to illustrate the relevance of assay performance to malaria control programs. Data and samples were collected between March–June 2018 during a cross-sectional household survey across three health areas with low, moderate, and high transmission intensities within Kinshasa Province, DRC. Samples from 1,431 participants were evaluated using RDT, microscopy, PCR, and BBA. P. falciparum parasite prevalence varied between diagnostic methods across all health areas, with the highest prevalence estimates observed in Bu (57.4–72.4% across assays), followed by Kimpoko (32.6–53.2%), and Voix du Peuple (3.1–8.4%). Using latent class analysis to compare these diagnostic methods against an “alloyed gold standard,” the most sensitive diagnostic method was BBA in Bu (high prevalence) and Voix du Peuple (low prevalence), while PCR diagnosis was most sensitive in Kimpoko (moderate prevalence). RDTs were consistently the most specific diagnostic method in all health areas. Among 9.0 million people residing in Kinshasa Province in 2018, the estimated P. falciparum prevalence by microscopy, PCR, and BBA were nearly double that of RDT. Comparison of malaria RDT, microscopy, PCR, and BBA results confirmed differences in sensitivity and specificity that varied by endemicity, with PCR and BBA performing best for detecting any P. falciparum infection. Prevalence estimates varied widely depending on assay type for parasite detection. Inherent differences in assay performance should be carefully considered when using community survey and surveillance data to guide policy decisions

Resistance to yellow spot in wheat grown under accelerated growth conditions

Yellow spot, also known as tan spot (YS), is a serious fungal foliar disease of wheat worldwide. The introduction of resistance to YS in wheat cultivars offers the most durable, economic, and environmentally safe management strategy. Adult plant resistance (APR) is preferred over seedling resistance to control other diseases in wheat and has the potential to offer non-race specific resistance to YS. The search for APR currently relies on screening vast numbers of wheat genotypes in the field, where expression is affected by environmental factors. We report a rapid phenotyping method for APR to YS that combines use of constant light and controlled temperatures to achieve accelerated growth conditions (AGC). A panel comprising 20 spring wheat genotypes was evaluated in four separate experiments: (1) seedling stage under regular greenhouse conditions; (2) adult-plant (AP) stage under AGC; (3) integrated seedling and AP disease assessment; and (4) AP stage in the field. Phenotypes from all AP experiments conducted under controlled and field conditions correlated well (r\ua0=\ua00.71–0.84), but correlations between AP and seedling phenotypes were weaker (r\ua0=\ua00.30–0.62). Moderate to high levels of APR were displayed by some genotypes (e.g. CIMMYT line ‘ZWW10-50’) that were equivalent to levels attained by seedling resistant cultivar ‘Leichhardt’. An integrated cycle requires only seven weeks to complete, and provides a useful tool for breeders and pathologists to efficiently phenotype APR to YS under controlled conditions

Imported Dengue Case Numbers and Local Climatic Patterns Are Associated with Dengue Virus Transmission in Florida, USA

Aedes aegypti mosquitoes are the main vector of dengue viruses globally and are present throughout much of the state of Florida (FL) in the United States of America. However, local transmission of dengue viruses in FL has mainly occurred in the southernmost counties; specifically Monroe and Miami-Dade counties. To get a better understanding of the ecologic risk factors for dengue fever incidence throughout FL, we collected and analyzed numerous environmental factors that have previously been connected to local dengue cases in disease-endemic regions. We analyzed these factors for each county-year in FL, between 2009–2019, using negative binomial regression. Monthly minimum temperature of 17.5–20.8 °C, an average temperature of 26.1–26.7 °C, a maximum temperature of 33.6–34.7 °C, rainfall between 11.4–12.7 cm, and increasing numbers of imported dengue cases were associated with the highest risk of dengue incidence per county-year. To our knowledge, we have developed the first predictive model for dengue fever incidence in FL counties and our findings provide critical information about weather conditions that could increase the risk for dengue outbreaks as well as the important contribution of imported dengue cases to local establishment of the virus in Ae. aegypti populations

Physiological Changes in Barley mlo-11 Powdery Mildew Resistance Conditioned by Tandem Repeat Copy Number

Wild barley accessions have evolved broad-spectrum defence against barley powdery mildew through recessive mlo mutations. However, the mlo defence response is associated with deleterious phenotypes with a cost to yield and fertility, with implications for natural fitness and agricultural productivity. This research elucidates the mechanism behind a novel mlo allele, designated mlo-11(cnv2), which has a milder phenotype compared to standard mlo-11. Bisulphite sequencing and histone ChIP-seq analyses using near-isogenic lines showed pronounced repression of the Mlo promoter in standard mlo-11 compared to mlo-11(cnv2), with repression governed by 24 nt heterochromatic small interfering RNAs. The mlo-11(cnv2) allele appears to largely reduce the physiological effects of mlo while still endorsing a high level of powdery mildew resistance. RNA sequencing showed that this is achieved through only partly restricted expression of Mlo, allowing adequate temporal induction of defence genes during infection and expression close to wild-type Mlo levels in the absence of infection. The two mlo-11 alleles showed copy number proportionate oxidase and peroxidase expression levels during infection, but lower amino acid and aromatic compound biosynthesis compared to the null allele mlo-5. Examination of highly expressed genes revealed a common WRKY W-box binding motif (consensus ACCCGGGACTAAAGG) and a transcription factor more highly expressed in mlo-11 resistance. In conclusion, mlo-11(cnv2) appears to significantly mitigate the trade-off between mlo defence and normal gene expression

