QTL discovery for agronomic and quality traits in diploid potato clones using PotatoMASH amplicon sequencing Article Swipe
Lea Vexler
,
María de la O Leyva‐Pérez
,
Agnieszka Konkolewska
,
Corentin R. Clot
,
Stephen Byrne
,
Denis Griffin
,
Tom Ruttink
,
Ronald C. B. Hutten
,
Christel Engelen
,
Richard G. F. Visser
,
Vanessa Prigge
,
Silke Wagener
,
Gisèle Lairy-Joly
,
Jan-David Driesprong
,
Ea Høegh Riis Sundmark
,
A. Nico O. Rookmaker
,
Herman J. van Eck
,
Dan Milbourne
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/g3journal/jkae164
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/g3journal/jkae164
We genotyped a population of 618 diploid potato clones derived from six independent potato-breeding programmes from NW-Europe. The diploids were phenotyped for 23 traits, using standardized protocols and common check varieties, enabling us to derive whole population estimators for most traits. We subsequently performed a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) for all traits with SNPs and short-read haplotypes derived from read-backed phasing. In this study, we used a marker platform called PotatoMASH (Potato Multi-Allele Scanning Haplotags); a pooled multiplex amplicon sequencing based approach. Through this method, neighboring SNPs within an amplicon can be combined to generate multiallelic short-read haplotypes (haplotags) that capture recombination history between the constituent SNPs and reflect the allelic diversity of a given locus in a different way than single bi-allelic SNPs. We found a total of 37 unique QTL across both marker types. A core of 10 QTL was detected with SNPs as well as with haplotags. Haplotags allowed to detect an additional 14 QTL not found based on the SNP set. Conversely, the bi-allelic SNP set also found 13 QTL not detectable using the haplotag set. We conclude that both marker types should routinely be used in parallel to maximize the QTL detection power. We report 19 novel QTL for nine traits: Skin Smoothness, Sprout Dormancy, Total Tuber Number, Tuber Length, Yield, Chipping Color, After-cooking Blackening, Cooking Type, and Eye depth.
Related Topics
Concepts
Biology
Quantitative trait locus
Amplicon
Ploidy
Amplicon sequencing
Genetics
Biotechnology
Gene
Polymerase chain reaction
16S ribosomal RNA
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/g3journal/jkae164
- https://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkae164/58600255/jkae164.pdf
- OA Status
- gold
- Cited By
- 3
- References
- 70
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4400809235
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4400809235Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/g3journal/jkae164Digital Object Identifier
- Title
-
QTL discovery for agronomic and quality traits in diploid potato clones using PotatoMASH amplicon sequencingWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-07-19Full publication date if available
- Authors
-
Lea Vexler, María de la O Leyva‐Pérez, Agnieszka Konkolewska, Corentin R. Clot, Stephen Byrne, Denis Griffin, Tom Ruttink, Ronald C. B. Hutten, Christel Engelen, Richard G. F. Visser, Vanessa Prigge, Silke Wagener, Gisèle Lairy-Joly, Jan-David Driesprong, Ea Høegh Riis Sundmark, A. Nico O. Rookmaker, Herman J. van Eck, Dan MilbourneList of authors in order
- Landing page
-
https://doi.org/10.1093/g3journal/jkae164Publisher landing page
- PDF URL
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https://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkae164/58600255/jkae164.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
- OA URL
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https://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkae164/58600255/jkae164.pdfDirect OA link when available
- Concepts
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Biology, Quantitative trait locus, Amplicon, Ploidy, Amplicon sequencing, Genetics, Biotechnology, Gene, Polymerase chain reaction, 16S ribosomal RNATop concepts (fields/topics) attached by OpenAlex
- Cited by
-
3Total citation count in OpenAlex
- Citations by year (recent)
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2025: 2, 2024: 1Per-year citation counts (last 5 years)
- References (count)
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70Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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