Tracking disease resistance deployment in potato breeding by enrichment sequencing

Armstrong, Miles; Vossen, Jack H.; Lim, Joanne Tze-Yin; Hutten, R.C.B.; Xu, Jianfei; Strachan, Shona; Harrower, Brian; Champouret, Nicolas; Gilroy, Eleanor M.; Hein, Ingo

doi:10.1111/pbi.12997

Cited by 59 publications

(60 citation statements)

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“…To confirm whether the resistance of 03112-233 to P. infestans isolate 90128 is caused by known or novel resistance genes, we conducted a dRenSeq analysis (Armstrong et al 2018). RenSeq-enriched pairedend Illumina reads from 03112-233 were mapped at mismatch rates of 0% and 2% against a panel of known functional NLRs: Rpi_ber, Rpi_chc, Rpi_R1, Rpi_R2, Rpi_R2-like, Rpi_R3a, Rpi_R3b, Rpi_R8, Figure 1 Comparison of detached leaves and in vitro plantlets of potato genotype 03112-233 after inoculation with P. infestans isolates 90128 and CN152.…”

Section: Resultsmentioning

confidence: 99%

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Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans

Duan

Armstrong

et al. 2020

G3 Genes|Genomes|Genetics

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Late blight, caused by Phytophthora infestans (P. infestans), is a devastating disease in potato worldwide. Our previous study revealed that the Solanum andigena genotype 03112-233 is resistant to P. infestans isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new R gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as SWEET compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between P. infestans and potato.

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Section: Resultsmentioning

confidence: 99%

“…Genomic DNA of 03112-233 was extracted according to the modified CTAB procedure of Doyle and Doyle (1987). NLRs enrichment and dRenSeq analysis were conducted as described by Armstrong et al (2018). Paired-end Illumina MiSeq sequencing was used to sequence the R-gene enriched samples.…”

Section: Dna Extraction and Drenseq Analysismentioning

confidence: 99%

Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans

Duan

Armstrong

et al. 2020

G3 Genes|Genomes|Genetics

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“…For the dRenSeq analysis, RenSeq reads were mapped against a bespoke set of functionally characterised NLRs, including their 5′ and 3′ flanking region (Armstrong et al 2018 ). In addition to the references described by Armstrong et al ( 2018 ), additional NLRs Gro1 - 4 [AY196151] (Paal et al 2004 ); Hero [AJ457051] (Ganal et al 1995 ); Mi1.1 [AF039681] and Mi1.2 [AF039682] (Milligan et al 1998 ); Rpi - abpt [FJ536324.1] (Lokossou et al 2009 ); Rpi - amr [KT373889] (Witek et al 2016 ); and Rpi - Ph - 3 [KJ563933.1] (Zhang et al 2014 ) were included. Only paired-end reads were mapped using the score-min parameter L, − 0.01, − 0.01.…”

Section: Methodsmentioning

confidence: 99%

“…Furthermore, RenSeq, which targets all 755 described NLRs in potato, has been successfully used to map and/or identify functional NLRs against late blight (Chen et al 2018 ; Jupe et al 2013 ; Witek et al 2016 ). Used as a diagnostic tool in wild species or varieties, and referred to as dRenSeq, the technology allows for the rapid assessment as to whether a resistance phenotype is based on already characterised resistances or a hitherto unknown gene (Armstrong et al 2018 ; Chen et al 2018 ; Jiang et al 2018 ; Van Weymers et al 2016 ). To compliment RenSeq-based mapping, we previously developed GenSeq, a targeted enrichment sequencing approach of 1980 single or low-copy number genes that can be placed on the individual potato chromosomes with high confidence (Chen et al 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Mapping the H2 resistance effective against Globodera pallida pathotype Pa1 in tetraploid potato

et al. 2019

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Key message The nematode resistance gene H2 was mapped to the distal end of chromosome 5 in tetraploid potato. Abstract The H2 resistance gene, introduced into cultivated potatoes from the wild diploid species Solanum multidissectum , confers a high level of resistance to the Pa1 pathotype of the potato cyst nematode Globodera pallida . A cross between tetraploid H2 -containing breeding clone P55/7 and susceptible potato variety Picasso yielded an F1 population that segregated approximately 1:1 for the resistance phenotype, which is consistent with a single dominant gene in a simplex configuration. Using genome reduction methodologies RenSeq and GenSeq, the segregating F1 population enabled the genetic characterisation of the resistance through a bulked segregant analysis. A diagnostic RenSeq analysis of the parents confirmed that the resistance in P55/7 cannot be explained by previously characterised resistance genes. Only the variety Picasso contained functionally characterised disease resistance genes Rpi - R1 , Rpi - R3a , Rpi - R3b variant, Gpa2 and Rx , which was independently confirmed through effector vacuum infiltration assays. RenSeq and GenSeq independently identified sequence polymorphisms linked to the H2 resistance on the top end of potato chromosome 5. Allele-specific KASP markers further defined the locus containing the H2 gene to a 4.7 Mb interval on the distal short arm of potato chromosome 5 and to positions that correspond to 1.4 MB and 6.1 MB in the potato reference genome. Electronic supplementary material The online version of this article (10.1007/s00122-019-03278-4) contains supplementary material, which is available to authorized users.

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“…Diversity Array Technology was effective in identifying genomic sequence variability in S. bulbocastanum and S. commersonii [130]. Resistance (R) gene enrichment sequencing (RenSeq) relies on the purification of predicted R genes from wild species for high-throughput sequencing [131] or to identify and track previously unknown R genes in cultivated germplasm [132]. Similarly, GenSeq uses single/low copy number genes to identify markers associated with resistance, when a known R gene is not present [133].…”

Section: Identifying Valuable Germplasmmentioning

confidence: 99%

Potato Germplasm Enhancement Enters the Genomics Era

2019

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The goal of germplasm enhancement is to introgress traits from wild crop relatives into cultivated material and eventually cultivars. It seeks to restore genetic diversity that has been lost over time or to augment cultivated material with novel alleles that improve parents in breeding programs. This paper discusses potato germplasm enhancement efforts in the past, focusing on effective examples such as disease resistance and processing quality. In addition, it outlines new strategies for enhancement efforts, shifting the focus from evaluating phenotypes to tracking and manipulating specific DNA sequences. In the genomics era, germplasm enhancement will increasingly be focused on identifying and introgressing alleles rather than traits. Alleles will come from a broad pool of genetic resources that include wild species relatives of potato, landraces, cultivated potato itself, and distantly-related species. Genomics tools will greatly increase the efficiency of introgressing multi-genic traits and will make it possible to identify rare alleles and utilize recessive alleles.

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Tracking disease resistance deployment in potato breeding by enrichment sequencing

Cited by 59 publications

References 32 publications

Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans

Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans

Mapping the H2 resistance effective against Globodera pallida pathotype Pa1 in tetraploid potato

Potato Germplasm Enhancement Enters the Genomics Era

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