Development and application of a 20K SNP array in potato

Vos, Peter G.

doi:10.18174/392278

Cited by 6 publications

(16 citation statements)

References 124 publications

(313 reference statements)

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“…These included both modern and old individuals from different market segments and geographic origins. Analysis of population structure in the panel displayed three sub-populations, as reported earlier (D'hoop et al 2008;Vos 2016). These sub-populations, hereafter referred to as BProcessing^, BOtherâ nd BStarch^, were used for analyses.…”

Section: Germplasm Collectionmentioning

confidence: 96%

“…Membership probability estimates from thirty runs were averaged and used to assign each individual to cluster groups (sub-populations). The sub-populations were denoted as BProcessing^, BOther^and BStarch^, based on prior knowledge that these three sub-populations existed in the panel (D'hoop et al 2008;Vos 2016).…”

Section: Population Structure Analysismentioning

confidence: 99%

“…For naive analyses, permutation testing was carried out with N = 1000 permutations at α = 0.05 to define the threshold value (−log 10 (P) = 5.0) (Churchill and Doerge 1994) (−log 10 (P) = 5.0). The support intervals of QTLs were set at 1.5 Mbp for non-introgressed regions and 2.5 Mbp for introgressed regions as described by Vos (2016).…”

Section: Significance Threshold and Qtl Support Intervalmentioning

confidence: 99%

“…Optimization of GWAS will likely identify loci with minor effects or those caused by rare variants with a low allele frequency. Certainly the population structure, distribution of the phenotypic values, as well as the ascertainment bias of SNPs in marker arrays should be considered beforehand as proposed by Vos (2016).…”

Section: Missing Heritabilitymentioning

confidence: 99%

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Genome-wide association analysis in tetraploid potato reveals four QTLs for protein content

et al. 2019

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Valorisation of tuber protein is relevant for the potato starch industry to create added-value and reduce impact on the environment. Hence, protein content has emerged as a key quality trait for innovative potato breeders. In this study, we estimated trait heritability, explored the relationship between protein content and tuber under-water weight (UWW), inferred haplotypes underlying quantitative trait loci (QTLs) and pinpointed candidate genes. We used a panel of varieties (N = 277) that was genotyped using the SolSTW 20 K Infinium single-nucleotide polymorphism (SNP) marker array. Protein content data were collected from multiple environments and years. Our genome-wide association study (GWAS) identified QTLs on chromosomes 3, 5, 7 and 12. Alleles of StCDF1 (maturity) were associated with QTLs found on chromosome 5. The QTLs on chromosomes 7 and 12 are presented here for the first time, whereas those on chromosomes 3 and 5 co-localized with loci reported in earlier studies. The candidate genes underlying the QTLs proposed here are relevant for functional studies. This study provides resources for genomics-enabled breeding for protein content in potato.

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Section: Germplasm Collectionmentioning

confidence: 96%

Section: Population Structure Analysismentioning

confidence: 99%

Section: Significance Threshold and Qtl Support Intervalmentioning

confidence: 99%

Section: Missing Heritabilitymentioning

confidence: 99%

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Genome-wide association analysis in tetraploid potato reveals four QTLs for protein content

et al. 2019

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“…This progress has allowed the development of new tools to dissect traits and to enhance breeding. Over the years, quantitative trait locus (QTL) mapping in populations (Brigneti et al 1997;Bryan et al 2002) and genome-wide association studies (GWAS) in variety panels Kloosterman et al 2013;Vos 2016) have been shown to function as suitable tools to perform genetic analysis in potato. Since the year 1980, genetic markers were developed and applied to construct chromosomal linkage maps in diploid potato (Bonierbale et al 1988;Van Os et al 2006).…”

Section: Modern Tools For the Dissection And Improvement Of Potato Trmentioning

confidence: 99%

Genetic and molecular approaches to valorise protein and fibre in potato

Klaassen¹

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Table of contents Chapter 1 General introduction Chapter 2 Genome-wide association analysis in tetraploid potato reveals four QTLs for protein content Chapter 3 Multi-allelic QTL analysis of protein content in a bi-parental population of cultivated tetraploid potato Chapter 4 Overexpression of a putative nitrate transporter (StNPF1.11) increases plant height, leaf chlorophyll content and tuber protein content of young potato plants Chapter 5 RG-I galactan side-chains are involved in the regulation of the water-binding capacity of potato cell walls

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Overview on domestication, breeding, genetic gain and improvement of tuber quality traits of potato using fast forwarding technique (GWAS): A review

et al. 2021

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Tuber quality is the subject of great interest among the processing industry and consumers worldwide. Being a polygenic trait, its enhancement requires a systematic understanding of their genetic complexity. Molecular genetics offered valuable solutions to the challenging endeavours of slow genetic gains in conventional potato breeding. With the advent of linkage maps, molecular markers and availability of next‐generation sequencing (NGS) platforms, the plant breeding programmes worldwide have achieved faster genetic gain due to marker‐assisted selection (MAS). Linkage mapping detects QTLs in biparental population; alternatively, genomic and phenotypic differences can be identified by extensive genotyping and phenotyping of a germplasm panel depicting natural biological diversity to reveal QTLs, in other words, marker‐trait associations. Due to advancements in the fields of genome sequencing and bioinformatics, researchers have preferred to use the genome‐wide association mapping (GWAS) method for detecting QTLs due to its higher resolution. In potato, GWAS identified causative allele(s)/loci and provides reliable platform for the development of diagnostic SNP markers by employing Infinium SolCAP SNP array. Later, KASP validation markers can be developed to be used as selection markers in order to bred improved cultivars. The current review focuses on recently used approaches for genetic analyses (linkage mapping or association mapping) regarding potato tuber quality traits, provides comprehensive knowledge about breeding, genetic gain, basic genetic and statistical GWAS concepts and subsequently highlights the genetic discoveries using GWAS and KASP markers.

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Development and application of a 20K SNP array in potato

Cited by 6 publications

References 124 publications

Genome-wide association analysis in tetraploid potato reveals four QTLs for protein content

Genome-wide association analysis in tetraploid potato reveals four QTLs for protein content

Genetic and molecular approaches to valorise protein and fibre in potato

Overview on domestication, breeding, genetic gain and improvement of tuber quality traits of potato using fast forwarding technique (GWAS): A review

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