Genome-wide association study of myrtle rust (Austropuccinia psidii) resistance in Eucalyptus obliqua (subgenus Eucalyptus)

Yong, Wilson Thau Lym; Ades, Peter K.; Runa, Fatima Akter; Bossinger, Gerd; Sandhu, K. S.; Potts, Brad M.; Tibbits, Josquin

doi:10.1007/s11295-021-01511-0

Cited by 13 publications

(10 citation statements)

References 77 publications

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“…Assessing phenotypic diversity, first the outliers should be removed from the raw data and then traits with high heritability estimates should be selected. At this stage, methods such as best linear unbiased estimator (BLUE) and best linear unbiased prediction (BLUP) are used to adjust the phenotypic scores based on the interactions of the genotype with the environment so that the power of GWAS is not negatively affected by this effect [ 55 , 58 ]. The number of individuals selected should also ensure sufficient genetic and phenotypic diversity in the study population.…”

Section: Experimental Approaches To Characterizing Disease Resistance...mentioning

confidence: 99%

“…Usually, these analyses are performed in replicated provenance or progeny trials using a randomized design (for example, randomized complete block design) to minimize environmental effects on the phenotype. In this case, based on the observed disease symptoms, a diverse range of disease responses from asymptomatic to the presence of obvious symptoms in different tissues are usually scored and raw data are obtained, the outliers removed and the adjusted phenotype values calculated using BLUP or BLUE [ 58 , 62 ]. The broad-sense heritability is also usually calculated for raw data to determine the genetic portion in controlling traits.…”

Section: Experimental Approaches To Characterizing Disease Resistance...mentioning

confidence: 99%

“…Five of these markers were located on each of chromosomes 3 and 4, and the rest were on the other chromosomes. Several genes (i.e., 67) identified around these markers (±5 kb of each SNP) indicate that resistance to the disease includes a wide range of responses, including PTI and basal resistance (asymptotic responses) to ETI (e.g., cell death and HR) [ 58 ]. The results of this study and other studies have shown that resistance to this disease in eucalyptus and other related trees is controlled by diverse loci with different effects, indicating the complexity of this trait [ 42 , 87 , 88 ].…”

Section: Experimental Approaches To Characterizing Disease Resistance...mentioning

confidence: 99%

“…Previous studies in Eucalyptus identified not only NBR-LRR genes, but also some other groups of R genes including kinases, hydrolases, and nucleotide-binding proteins and transcription factors (e.g., WRKY and bHLH) to be involved in resistance against myrtle rust. The presence of different R gene families in plants and trees allows effective identification of pathogenic effectors that change over time [ 42 , 58 , 89 ]. In previous studies, many SNPs of resistance to this disease and other fungal diseases were mainly located on chromosome 3 [ 43 , 52 , 89 , 90 ].…”

Section: Experimental Approaches To Characterizing Disease Resistance...mentioning

confidence: 99%

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Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection

Younessi-Hamzekhanlu

Gailing²

2022

IJMS

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The ecological and economic importance of forest trees is evident and their survival is necessary to provide the raw materials needed for wood and paper industries, to preserve the diversity of associated animal and plant species, to protect water and soil, and to regulate climate. Forest trees are threatened by anthropogenic factors and biotic and abiotic stresses. Various diseases, including those caused by fungal pathogens, are one of the main threats to forest trees that lead to their dieback. Genomics and transcriptomics studies using next-generation sequencing (NGS) methods can help reveal the architecture of resistance to various diseases and exploit natural genetic diversity to select elite genotypes with high resistance to diseases. In the last two decades, QTL mapping studies led to the identification of QTLs related to disease resistance traits and gene families and transcription factors involved in them, including NB-LRR, WRKY, bZIP and MYB. On the other hand, due to the limitation of recombination events in traditional QTL mapping in families derived from bi-parental crosses, genome-wide association studies (GWAS) that are based on linkage disequilibrium (LD) in unstructured populations overcame these limitations and were able to narrow down QTLs to single genes through genotyping of many individuals using high-throughput markers. Association and QTL mapping studies, by identifying markers closely linked to the target trait, are the prerequisite for marker-assisted selection (MAS) and reduce the breeding period in perennial forest trees. The genomic selection (GS) method uses the information on all markers across the whole genome, regardless of their significance for development of a predictive model for the performance of individuals in relation to a specific trait. GS studies also increase gain per unit of time and dramatically increase the speed of breeding programs. This review article is focused on the progress achieved in the field of dissecting forest tree disease resistance architecture through GWAS and QTL mapping studies. Finally, the merit of methods such as GS in accelerating forest tree breeding programs is also discussed.

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Section: Experimental Approaches To Characterizing Disease Resistance...mentioning

confidence: 99%

Section: Experimental Approaches To Characterizing Disease Resistance...mentioning

confidence: 99%

Section: Experimental Approaches To Characterizing Disease Resistance...mentioning

confidence: 99%

Section: Experimental Approaches To Characterizing Disease Resistance...mentioning

confidence: 99%

See 2 more Smart Citations

Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection

Younessi-Hamzekhanlu

Gailing²

2022

IJMS

View full text Add to dashboard Cite

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“…Hypersensitive individuals display localised necrotic regions on young leaves indicating a rapid resistance response. Genomic approaches have been utilised to better understand pathways and genetic architecture associated with host resistance to A. psidii [19][20][21][22][23][24]. Gene expression analysis has indicated that early recognition of the pathogen within 24 h post-infection and activation of defence responses discriminate resistant individuals of Eucalyptus grandis and Syzygium luehmannii from susceptible individuals [21,23].…”

Section: Introductionmentioning

confidence: 99%

Both Constitutive and Infection-Responsive Secondary Metabolites Linked to Resistance against Austropuccinia psidii (Myrtle Rust) in Melaleuca quinquenervia

et al. 2022

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Austropuccinia psidii is a fungal plant pathogen that infects species within the Myrtaceae, causing the disease myrtle rust. Myrtle rust is causing declines in populations within natural and managed ecosystems and is expected to result in species extinctions. Despite this, variation in response to A. psidii exist within some species, from complete susceptibility to resistance that prevents or limits infection by the pathogen. Untargeted metabolomics using Ultra Performance Liquid Chromatography with Ion Mobility followed by analysis using MetaboAnalyst 3.0, was used to explore the chemical defence profiles of resistant, hypersensitive and susceptible phenotypes within Melaleuca quinquenervia during the early stages of A. psidii infection. We were able to identify three separate pools of secondary metabolites: (i) metabolites classified structurally as flavonoids that were naturally higher in the leaves of resistant individuals prior to infection, (ii) organoheterocyclic and carbohydrate-related metabolites that varied with the level of host resistance post-infection, and (iii) metabolites from the terpenoid pathways that were responsive to disease progression regardless of resistance phenotype suggesting that these play a minimal role in disease resistance during the early stages of colonization of this species. Based on the classes of these secondary metabolites, our results provide an improved understanding of key pathways that could be linked more generally to rust resistance with particular application within Melaleuca.

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Population Genomics of Eucalypts

Jordan

Prober

Andrew

et al. 2023

Population Genomics

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Genome-wide association study of myrtle rust (Austropuccinia psidii) resistance in Eucalyptus obliqua (subgenus Eucalyptus)

Cited by 13 publications

References 77 publications

Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection

Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection

Both Constitutive and Infection-Responsive Secondary Metabolites Linked to Resistance against Austropuccinia psidii (Myrtle Rust) in Melaleuca quinquenervia

Population Genomics of Eucalypts

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