An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci

Jonathan Fresnedo-Ramírez; Shanshan Yang; Qi Sun; Linda M. Cote; Peter A. Schweitzer; Bruce I. Reisch; Craig A. Ledbetter; James J. Luby; Matthew D. Clark; Jason P. Londo; David M. Gadoury; Pál Kozma; Lance Cadle-Davidson

doi:10.1007/s11032-017-0739-0

An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci

Jonathan Fresnedo-Ramírez, Shanshan Yang, Qi Sun, Linda M. Cote, Peter A. Schweitzer, Bruce I. Reisch, Craig A. Ledbetter, James J. Luby, Matthew D. Clark, Jason P. Londo, David M. Gadoury, Pál Kozma, Lance Cadle-Davidson

Horticultural Science

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

14 Scopus citations

Abstract

Resistance breeding often requires the introgression and tracking of resistance loci from wild species into domesticated backgrounds, typically with the goal of pyramiding multiple resistance genes, to provide durable disease resistance to breeding selections and ultimately cultivars. While molecular markers are commonly used to facilitate these efforts, high genetic diversity and divergent marker technologies can complicate marker-assisted breeding strategies. Here, amplicon sequencing (AmpSeq) was used to integrate SNP markers with dominant presence/absence markers derived from genotyping-by-sequencing and other genotyping technologies, for the simultaneous tracking of five loci for resistance to grapevine powdery mildew. SNP haploblocks defined the loci for REN1, REN2 and REN3, which confer quantitative resistance phenotypes that are challenging to measure via field ratings of natural infections. Presence/absence markers for RUN1 and REN4 were validated to predict qualitative resistance phenotypes and corresponded with previous presence/absence fluorescent electrophoretic assays. Thus, 37 AmpSeq-derived markers were identified for the five loci, and markers for REN1, REN2, REN4 and RUN1 were used for multiplexed screening and selection within diverse breeding germplasm. Poor transferability of SNP markers indicated imperfect marker-trait association in some families. Together, AmpSeq SNP haploblocks and presence/absence markers provide a high-throughput, cost-effective tool to integrate divergent technologies for marker-assisted selection and genetic analysis of introgressed disease resistance loci in grapevine.

Original language	English (US)
Article number	145
Journal	Molecular Breeding
Volume	37
Issue number	12
DOIs	https://doi.org/10.1007/s11032-017-0739-0
State	Published - Dec 1 2017

Bibliographical note

Funding Information:
Acknowledgements We would like to thank Michelle Schaub, Hema Kasinathan, Anna Nowogrodzki, Paige Appleton, Mary Jean Welser and Jackie Lillis for their technical support phenotyping powdery mildew resistance. We thank Steve Luce and Mike Colizzi; Norma Ambriz and Jacob Andresen; and Peter Hemstad from Cornell University, USDA-ARS Parlier, and the University of Minnesota, respectively, for help maintaining the mapping families used in this study. The authors gratefully acknowledge the USDA-NIFA Specialty Crop Research Initiative (award no. 2011-51181-30635) for funding the VitisGen project (http://www. vitisgen.org/) and support for JFR, as well as the National Grape and Wine Initiative for support for SY.

Publisher Copyright:
© 2017, This is a U.S. government work.

Keywords

Disease resistance
Erysiphe necator
Marker-assisted breeding
Marker-assisted seedling selection
Uncinula necator
Vitis

Access

10.1007/s11032-017-0739-0

OpenUrl availability

Full text

Cite this

Fresnedo-Ramírez, J., Yang, S., Sun, Q., Cote, L. M., Schweitzer, P. A., Reisch, B. I., Ledbetter, C. A., Luby, J. J., Clark, M. D., Londo, J. P., Gadoury, D. M., Kozma, P., & Cadle-Davidson, L. (2017). An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci. Molecular Breeding, 37(12), Article 145. https://doi.org/10.1007/s11032-017-0739-0

Fresnedo-Ramírez, J, Yang, S, Sun, Q, Cote, LM, Schweitzer, PA, Reisch, BI, Ledbetter, CA, Luby, JJ , Clark, MD, Londo, JP, Gadoury, DM, Kozma, P & Cadle-Davidson, L 2017, 'An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci', Molecular Breeding, vol. 37, no. 12, 145. https://doi.org/10.1007/s11032-017-0739-0

