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Barley yellow dwarf resistance in cereal crops : genetics and resistance mechanisms


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Choudhury, S 2019 , 'Barley yellow dwarf resistance in cereal crops : genetics and resistance mechanisms', PhD thesis, University of Tasmania.

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Barley yellow dwarf (BYD) is one of the most widespread and serious viral diseases in the world. The causal agent, Barley yellow dwarf virus (BYDV) can infect cereal crops including wheat, barley and oats, leading to significant yield losses. There are several strains of BYDV, among the BYDV strains (PAV, MAV, SGV, RPV and RMV), BYDV-PAV is the most common and prevailing strain in Australia. Breeding BYD resistant/tolerant crops has become one of the top priorities for controlling BYDV. A proper resistance screening method is crucial for selecting resistant genotypes in a breeding program. In this study, we developed a reliable screening method for BYDV-PAV resistance of cereal crops under glasshouse conditions. At two-leaf stage, inoculation of 5-10 viruliferous aphids per plant for four days was shown to be a quick and effective screening technique for selecting BYD resistance in wheat, barley and oats. Visual evaluation of symptoms on barley and oats is considered adequate for evaluating BYD resistance. For wheat, it is necessary to assess BYD resistance by enzyme-linked immunosorbent assay (ELISA) or tissue blot immunoassay (TBIA) and measuring plant biomass (at early stage) and grain number and yield (at late stage).
To gain a better understanding of plant defence mechanisms of BYD resistance genes (Bdv2 and Ryd2) against BYDV-PAV infection, we investigated the differences in agronomical, biochemical and histological changes between susceptible and resistant wheat and barley cultivars. Following BYDV infection, root growth and total dry matter of susceptible genotypes showed greater reduction than those of resistant genotypes. Virus multiplication in the phloem resulted in altered allocation of sugar, i.e. reduced sugar transport and accumulation of sugars, and altered leaf ultrastructure, coupled with necrosis in vascular bundles. Increased production of phenolic compounds may play a role in the resistance and defensive mechanisms of both Bdv2 and Ryd2 against virus infection.
We compared different physiological measures such as gas exchange parameters, quantum yield of PSII (chlorophyll fluorescence Fv/Fm ratio), chlorophyll content, dry biomass, leaf area and relative water, and yield attributes and pasting properties under BYDV stress. We used four wheat genotypes subjected to different BYDV treatments under field conditions to determine any differences for these traits between susceptible and resistant genotypes under BYDV infection. We also confirmed BYDV infection using TBIA. Pasting properties were hardly affected by BYDV infection, with genotype having a larger effect than infection. Grain yield showed positive correlations with all gas exchange parameters, chlorophyll fluorescence, chlorophyll content, leaf area, relative water content and biomass weight; grain yield negatively correlated with TBIA and visual symptom scores. The results suggest that stomatal conductance, transpiration rate and chlorophyll fluorescence measurements are suitable for assessment of BYDV infection and screening BYD susceptible and resistant wheat genotypes.
Identifying new resistance genes/quantitative trait locus (QTL) is an essential, first step in the development of breeding-based control mechanisms of barely yellow dwarf virus. A genome-wide association study (GWAS) was performed on 335 wheat accessions using a recently developed, high-density wheat single nucleotide polymorphism (SNP) array. All accessions were assessed for BYD resistance under different environments. Marker-trait associations were performed using a general linear model (GLM) and a mixed linear model (MLM). A total of 36 significant marker-trait associations were identified, four of which arose consistently across three models. Five novel QTL on chromosomes 2A, 2B, 6A 7A and 7B, with the nearest markers of IWA3520, IWB24938, WB69770, IWB57703 and IWB65432, respectively were consistently detected in two models. This was the first GWAS study on BYD resistance in wheat accessions. Several wheat genotypes showed consistent resistance in different field trials. None of these genotypes contained Bdv2, Bdv3 or Bdv4 gene. These genotypes will be used in our further research to confirm the QTL identified in this research or map new QTL for BYD resistance.
A double haploid (DH) population from the cross between XuBYDV (introduced from China and showed very good resistance to BYD) and H-120 (also introduced from China but BYD sensitive) was used to identify new QTL for BYD resistance. This population was genotyped using a high-density wheat SNP array containing iSelect 90K SNPs. Each plant of the DH lines was inoculated with 5-10 viruliferous aphids for four days. Disease resistance of BYDV inoculated DH lines was assessed at heading stage and BYDV infection was tested by Tissue blot immunoassay (TBIA). Three new significant QTL were identified on chromosomes 5A, 6A and 7A for both symptom score and TBIA score, all three resistance alleles being from XuBYDV. Some lines with resistance alleles from these three QTL showed high level resistance to BYD. These new QTL will be useful in breeding programs for pyramiding BYD resistance genes.
In conclusion, several QTL were identified for BYD resistance based on visual symptom score and TBIA score. The QTL identified for TBIA score and symptom score were located at different positions to those for BYD resistance. A total of five significant QTL were identified through genome wide association studies. Some of the genotypes in the study showed similar or even better resistance to BYD than those genotypes with known resistance gene (Bdv2). These genotypes and the five identified QTL will be useful for breeders to generate combinations with and without Bdv2 to achieve higher levels more stable BYD resistance.

Item Type: Thesis - PhD
Authors/Creators:Choudhury, S
Keywords: Virus infection, defence mechanisms, resistance genes, quantitative trait loci, Genome-wide association study
DOI / ID Number: 10.25959/100.00031438
Copyright Information:

Copyright 2018 the author

Additional Information:

Chapter 2 appears to be the equivalent of a post-peer-review, pre-copyedit version of an article published in Euphytica. The final authenticated version is available online at:

Chapter 3 appears to be the equivalent of the peer reviewed version of the following article: Choudhury, S., Al-Shammari, D., Hu, H., Meinke, H., Westmore, G., Birchall, C., Larkin, P., Zhou, M., 2018. A screening method to detect BYDV‐PAV resistance in cereals under glasshouse conditions, Plant pathology, 67(9), 1987-1996, which has been published in final form at This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions

Chapter 4 appears to be the equivalent of a post-print version of an article published as: Choudhury, S., Hu, H., Larkin, P., Meinke, H., Shabala, S., Ahmed, I. Zhou, M., 2018. Agronomical, biochemical and histological response of resistant and susceptible wheat and barley under BYDV stress, PeerJ 6, e4833. 2018. Copyright Choudhury et al. Distributed under Creative Commons Attribution 4.0 International (CC BY 4.0) license (

Chapter 5 appears to be the equivalent of a pre-print version of an article published as: Choudhury, S., Larkin, P., Meinke, H., Hasanuzzaman, M., Johnson, P., Zhou, M. 2019. Barley yellow dwarf virus infection affects physiology, morphology, grain yield and flour pasting properties of wheat, Crop & Pasture Science, 70(1), 16-25

Chapter 6 appears to be the equivalent of a pre-print version of an article published as: Choudhury, S., Larkin, P., Xu, R., Hayden, M., Forrest, K., Meinke, H., Hu, H., Zhou, M., Fan, Y., 2019. Genome wide association study reveals novel QTL genes for barley yellow dwarf virus resistance in wheat, BMC genomics, 20, 891. The Author(s). 2019 Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

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