Towards efficient isolation of R gene orthologs from multiple genotypes: Optimization of Long Range-PCR

Maria J. Sanchez; James M. Bradeen

doi:10.1007/s11032-005-4475-5

Towards efficient isolation of R gene orthologs from multiple genotypes: Optimization of Long Range-PCR

Maria J. Sanchez, James M. Bradeen

Plant Pathology

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

Abstract

Resistance (R) genes and the proteins they encode are key components of the defense system of plants. The exploration of R gene diversity enables the study of R gene evolution and may facilitate the isolation of new and functional alleles. Most cloned R genes occur in clusters of related sequences. Thus, the development of a tool for reliable recovery of orthologous R gene sequences to the exclusion of paralogous sequences will facilitate R gene diversity analysis. The late blight resistance gene RB is a single functional locus embedded within a cluster of related sequences. Previously, the functional RB allele was cloned from wild potato using a Long Range-PCR (LR-PCR) technique, suggesting this method may be a promising tool for recovery of R gene orthologs in other genotypes. Using the RB gene as a model, we explored the limitations and improved three technical aspects of LR-PCR for multi-genotype applications. We present improved primers for the recovery of the RB locus and have identified efficient DNA extraction procedures and reliable amplification systems. We document that consensus sequences built from three independently generated LR-PCR clones can be up to 100% accurate. Our results show encouraging advances toward successful application of LR-PCR for isolating alleles from orthologous R gene loci.

Original language	English (US)
Pages (from-to)	137-148
Number of pages	12
Journal	Molecular Breeding
Volume	17
Issue number	2
DOIs	https://doi.org/10.1007/s11032-005-4475-5
State	Published - Feb 2006

Bibliographical note

Funding Information:
This project was partially funded by the NSF Potato Genome Grant (DBI0218166) and by the Minnesota Rapid Agricultural Response Fund. We thank Dr. John Helgeson, USDA-ARS and University of Wisconsin for providing S. bulbo-castanum genotype PT29. We also thank Dr. Deborah Samac and Dr. Georgiana May for thoughtful advice and insight and the staff and graduate students at the Potato Pathology and Genomic Lab for their support. Computer support from the University of Minnesota Supercomputing Institute is gratefully acknowledged. Reference to a specific product by name is necessary for factual reporting of our results and should not be construed as an endorsement to the exclusion of similar products.

Keywords

Allelic mining
LR-PCR
Potato
R genes
RB gene

Publisher link

10.1007/s11032-005-4475-5

Find It

Find It at U of M Libraries

Cite this

@article{36a17aa5614d43288ad30564f30ad21b,

title = "Towards efficient isolation of R gene orthologs from multiple genotypes: Optimization of Long Range-PCR",

abstract = "Resistance (R) genes and the proteins they encode are key components of the defense system of plants. The exploration of R gene diversity enables the study of R gene evolution and may facilitate the isolation of new and functional alleles. Most cloned R genes occur in clusters of related sequences. Thus, the development of a tool for reliable recovery of orthologous R gene sequences to the exclusion of paralogous sequences will facilitate R gene diversity analysis. The late blight resistance gene RB is a single functional locus embedded within a cluster of related sequences. Previously, the functional RB allele was cloned from wild potato using a Long Range-PCR (LR-PCR) technique, suggesting this method may be a promising tool for recovery of R gene orthologs in other genotypes. Using the RB gene as a model, we explored the limitations and improved three technical aspects of LR-PCR for multi-genotype applications. We present improved primers for the recovery of the RB locus and have identified efficient DNA extraction procedures and reliable amplification systems. We document that consensus sequences built from three independently generated LR-PCR clones can be up to 100% accurate. Our results show encouraging advances toward successful application of LR-PCR for isolating alleles from orthologous R gene loci.",

keywords = "Allelic mining, LR-PCR, Potato, R genes, RB gene",

author = "Sanchez, {Maria J.} and Bradeen, {James M.}",

note = "Funding Information: This project was partially funded by the NSF Potato Genome Grant (DBI0218166) and by the Minnesota Rapid Agricultural Response Fund. We thank Dr. John Helgeson, USDA-ARS and University of Wisconsin for providing S. bulbo-castanum genotype PT29. We also thank Dr. Deborah Samac and Dr. Georgiana May for thoughtful advice and insight and the staff and graduate students at the Potato Pathology and Genomic Lab for their support. Computer support from the University of Minnesota Supercomputing Institute is gratefully acknowledged. Reference to a specific product by name is necessary for factual reporting of our results and should not be construed as an endorsement to the exclusion of similar products.",

