Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 488841
Title Possibilities and challenges of the potato genome sequence
Author(s) Visser, R.G.F.; Bachem, C.W.B.; Borm, T.J.A.; Boer, J.M. de; Eck, H.J. van; Finkers, H.J.; Linden, G. van der; Maliepaard, C.A.; Uitdewilligen, J.G.A.M.L.; Voorrips, R.E.; Vos, P.G.; Wolters, A.M.A.
Source Potato Research 57 (2014)3-4. - ISSN 0014-3065 - p. 327 - 330.
DOI https://doi.org/10.1007/s11540-015-9282-8
Department(s) Plant Breeding
PBR Breeding for growth and development
Plant Breeding
PBR Biodiversity and genetic variation
PRI Biodiversity and Breeding
PBR Quantitative aspects of Plant Breeding
EPS
Publication type Refereed Article in a scientific journal
Publication year 2014
Keyword(s) construction
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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