Applied phenomics and genomics for improving barley yellow dwarf resistance in winter wheat

Barley yellow dwarf (BYD) is one of the major viral diseases of cereals. Phenotyping BYD in wheat is extremely challenging due to similarities to other biotic and abiotic stresses. Breeding for resistance is additionally challenging as the wheat primary germplasm pool lacks genetic resistance, with most of the few resistance genes named to date originating from a wild relative species. The objectives of this study were to, i) evaluate the use of high-throughput phenotyping (HTP) from unmanned aerial systems to improve BYD assessment and selection, ii) identify genomic regions associated with BYD resistance, and iii) evaluate genomic prediction models ability to predict BYD resistance. Up to 107 wheat lines were phenotyped during each of five field seasons under both insecticide treated and untreated plots. Across all seasons, BYD severity was lower with the insecticide treatment and plant height (PTHTM) and grain yield (GY) showed increased values relative to untreated entries. Only 9.2% of the lines were positive for the presence of the translocated segment carrying resistance gene Bdv2 on chromosome 7DL. Despite the low frequency, this region was identified through association mapping. Furthermore, we mapped a potentially novel genomic region for resistance on chromosome 5AS. Given the variable heritability of the trait (0.211 0.806), we obtained relatively good predictive ability for BYD severity ranging between 0.06 0.26. Including Bdv2 on the predictive model had a large effect for predicting BYD but almost no effect for PTHTM and GY. This study was the first attempt to characterize BYD using field-HTP and apply GS to predict the disease severity. These methods have the potential to improve BYD characterization and identifying new sources of resistance will be crucial for delivering BYD resistant germplasm.

Genome sequence of the English grain aphid, Sitobion avenae and its endosymbiont Buchnera aphidicola

The English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and one of the principal vectors of Barley Yellow Dwarf Virus (BYDV) leading to significant reductions in grain yield, annually. Emerging resistance to and increasing regulation of insecticides has resulted in limited options for their control. Using PacBio HiFi data, we have produced a high quality draft assembly of the S. avenae genome; generating a primary assembly with a total assembly size of 475.7 Mb, and an alternate assembly with a total assembly size of 430.8 Mb. Our primary assembly was highly contiguous with only 326 contigs and a contig N50 of 15.95 Mb. Assembly completeness was estimated at 97.7% using BUSCO analysis and 31,007 and 29,037 protein coding genes were predicted from the primary and alternate assemblies, respectively. This assembly, which is to our knowledge the first for an insecticide resistant clonal lineage of English grain aphid, will provide novel insight into the molecular and mechanistic determinants of resistance and will facilitate future research into mechanisms of viral transmission and aphid behavior.

Advances in understanding the biology and epidemiology of barley yellow dwarf virus (BYDV)

A tri-trophic network of domesticated grasses (host), various aphids (vector) and barley yellow dwarf virus (pathogen) species has been spread by humans from Eurasia to the rest of the world. Understanding how climate, natural and agricultural landscapes challenge pathogens, vectors, and their natural enemies and shape their dynamics is the key to managing this pathosystem. This chapter provides an overview of this complex system and its evolution. The chapter includes a case study of biological control of aphids causing wheat BYDV in Brazil. The current challenge is to create tools that integrate knowledge of this complex pathosystem and facilitate monitoring and decision making for rational management to reduce the burden of disease.

Resistance breeding in barley against Barley yellow dwarf virus (BYDV): avoiding negative impacts on anatomy and physiology

Barley yellow dwarf (BYD) is one of the most widespread and damaging viral diseases of grasses and cereal crops worldwide. Due to an increasing risk of food losses e.g. in barley by Barley yellow dwarf virus (BYDV) as a consequence of climate change, associated by a strong demand to decrease the use of chemical insecticides, breeding for BYDV resistance is of prime importance today. This chapter describes the negative impact of BYDV on barley on multiple levels (anatomy, physiology and agronomic traits). It also demonstrates the benefits of BYDV resistance regarding a reduction in yield losses but also a decreased spread of BYDV in the field due to effects on the tritrophic interaction of virus, vector and plant. Until now, several genes and QTL are known that mediate tolerance or resistance against BYDV, respectively. The combination of genomic tools and phenotyping is the basis for the identification of these genes and recent developments facilitate to enhance this process.

