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Genetic and physiological mechanisms of barley yellow dwarf virus resistance in barley

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Hu, H ORCID: 0000-0003-4023-9537 2020 , 'Genetic and physiological mechanisms of barley yellow dwarf virus resistance in barley', PhD thesis, University of Tasmania.

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Abstract

Barley yellow dwarf virus (BYDV) infection often results in substantial yield losses in susceptible cereal crops. Major symptoms of BYDV infection in cereals include plant dwarfing and colour changes of leaf blades along the vascular bundles, especially of leaf tips. A full understanding of physiological and molecular mechanisms contributing to resistance provides salient information for breeding BYD resistant varieties and developing strategies to address the problem. A review was conducted (Chapter 2) for BYDV infection mechanisms and summarised current information on known resistance genes, molecular markers and the use of transgenic techniques in breeding of BYD resistant varieties. Cereal yellow dwarf viruses (CYDVs) are also discussed as both BYDV and CYDV belong to the family Luteoviridae.
For effective control of Barley yellow dwarf virus through breeding, the identification of genetic sources of resistance is the key to success. For this purpose, a genome-wide association study using 187 barley accessions was conducted in 2015 and 2017 (Chapter 3). The genotypes were inoculated with BYDV-PAV, one of the most widespread strains, and their reaction was scored based on leaf discoloration. Accession reaction ranged from highly resistant to highly susceptible and a significant correlation was found between the two years. There were 10 and 13 significant marker-trait associations representing 6 and 5 QTL in 2015 and 2017, respectively. These markers were located on chromosome 2H, 3H, 5H and 6H. Among them, five markers were commonly detected in both trials. Our study provides potential novel genes for future breeding for BYD resistance. Several barley genotypes showed consistently higher resistance in the two trials. These genotypes will be used in further research to confirm and characterise the QTL identified for BYD resistance.
A preliminary observation of a DH population originated from a cultivated barley (cv. Franklin) with a known resistance gene and a wild barley (cv. TAM407227) showed segregation in BDY resistance with some lines showing better resistance than Franklin. Further phenotyping of BYD resistance was conducted in three trials with two in Tasmania (TAS) and one in Western Australia (WA) (Chapter 4). Two Quantitative trait loci (QTL) were identified both trials, one on chromosome 3H and the other on chromosome 5H. The QTL on chromosome 3H corresponds to the known major resistance gene Ryd2. The other QTL, Qbyd-5H, represents a potential new resistance locus and contributed for 7% ~10.4% of the phenotypic variation. It was mapped within the interval of 125.76~139.24 cM of chromosome 5H. Two additional minor effect QTL were identified on chromosome 7H from the WA trial, contributing slightly less effects on BYD tolerance. The consistently detected new gene on chromosome 5H will potentially serve as a novel source of tolerance to achieve more sustainable resistance to BYDV in barley.
A different DH population derived from a cross between the resistant genotype Gairdner and a Chinese genotype YSM1 was also used to identify QTL for BYD resistance. The population was artificially inoculated with BYDV-PAV, one of the most prevalent and damaging species. Both parents showed medium resistance to BYDV while the DH lines showed a wide segregation, indicating that different resistance genes existed in the two parent genotypes. Based on visual symptom scores, two QTL were identified for BYD resistance. They were located on chromosomes 3H and 2H and determined nearly 20% of the phenotypic variation. A QTL for plant height was close to the known 3H QTL for BYD resistance but this QTL was more likely the denso gene. A QTL for leaf chlorophyll content was located on 2H at a similar position to the new one for BYD resistance identified in this study. However, as the disease evaluation was only done in one single trial, more phenotyping will be conducted in follow-on studies for confirm the new QTL.
Plant response to BYDV is controlled by multiple environment and intrinsic factors. Among them, heading date (HD), an important agronomic trait that influences plant adaptability to varying environment and grain yield, constitutes an important factor determining the fate of plant upon disease attack. Studies demonstrated that younger plants are more prone to contracting BYD and manifesting severer symptom than old plants. Thus, escaping BYD epidemic season through early heading will equip plants with field resistance. Days to heading had a significant and negative correlation with BYD resistance, thus QTL for heading date were also investigated for the above population which were used for the identification of QTL for BYD resistance (Chapter 5). Another DH population originated from a different cultivated barley and wild barley was also added to the study. The two DH populations were sown in three seasons. Using three times of sowing (TOSs) differing in daylength and temperature, I investigated quantitative trait loci (QTL) controlling HD from both different populations and growing seasons. Fourteen QTL were identified for HD from different populations and sowing dates. The expression of HD related genes varied with the TOS, suggesting a significant QTL × environment interaction. By comparing the positions of previously mapped HD genes and those of QTL detected in this population, eleven of the fourteen QTL identified in this study were found to be located at similar positions to those reported genes for HD. Among the three new potential QTL, one was located at 73.5 cM on chromosome 2H, explaining 19.2% and 4.6% HD of DH lines in spring and summer growing, respectively. The wild barley parent TAM407227 contributed the early maturity allele. HORVU2Hr1G088460 within the interval of QTL could be the candidate gene. The second new QTL was identified on chromosome 3H from a summer sowing trial and the third one on chromosome 4H affected HD of DH lines only under spring sowing condition. These new QTL identified will provide alternative genetic resources for plant breeders developing barley varieties with improved HD adaptability to varying environments. None of the QTL for HD were located at similar positions to these for BYD resistance identified in this study.
In conclusion, several QTL were identified for BYD resistance based on visual symptom score, ELISA test and growth parameters including plant height and leaf chlorophyll index. The QTL identified were located at various positions of barley genome, including the one on chromosome 3H which is the Ryd2 gene. Identification of these potential genes not only warrants further fine mapping of resistance QTL but suggests future possibility of enhancing BYD resistance by genetic improvement.

Item Type: Thesis - PhD
Authors/Creators:Hu, H
Keywords: barley, molecular mapping, resistance, BYD, virus
Copyright Information:

Copyright 2019 the author

Additional Information:

Chapter 2 appears to be the equivalent of a post-print version of an article published as: Choudhury, S., Hu, H., Meinke, H., Shabala, S., Westmore, G., Larkin, P., Zhou, M., 2017. Barley yellow dwarf viruses: infection mechanisms and breeding strategies, Euphytica, 213(8), 168. Post-prints are subject to Springer Nature re-use terms

Chapter 4 appears to be the equivalent of a post-print version of an article published as: Hu, H., Choudhury, S., Shabala, S., Gupta, S., Zhou, M., 2019. Genomic regions on chromosome 5H containing a novel QTL conferring barley yellow dwarf virus-PAV (BYDV-PAV) tolerance in barley, Scientific reports, 9, 11298. © The Author(s) 2019. This article is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0), (https://creativecommons.org/licenses/by/4.0/) which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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

Chapter 6 appears to be the equivalent of a post-print version of an article published as: Hu, H., Ahmed, I., Choudhury, S., Fan, Y., Shabala, S., Zhang, G., Harrison, M., Meinke, H. Zhou, M., 2019. Wild barley shows a wider diversity in genes regulating heading date compared with cultivated barley, Euphytica, 215(4), 75. Post-prints are subject to Springer Nature re-use terms

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