2018
DOI: 10.1111/pbi.12997
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Tracking disease resistance deployment in potato breeding by enrichment sequencing

Abstract: Summary Following the molecular characterisation of functional disease resistance genes in recent years, methods to track and verify the integrity of multiple genes in varieties are needed for crop improvement through resistance stacking. Diagnostic resistance gene enrichment sequencing ( dR enSeq) enables the high‐confidence identification and complete sequence validation of known functional resistance genes in crops. As demonstrated for tetraploid potato varieties, the metho… Show more

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Cited by 59 publications
(60 citation statements)
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References 32 publications
(43 reference 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%
See 1 more Smart Citation
“…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%
“…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%
“…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%
“…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%