Dissection of Potato Complex Traits by Linkage and Association Genetics as Basis for Developing Molecular Diagnostics in Breeding Programs

Gebhardt, Christiane; Urbany, Claude; Stich, Benjamin

doi:10.1007/978-94-007-7575-6_3

Cited by 10 publications

(10 citation statements)

References 213 publications

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“…Alternatively, the StCDF1 locus might be less influential on natural variation of plant maturity when the plants are cultivated in a geographical region with shorter day length during the growing season such as Northern Spain. The length of the vegetation period recorded by breeders as plant maturity or ‘earliness’ is certainly a polygenic trait that is influenced by additional developmental processes and additional loci as demonstrated in previous linkage and association mapping studies for plant maturity, reviewed in (Gebhardt et al 2014 ).…”

Section: Discussionmentioning

confidence: 97%

Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.)

Schönhals

Ortega²,

Barandalla

et al. 2016

Theor Appl Genet

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Key messageSNPs in candidate genesPain-1,InvCD141(invertases),SSIV(starch synthase),StCDF1(transcription factor),LapN(leucine aminopeptidase), and cytoplasm type are associated with potato tuber yield, starch content and/or starch yield.AbstractTuber yield (TY), starch content (TSC), and starch yield (TSY) are complex characters of high importance for the potato crop in general and for industrial starch production in particular. DNA markers associated with superior alleles of genes that control the natural variation of TY, TSC, and TSY could increase precision and speed of breeding new cultivars optimized for potato starch production. Diagnostic DNA markers are identified by association mapping in populations of tetraploid potato varieties and advanced breeding clones. A novel association mapping population of 282 genotypes including varieties, breeding clones and Andean landraces was assembled and field evaluated in Northern Spain for TY, TSC, TSY, tuber number (TN) and tuber weight (TW). The landraces had lower mean values of TY, TW, TN, and TSY. The population was genotyped for 183 microsatellite alleles, 221 single nucleotide polymorphisms (SNPs) in fourteen candidate genes and eight known diagnostic markers for TSC and TSY. Association test statistics including kinship and population structure reproduced five known marker–trait associations of candidate genes and discovered new ones, particularly for tuber yield and starch yield. The inclusion of landraces increased the number of detected marker–trait associations. Integration of the present association mapping results with previous QTL linkage mapping studies for TY, TSC, TSY, TW, TN, and tuberization revealed some hot spots of QTL for these traits in the potato genome. The genomic positions of markers linked or associated with QTL for complex tuber traits suggest high multiplicity and genome wide distribution of the underlying genes.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2665-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 97%

Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.)

Schönhals

Ortega²,

Barandalla

et al. 2016

Theor Appl Genet

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“…The increasing knowledge about the geno-phenotypic relationships and the availability of new technologies has allowed for the development of ‘precision breeding.’ Precision breeding increases the efficiency in selection of targeted traits through genetics techniques (e.g., marker assisted selection, MAS) and shorten the selection cycle ( Gebhardt, 2013 ). These have been used to identify disease resistance genes in wild relatives and to cross them into commercial potatoes ( Gebhardt et al, 2014 ). The knockout of the vacuolar invertase gene, Vinv , in potato tubers resulted in cold induced-sweetening inhibition and high quality processed tubers ( Clasen et al, 2016 ).…”

Section: The Role Of Genomics In Potato Quality Improvementmentioning

confidence: 99%

Assuring Potato Tuber Quality during Storage: A Future Perspective

et al. 2017

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Potatoes represent an important staple food crop across the planet. Yet, to maintain tuber quality and extend availability, there is a necessity to store tubers for long periods often using industrial-scale facilities. In this context, preserving potato quality is pivotal for the seed, fresh and processing sectors. The industry has always innovated and invested in improved post-harvest storage. However, the pace of technological change has and will continue to increase. For instance, more stringent legislation and changing consumer attitudes have driven renewed interest in creating alternative or complementary post-harvest treatments to traditional chemically reliant sprout suppression and disease control. Herein, the current knowledge on biochemical factors governing dormancy, the use of chlorpropham (CIPC) as well as existing and chemical alternatives, and the effects of pre- and post-harvest factors to assure potato tuber quality is reviewed. Additionally, the role of genomics as a future approach to potato quality improvement is discussed. Critically, and through a more industry targeted research, a better mechanistic understanding of how the pre-harvest environment influences tuber quality and the factors which govern dormancy transition should lead to a paradigm shift in how sustainable storage can be achieved.

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“…Marker-assisted selection approaches, however, have the potential to increase the gain from selection (Gebhardt, 2013 ). Although many quantitative trait loci (QTL) have been identified (for review see Gebhardt et al, 2014 ), the impact of marker-assisted selection for improving truly quantitative traits in potato breeding is limited (Slater et al, 2016 ). This is attributed to the low proportion of variance explained by most of the identified QTL as well as the fact that many identified QTL are specific to a particular phenotyping environment or genetic background.…”

Section: Introductionmentioning

confidence: 99%

Prospects and Potential Uses of Genomic Prediction of Key Performance Traits in Tetraploid Potato

Stich

Inghelandt

2018

Front. Plant Sci.

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Genomic prediction is a routine tool in breeding programs of most major animal and plant species. However, its usefulness for potato breeding has not yet been evaluated in detail. The objectives of this study were to (i) examine the prospects of genomic prediction of key performance traits in a diversity panel of tetraploid potato modeling additive, dominance, and epistatic effects, (ii) investigate the effects of size and make up of training set, number of test environments and molecular markers on prediction accuracy, and (iii) assess the effect of including markers from candidate genes on the prediction accuracy. With genomic best linear unbiased prediction (GBLUP), BayesA, BayesCπ, and Bayesian LASSO, four different prediction methods were used for genomic prediction of relative area under disease progress curve after a Phytophthora infestans infection, plant maturity, maturity corrected resistance, tuber starch content, tuber starch yield (TSY), and tuber yield (TY) of 184 tetraploid potato clones or subsets thereof genotyped with the SolCAP 8.3k SNP array. The cross-validated prediction accuracies with GBLUP and the three Bayesian approaches for the six evaluated traits ranged from about 0.5 to about 0.8. For traits with a high expected genetic complexity, such as TSY and TY, we observed an 8% higher prediction accuracy using a model with additive and dominance effects compared with a model with additive effects only. Our results suggest that for oligogenic traits in general and when diagnostic markers are available in particular, the use of Bayesian methods for genomic prediction is highly recommended and that the diagnostic markers should be modeled as fixed effects. The evaluation of the relative performance of genomic prediction vs. phenotypic selection indicated that the former is superior, assuming cycle lengths and selection intensities that are possible to realize in commercial potato breeding programs.

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Dissection of Potato Complex Traits by Linkage and Association Genetics as Basis for Developing Molecular Diagnostics in Breeding Programs

Cited by 10 publications

References 213 publications

Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.)

Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.)

Assuring Potato Tuber Quality during Storage: A Future Perspective

Prospects and Potential Uses of Genomic Prediction of Key Performance Traits in Tetraploid Potato

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