Nucleus

In our application of AuNPs on the leaf surface, we were pushing the Barley Yellow Dwarf Virus (BYDV-PAV) source and Gold nanoparticles (AuNPs) into the plant cell system up on the events of systemic plant defense response. In the infected host cell, the viral coat protein is the first obvious in the cytoplasm. When nanoparticles are applied on leaf surfaces, a large surface area relative to their volume happens. AuNPs solutions are more active and dispersed ooplasm. The correlation between Zeta potential value and Zeta sizer is inverse proportion. Filaments are visible in the nucleopores, the nuclear outline is distorted, and massive clumping of heterochromatin begins as declared. It was mostly found in or around regions of ribosome-associated filaments. Our present study combines TEM and nucleus content in the presence of AuNPS to explore the level of repair mechanism illustrating in TEM micrographs, showing Polyploidy nucleus and segregated chromatin. Multi membranous structure, imaging the AuNPs inside and around the nucleus and Pseudo crystal array is enveloped in an endoplasmic reticulum cisterna (ER).

Cell Wall

The application of AuNPs on the infected barley cultivar had great damage results on Barley Yellow Dwarf Virus (BYDV-PAV) particles in TEM. Observation of TEM images provided an insight into the transport of AuNPs through the plasmodesmata endoplasmic reticulum route, where they likely accumulated as the channels narrowed. The cytoplasmic parenchyma cell components do not have an intact peripheral location, but taking irregular shapes, internal movement between adjacent two cells seems to be the VLPs moved toward via plasmodesmata. TEM micrographs; showing different abnormalities in the cell wall due to viral infection. Application of AuNPs revealed sticky Integrated AuNPs inside the cell wall with low and high density. The mechanical transportation of the virus through the sieve elements with endosomes was observed. The mechanical transportation of virus particles through the cell wall with some vesicles, amorphous inclusions, and filamentous particles was proved through the sieve elements with filamentous strands.

Chloroplast and Mitochondria

Photosynthesis is a crucial process for plants on earth that changes light energy to chemical energy. Virus infection can cause dramatic photosynthesis changes: respiration and the translocation of carbohydrates and other substances around the host plant. Chlorosis in virus-infected leaves like Barley Yellow Dwarf Virus (BYDV- PAV).infection can result from damage to chloroplasts resulting from inhibition of photosynthetic activity. Our present study combines TEM and chlorophyll-level content in the presence of Gold nanoparticles (AuNPS) to explore the repair mechanism for the yellowing leaf symptom development caused by infection with BYDV- PAV by illustrating TEM micrographs; showing fragmentized grana, deformation of the myelin like bodies (MLB), many vesicles; osmiophilic lipid granules/plastoglobulus, starch body, and plasmolysis in the chloroplast, distribution of AuNPs & VLPs near and inside the chloroplast. Mitochondria, Double-membrane-bound organelle, Distorted mitochondrion, Amorphous inclusion bodies.

Cytoplasmic Matrix and Viroplasms Inclusions in the Presence of Gold Nanoparticles (AuNPs)

Cellular ultrastructure micrographs revealed striking changes resulting from the Barley Yellow Dwarf Virus (BYDV-PAV) infection in Electron microscopy. In the cytoplasm, the Gold nanoparticles (AuNPs) may bind with different cytoplasmic organelles and interfere with the treated site’s metabolic processes. The micrographs of the treated plant leave with AuNPs showing; Endosomes, amorphous bodies, slender filaments fibers, myelin bodies with a high concentration of virus particles, and Gold Nanoparticles distributed in a circulated shape in the cytoplasm with virus particles.