Genetic characterization of resistance to Pyrenophora teres f. teres in the international barley differential Canadian Lake Shore

Genetic resistance to net form of net blotch in the international barley differential Canadian Lake Shore (CLS) was characterized and mapped. A doubled haploid (DH) population generated from a cross between CLS and susceptible cultivar Harrington was evaluated at the seedling stage using eight diverse Pyrenophora teres f. teres (Ptt) isolates and at the adult stage in the field using natural inoculum. To effectively map the CLS resistance, comparative marker frequency analysis (MFA) was performed using 8,762 polymorphic DArT-seq markers, where 'resistant' and 'susceptible' groups each comprised 40 DH lines displaying the most extreme phenotypes. Five DArTseq markers were consistently detected in eight disease assays, which was designated qPttCLS and deemed to harbor the locus underpinning CLS resistance. Four of these markers were present onto the barley DArTseq physical map and spans a region between 398203862 and 435526243 bp which were found to consist several genes involved in important plant functions such as disease response and signaling pathways. While MFA only detected the 3H region, genetic analyses based on segregation patterns were inconsistent, suggesting complex inheritance or variation in phenotypic expression of qPttCLS, particularly in the field. This study represents progress toward connecting Ptt pathotype surveys with the corresponding resistance genes in barley differentials. The markers associated with qPttCLS are useful for marker-assisted selection in breeding programs

Into the vault of the Vavilov wheats: old diversity for new alleles

Intensive selection in wheat (Triticum aestivum L.) breeding programs over the past 100 years has led to a genetic bottleneck in modern bread wheat. Novel allelic variation is needed to break the yield plateau, particularly in the face of climate change and rapidly evolving pests and pathogens. Landraces preserved in seed banks likely harbour valuable sources of untapped genetic diversity because they were cultivated for thousands of years under diverse eco-geographical conditions prior to modern breeding. We performed the first genetic characterisation of bread wheat accessions sourced from the N. I. Vavilov Institute of Plant Genetic Resources (VIR) in St Petersburg, Russia. A panel comprising 295 accessions, including landraces, breeding lines and cultivars was subject to single seed descent (SSD) and genotyped using the genotyping-by-sequencing Diversity Arrays Technology platform (DArT-seq); returning a total of 34,311 polymorphic markers (14,228 mapped and 20,083 unmapped). Cluster analysis identified two distinct groups; one comprising mostly breeding lines and cultivars, and the other comprising landraces. Diversity was benchmarked in comparison to a set of standards, which revealed a high degree of genetic similarity among breeding material from Australia and the International Maize and Wheat Improvement Center (CIMMYT). Further, 11,025 markers (1888 mapped and 9137 unmapped) were polymorphic in the diversity panel only, thus representing allelic diversity potentially not present in Australian or CIMMYT germplasm. Open-access to DArT-seq markers and seed for SSD lines will empower researchers, pre-breeders and breeders to rediscover genetic diversity in the VIR collection and accelerate utilisation of novel alleles to improve wheat

Standing on the shoulders of giants: Vavilov's wheat collection and sources of resistance

Nikolai Ivanovich Vavilov was a renowned Russian botanist and geneticist, best known for his theory relating to “the centres of origin of cultivated plants”. Inspired by his idol, Charles Darwin, he travelled the world in the early 1900s collecting more seeds, tubers and fruits than any person in history. The collections, including many wheat landraces, were stored in a seed bank in Leningrad, now known as the N. I. Vavilov Institute of Plant Genetic Resources in St Petersburg, Russia. Remarkably, the unique seed collection survived the “Siege of Leningrad” during World War II. However, Vavilov himself faced an ironic fate – he was arrested for criticising the non-Mendelian concepts of a Soviet biologist, Trofim Lysenko, who had the support of Joseph Stalin. Vavilov was sentenced to death in July 1941, but in 1942 his sentence was reduced to 20 years imprisonment. Despite this, he died of starvation in prison in 1943. Following in the footsteps of the Great Russian scientist and his colleagues, we performed the world’s first genetic analysis of Vavilov’s wheat seeds. A total of 295 diverse wheats collected from around the world were examined using 34,000 DNA markers. The genomic analysis revealed a massive array of allelic diversity that is absent in modern germplasm. We provide a summary of our ongoing efforts to discover new genes for disease resistance hidden in the Vavilov treasures. By combining several breeding technologies, we are rapidly mining new sources of resistance to major foliar diseases of wheat, including the rapidly evolving rust diseases (stripe, leaf and stem rust) and yellow spot disease