Identification of additional fire blight resistance candidate genes following MinION Oxford Nanopore sequencing and assembly of BAC clone spanning the Malus fusca resistance locus

Emeriewen, Ofere Francis; Piazza, Stefano; Cestaro, Alessandro; Flachowsky, Henryk; Malnoy, Mickaël; Peil, Andreas

doi:10.1007/s42161-022-01223-x

Cited by 9 publications

(9 citation statements)

References 45 publications

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“…are not products of coevolution with the Erwinia due to their lack of positioning within clusters of paralogs (i.e., arrays). However, the results presented by Emeriewen et al (2022) and our genome support a co-evolutionary origin of the fire blight resistance in M. fusca. Our assembly demonstrates that the Emeriewen et al (2022) candidate R-gene was located within a tandem array of similar R-genes, which also span into other Malus spp.…”

Section: Comparing Apples To Apples: Synteny Within Malussupporting

confidence: 48%

“…However, the results presented by Emeriewen et al (2022) and our genome support a co-evolutionary origin of the fire blight resistance in M. fusca. Our assembly demonstrates that the Emeriewen et al (2022) candidate R-gene was located within a tandem array of similar R-genes, which also span into other Malus spp. and domesticated cultivars.…”

Section: Comparing Apples To Apples: Synteny Within Malussupporting

confidence: 48%

“…In that research, a genetic map was developed positioning a QTL on Chromosome 10 (FB_Mfu10) that explained 66% of the variation (Emeriewen et al, 2017(Emeriewen et al, , 2020. Further analysis of that region using Illumina-and Nanopore-sequenced BACs, identified a potential candidate gene, as well as other repetitive fragments of high sequence similarity to the candidate gene (Emeriewen et al, 2018(Emeriewen et al, , 2022. We sought to leverage our highly contiguous assembly of this fire blight resistant M. fusca accession to help in resolving this important locus and further analyze the genes therein, which likely contribute to this resistance trait.…”

Section: Comparing Apples To Apples: Synteny Within Malusmentioning

confidence: 99%

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A haplotype resolved chromosome‐scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus

Mansfeld,

Yocca,

et al. 2023

The Plant Journal

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SUMMARYThe Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation for M. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.

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Section: Comparing Apples To Apples: Synteny Within Malussupporting

confidence: 48%

Section: Comparing Apples To Apples: Synteny Within Malussupporting

confidence: 48%

Section: Comparing Apples To Apples: Synteny Within Malusmentioning

confidence: 99%

See 1 more Smart Citation

A haplotype resolved chromosome‐scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus

Mansfeld,

Yocca,

et al. 2023

The Plant Journal

View full text Add to dashboard Cite

show abstract

“…are not products of coevolution with the Erwinia due to their lack of positioning within clusters of paralogs (i.e., arrays). However, the results presented by Emeriewen et al, (2022) and our genome support a co-evolutionary origin of the fire blight resistance in M. fusca. Our assembly demonstrates that the Emeriewen et al, (2022) candidate R-gene was located within a tandem array of similar Rgenes, which also span into other Malus spp.…”

Section: Resolving the Fire Blight Resistance Locus (Fb_mfu10)supporting

confidence: 48%

“…Within the fine-mapped boundaries identified by Emeriewen et al, (2018) we identified several genes including a tandem duplication array consisting of four copies ( MfusH1_10g02031, MfusH1_10g02036, MfusH1_10g02040, and MfusH1_10g02042 ) of the G-type lectin S-receptor-like serine/threonine-protein kinase genes implicated by Emeriewen et al, (2018;2022). Since similar resistance receptors ( i.e., R-genes) are often part of such tandem duplications; we hypothesized that apart from sequence polymorphism, copy number variation (CNV) within this locus could potentially contribute to the resistance phenotype.…”

Section: Resultsmentioning

confidence: 84%

A haplotype resolved chromosome-scale assembly of North American wild appleMalus fuscaand comparative genomics of the fire blightMfu10locus. Genome of the Pacific CrabappleMalus fusca

Mansfeld

Yocca

et al. 2023

Preprint

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The Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus x domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca has been hampered by the lack of genomic resources. Here, we present a high-quality, haplotype-resolved, chromosome-scale genome assembly and annotation for M. fusca. The genome was assembled using high-fidelity long-reads and scaffolded using genetic maps and high-throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co-linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference-quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA-informed introgression breeding.

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Mfu16 is an unstable fire blight resistance QTL on linkage group 16 of Malus fusca MAL0045

et al. 2023

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A strong fire blight resistance QTL (Mfu10) was previously detected on linkage group 10 (LG10) of Malus fusca accession MAL0045, using several strains of the causative bacterium, Erwinia amylovora. As no strain capable of breaking the resistance of MAL0045 has been found, we hypothesized that another locus contributes to its fire blight resistance. However, none was detected with strains previously tested on the progeny. Here, an avrRpt2EA mutant strain (Ea1038) with the chromosomal S-allele deleted and complemented with the less aggressive C-allele, was used to phenotype MAL0045 × ‘Idared’ progeny. We performed phenotype-genotype analyses using the first genetic map of MAL0045, which is scarcely dense, and a recently constructed saturated map. As expected, Mfu10 was detected on LG10 with Ea1038, as was previously with other strains. Interestingly, a QTL with a logarithm of odds (LOD) thresholds of 5.5 and 2.9, significant at the genome-wide and chromosome levels, respectively, was detected with Ea1038 on LG16 (Mfu16) in a subset of 76 individuals, but only using the saturated map. Progenies carrying both Mfu10 and Mfu16 were significantly more resistant than progenies carrying only Mfu10. However, the LOD of Mfu16 diminished to 2.6 in a larger subset of individuals. We hypothesize that Mfu16 is present in the genome of MAL0045 albeit unstable in the progeny.

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Identification of additional fire blight resistance candidate genes following MinION Oxford Nanopore sequencing and assembly of BAC clone spanning the Malus fusca resistance locus

Cited by 9 publications

References 45 publications

A haplotype resolved chromosome‐scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus

A haplotype resolved chromosome‐scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus

A haplotype resolved chromosome-scale assembly of North American wild appleMalus fuscaand comparative genomics of the fire blightMfu10locus. Genome of the Pacific CrabappleMalus fusca

Mfu16 is an unstable fire blight resistance QTL on linkage group 16 of Malus fusca MAL0045

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