@article{d1db5fc71fae46a0a8ae3b551214b302,

title = "An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci",

abstract = "Resistance breeding often requires the introgression and tracking of resistance loci from wild species into domesticated backgrounds, typically with the goal of pyramiding multiple resistance genes, to provide durable disease resistance to breeding selections and ultimately cultivars. While molecular markers are commonly used to facilitate these efforts, high genetic diversity and divergent marker technologies can complicate marker-assisted breeding strategies. Here, amplicon sequencing (AmpSeq) was used to integrate SNP markers with dominant presence/absence markers derived from genotyping-by-sequencing and other genotyping technologies, for the simultaneous tracking of five loci for resistance to grapevine powdery mildew. SNP haploblocks defined the loci for REN1, REN2 and REN3, which confer quantitative resistance phenotypes that are challenging to measure via field ratings of natural infections. Presence/absence markers for RUN1 and REN4 were validated to predict qualitative resistance phenotypes and corresponded with previous presence/absence fluorescent electrophoretic assays. Thus, 37 AmpSeq-derived markers were identified for the five loci, and markers for REN1, REN2, REN4 and RUN1 were used for multiplexed screening and selection within diverse breeding germplasm. Poor transferability of SNP markers indicated imperfect marker-trait association in some families. Together, AmpSeq SNP haploblocks and presence/absence markers provide a high-throughput, cost-effective tool to integrate divergent technologies for marker-assisted selection and genetic analysis of introgressed disease resistance loci in grapevine.",

keywords = "Disease resistance, Erysiphe necator, Marker-assisted breeding, Marker-assisted seedling selection, Uncinula necator, Vitis",

author = "Jonathan Fresnedo-Ram{\'i}rez and Shanshan Yang and Qi Sun and Cote, {Linda M.} and Schweitzer, {Peter A.} and Reisch, {Bruce I.} and Ledbetter, {Craig A.} and Luby, {James J.} and Clark, {Matthew D.} and Londo, {Jason P.} and Gadoury, {David M.} and P{\'a}l Kozma and Lance Cadle-Davidson",

note = "Funding Information: Acknowledgements We would like to thank Michelle Schaub, Hema Kasinathan, Anna Nowogrodzki, Paige Appleton, Mary Jean Welser and Jackie Lillis for their technical support phenotyping powdery mildew resistance. We thank Steve Luce and Mike Colizzi; Norma Ambriz and Jacob Andresen; and Peter Hemstad from Cornell University, USDA-ARS Parlier, and the University of Minnesota, respectively, for help maintaining the mapping families used in this study. The authors gratefully acknowledge the USDA-NIFA Specialty Crop Research Initiative (award no. 2011-51181-30635) for funding the VitisGen project (http://www. vitisgen.org/) and support for JFR, as well as the National Grape and Wine Initiative for support for SY. Publisher Copyright: {\textcopyright} 2017, This is a U.S. government work.",

year = "2017",

month = dec,

day = "1",

doi = "10.1007/s11032-017-0739-0",

language = "English (US)",

volume = "37",

journal = "Molecular Breeding",

issn = "1380-3743",

publisher = "Springer Netherlands",

number = "12",

}

TY - JOUR

T1 - An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci

AU - Fresnedo-Ramírez, Jonathan

AU - Yang, Shanshan

AU - Sun, Qi

AU - Cote, Linda M.

AU - Schweitzer, Peter A.

AU - Reisch, Bruce I.

AU - Ledbetter, Craig A.

AU - Luby, James J.

AU - Clark, Matthew D.

AU - Londo, Jason P.

AU - Gadoury, David M.

