Possibilities and challenges of the potato genome sequence

R.G.F. Visser, C.W.B. Bachem, T.J.A. Borm, J.M. de Boer, H.J. van Eck, H.J. Finkers, G. van der Linden, C.A. Maliepaard, J.G.A.M.L. Uitdewilligen, R.E. Voorrips, P.G. Vos, A.M.A. Wolters

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

Abstract

This paper describes the progress that has been made since the draft genome sequence of potato has been obtained and the analyses that need to be done to make further progress. Although sequencing has become less expensive and read lengths have increased, making optimal use of the information obtained is still difficult, certainly in the tetraploid potato crop. Major challenges in potato genomics are standardized genome assembly and haplotype analysis. Sequencing methods need to be improved further to achieve precision breeding. With the current new generation sequencing technology, the focus in potato breeding will shift from phenotype improvement to genotype improvement. In this respect, it is essential to realize that different alleles of the same gene can lead to different phenotypes depending on the genetic background and that there is significant epistatic interaction between different alleles. Genome-wide association studies will gain statistical power when binary single nucleotide polymorphism (SNP) data can be replaced with multi-allelic haplotype data. Binary SNP can be distributed across the many different alleles per locus or may be haplotype-specific, and potentially tag specific alleles which clearly differ in their contribution to a certain trait value. Assembling reads from the same linkage phase proved to allow constructing sufficiently long haplotype tracts to ensure their uniqueness. Combining large phenotyping data sets with modern approaches to sequencing and haplotype analysis and proper software will allow the efficiency of potato breeding to increase.
Original languageEnglish
Pages (from-to)327-330
JournalPotato Research
Volume57
Issue number3-4
DOIs
Publication statusPublished - 2014

Fingerprint

Solanum tuberosum
Haplotypes
haplotypes
potatoes
Genome
Alleles
genome
Breeding
alleles
phenotype
single nucleotide polymorphism
Single Nucleotide Polymorphism
breeding
genome assembly
Phenotype
Tetraploidy
Genome-Wide Association Study
Genomics
genetic background
tetraploidy

Keywords

  • construction

Cite this

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title = "Possibilities and challenges of the potato genome sequence",
abstract = "This paper describes the progress that has been made since the draft genome sequence of potato has been obtained and the analyses that need to be done to make further progress. Although sequencing has become less expensive and read lengths have increased, making optimal use of the information obtained is still difficult, certainly in the tetraploid potato crop. Major challenges in potato genomics are standardized genome assembly and haplotype analysis. Sequencing methods need to be improved further to achieve precision breeding. With the current new generation sequencing technology, the focus in potato breeding will shift from phenotype improvement to genotype improvement. In this respect, it is essential to realize that different alleles of the same gene can lead to different phenotypes depending on the genetic background and that there is significant epistatic interaction between different alleles. Genome-wide association studies will gain statistical power when binary single nucleotide polymorphism (SNP) data can be replaced with multi-allelic haplotype data. Binary SNP can be distributed across the many different alleles per locus or may be haplotype-specific, and potentially tag specific alleles which clearly differ in their contribution to a certain trait value. Assembling reads from the same linkage phase proved to allow constructing sufficiently long haplotype tracts to ensure their uniqueness. Combining large phenotyping data sets with modern approaches to sequencing and haplotype analysis and proper software will allow the efficiency of potato breeding to increase.",
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Possibilities and challenges of the potato genome sequence. / Visser, R.G.F.; Bachem, C.W.B.; Borm, T.J.A.; de Boer, J.M.; van Eck, H.J.; Finkers, H.J.; van der Linden, G.; Maliepaard, C.A.; Uitdewilligen, J.G.A.M.L.; Voorrips, R.E.; Vos, P.G.; Wolters, A.M.A.

In: Potato Research, Vol. 57, No. 3-4, 2014, p. 327-330.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - Possibilities and challenges of the potato genome sequence

AU - Visser, R.G.F.

AU - Bachem, C.W.B.

AU - Borm, T.J.A.

AU - de Boer, J.M.

AU - van Eck, H.J.

AU - Finkers, H.J.

AU - van der Linden, G.

AU - Maliepaard, C.A.

AU - Uitdewilligen, J.G.A.M.L.

AU - Voorrips, R.E.

AU - Vos, P.G.

AU - Wolters, A.M.A.

PY - 2014

Y1 - 2014

N2 - This paper describes the progress that has been made since the draft genome sequence of potato has been obtained and the analyses that need to be done to make further progress. Although sequencing has become less expensive and read lengths have increased, making optimal use of the information obtained is still difficult, certainly in the tetraploid potato crop. Major challenges in potato genomics are standardized genome assembly and haplotype analysis. Sequencing methods need to be improved further to achieve precision breeding. With the current new generation sequencing technology, the focus in potato breeding will shift from phenotype improvement to genotype improvement. In this respect, it is essential to realize that different alleles of the same gene can lead to different phenotypes depending on the genetic background and that there is significant epistatic interaction between different alleles. Genome-wide association studies will gain statistical power when binary single nucleotide polymorphism (SNP) data can be replaced with multi-allelic haplotype data. Binary SNP can be distributed across the many different alleles per locus or may be haplotype-specific, and potentially tag specific alleles which clearly differ in their contribution to a certain trait value. Assembling reads from the same linkage phase proved to allow constructing sufficiently long haplotype tracts to ensure their uniqueness. Combining large phenotyping data sets with modern approaches to sequencing and haplotype analysis and proper software will allow the efficiency of potato breeding to increase.

AB - This paper describes the progress that has been made since the draft genome sequence of potato has been obtained and the analyses that need to be done to make further progress. Although sequencing has become less expensive and read lengths have increased, making optimal use of the information obtained is still difficult, certainly in the tetraploid potato crop. Major challenges in potato genomics are standardized genome assembly and haplotype analysis. Sequencing methods need to be improved further to achieve precision breeding. With the current new generation sequencing technology, the focus in potato breeding will shift from phenotype improvement to genotype improvement. In this respect, it is essential to realize that different alleles of the same gene can lead to different phenotypes depending on the genetic background and that there is significant epistatic interaction between different alleles. Genome-wide association studies will gain statistical power when binary single nucleotide polymorphism (SNP) data can be replaced with multi-allelic haplotype data. Binary SNP can be distributed across the many different alleles per locus or may be haplotype-specific, and potentially tag specific alleles which clearly differ in their contribution to a certain trait value. Assembling reads from the same linkage phase proved to allow constructing sufficiently long haplotype tracts to ensure their uniqueness. Combining large phenotyping data sets with modern approaches to sequencing and haplotype analysis and proper software will allow the efficiency of potato breeding to increase.

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M3 - Article

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SP - 327

EP - 330

JO - Potato Research

JF - Potato Research

SN - 0014-3065

IS - 3-4

ER -