year = "2006",

month = feb,

doi = "10.1007/s11032-005-4475-5",

language = "English (US)",

volume = "17",

pages = "137--148",

journal = "Molecular Breeding",

issn = "1380-3743",

publisher = "Springer Netherlands",

number = "2",

}

TY - JOUR

T1 - Towards efficient isolation of R gene orthologs from multiple genotypes

T2 - Optimization of Long Range-PCR

AU - Sanchez, Maria J.

AU - Bradeen, James M.

N1 - Funding Information: This project was partially funded by the NSF Potato Genome Grant (DBI0218166) and by the Minnesota Rapid Agricultural Response Fund. We thank Dr. John Helgeson, USDA-ARS and University of Wisconsin for providing S. bulbo-castanum genotype PT29. We also thank Dr. Deborah Samac and Dr. Georgiana May for thoughtful advice and insight and the staff and graduate students at the Potato Pathology and Genomic Lab for their support. Computer support from the University of Minnesota Supercomputing Institute is gratefully acknowledged. Reference to a specific product by name is necessary for factual reporting of our results and should not be construed as an endorsement to the exclusion of similar products.

PY - 2006/2

Y1 - 2006/2

N2 - Resistance (R) genes and the proteins they encode are key components of the defense system of plants. The exploration of R gene diversity enables the study of R gene evolution and may facilitate the isolation of new and functional alleles. Most cloned R genes occur in clusters of related sequences. Thus, the development of a tool for reliable recovery of orthologous R gene sequences to the exclusion of paralogous sequences will facilitate R gene diversity analysis. The late blight resistance gene RB is a single functional locus embedded within a cluster of related sequences. Previously, the functional RB allele was cloned from wild potato using a Long Range-PCR (LR-PCR) technique, suggesting this method may be a promising tool for recovery of R gene orthologs in other genotypes. Using the RB gene as a model, we explored the limitations and improved three technical aspects of LR-PCR for multi-genotype applications. We present improved primers for the recovery of the RB locus and have identified efficient DNA extraction procedures and reliable amplification systems. We document that consensus sequences built from three independently generated LR-PCR clones can be up to 100% accurate. Our results show encouraging advances toward successful application of LR-PCR for isolating alleles from orthologous R gene loci.

AB - Resistance (R) genes and the proteins they encode are key components of the defense system of plants. The exploration of R gene diversity enables the study of R gene evolution and may facilitate the isolation of new and functional alleles. Most cloned R genes occur in clusters of related sequences. Thus, the development of a tool for reliable recovery of orthologous R gene sequences to the exclusion of paralogous sequences will facilitate R gene diversity analysis. The late blight resistance gene RB is a single functional locus embedded within a cluster of related sequences. Previously, the functional RB allele was cloned from wild potato using a Long Range-PCR (LR-PCR) technique, suggesting this method may be a promising tool for recovery of R gene orthologs in other genotypes. Using the RB gene as a model, we explored the limitations and improved three technical aspects of LR-PCR for multi-genotype applications. We present improved primers for the recovery of the RB locus and have identified efficient DNA extraction procedures and reliable amplification systems. We document that consensus sequences built from three independently generated LR-PCR clones can be up to 100% accurate. Our results show encouraging advances toward successful application of LR-PCR for isolating alleles from orthologous R gene loci.

KW - Allelic mining

KW - LR-PCR

KW - Potato

KW - R genes

KW - RB gene

UR - http://www.scopus.com/inward/record.url?scp=33644781963&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33644781963&partnerID=8YFLogxK

U2 - 10.1007/s11032-005-4475-5

DO - 10.1007/s11032-005-4475-5

M3 - Article

AN - SCOPUS:33644781963

SN - 1380-3743

VL - 17

SP - 137

EP - 148

JO - Molecular Breeding

JF - Molecular Breeding

IS - 2

ER -

Towards efficient isolation of R gene orthologs from multiple genotypes: Optimization of Long Range-PCR

Abstract

Bibliographical note

Keywords

Publisher link

Find It

Other files and links

Fingerprint

Cite this