AU - Kozma, Pál

AU - Cadle-Davidson, Lance

N1 - Funding Information: Acknowledgements We would like to thank Michelle Schaub, Hema Kasinathan, Anna Nowogrodzki, Paige Appleton, Mary Jean Welser and Jackie Lillis for their technical support phenotyping powdery mildew resistance. We thank Steve Luce and Mike Colizzi; Norma Ambriz and Jacob Andresen; and Peter Hemstad from Cornell University, USDA-ARS Parlier, and the University of Minnesota, respectively, for help maintaining the mapping families used in this study. The authors gratefully acknowledge the USDA-NIFA Specialty Crop Research Initiative (award no. 2011-51181-30635) for funding the VitisGen project (http://www. vitisgen.org/) and support for JFR, as well as the National Grape and Wine Initiative for support for SY. Publisher Copyright: © 2017, This is a U.S. government work.

PY - 2017/12/1

Y1 - 2017/12/1

N2 - Resistance breeding often requires the introgression and tracking of resistance loci from wild species into domesticated backgrounds, typically with the goal of pyramiding multiple resistance genes, to provide durable disease resistance to breeding selections and ultimately cultivars. While molecular markers are commonly used to facilitate these efforts, high genetic diversity and divergent marker technologies can complicate marker-assisted breeding strategies. Here, amplicon sequencing (AmpSeq) was used to integrate SNP markers with dominant presence/absence markers derived from genotyping-by-sequencing and other genotyping technologies, for the simultaneous tracking of five loci for resistance to grapevine powdery mildew. SNP haploblocks defined the loci for REN1, REN2 and REN3, which confer quantitative resistance phenotypes that are challenging to measure via field ratings of natural infections. Presence/absence markers for RUN1 and REN4 were validated to predict qualitative resistance phenotypes and corresponded with previous presence/absence fluorescent electrophoretic assays. Thus, 37 AmpSeq-derived markers were identified for the five loci, and markers for REN1, REN2, REN4 and RUN1 were used for multiplexed screening and selection within diverse breeding germplasm. Poor transferability of SNP markers indicated imperfect marker-trait association in some families. Together, AmpSeq SNP haploblocks and presence/absence markers provide a high-throughput, cost-effective tool to integrate divergent technologies for marker-assisted selection and genetic analysis of introgressed disease resistance loci in grapevine.

AB - Resistance breeding often requires the introgression and tracking of resistance loci from wild species into domesticated backgrounds, typically with the goal of pyramiding multiple resistance genes, to provide durable disease resistance to breeding selections and ultimately cultivars. While molecular markers are commonly used to facilitate these efforts, high genetic diversity and divergent marker technologies can complicate marker-assisted breeding strategies. Here, amplicon sequencing (AmpSeq) was used to integrate SNP markers with dominant presence/absence markers derived from genotyping-by-sequencing and other genotyping technologies, for the simultaneous tracking of five loci for resistance to grapevine powdery mildew. SNP haploblocks defined the loci for REN1, REN2 and REN3, which confer quantitative resistance phenotypes that are challenging to measure via field ratings of natural infections. Presence/absence markers for RUN1 and REN4 were validated to predict qualitative resistance phenotypes and corresponded with previous presence/absence fluorescent electrophoretic assays. Thus, 37 AmpSeq-derived markers were identified for the five loci, and markers for REN1, REN2, REN4 and RUN1 were used for multiplexed screening and selection within diverse breeding germplasm. Poor transferability of SNP markers indicated imperfect marker-trait association in some families. Together, AmpSeq SNP haploblocks and presence/absence markers provide a high-throughput, cost-effective tool to integrate divergent technologies for marker-assisted selection and genetic analysis of introgressed disease resistance loci in grapevine.

KW - Disease resistance

KW - Erysiphe necator

KW - Marker-assisted breeding

KW - Marker-assisted seedling selection

KW - Uncinula necator

KW - Vitis

UR - http://www.scopus.com/inward/record.url?scp=85033731790&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85033731790&partnerID=8YFLogxK

U2 - 10.1007/s11032-017-0739-0

DO - 10.1007/s11032-017-0739-0

M3 - Article

AN - SCOPUS:85033731790

SN - 1380-3743

VL - 37

JO - Molecular Breeding

JF - Molecular Breeding

IS - 12

M1 - 145

ER -

An integrative AmpSeq platform for highly multiplexed marker-assisted pyramiding of grapevine powdery mildew resistance loci

Abstract

Bibliographical note

Keywords

Access

OpenUrl availability

Other files and links

Fingerprint

Cite this