Genetic mapping in polyploids

Bourke, Peter M.

doi:10.18174/444415

Cited by 5 publications

(16 citation statements)

References 375 publications

(786 reference statements)

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“…To estimate the presence of parental haplotypes in the offspring, we calculated IBD probabilities as described by Bourke ( 2014 ). A schematic overview of the method is shown in Fig.…”

Section: Methodsmentioning

confidence: 99%

“…QTL analysis was performed on block-corrected mean phenotypic values using an IBD probability model, as described before for tetraploids (Bourke 2014 ). An additive model modified from Kempthorne ( 1957 ) as suggested by Hackett et al ( 2013 , 2014 ) was modified to the hexaploid level: where α i and X i are the main effects and indicator variables for allele i , respectively.…”

Section: Methodsmentioning

confidence: 99%

“…Such haplotypes can be identified based on the configuration of neighbouring alleles. Methods for reconstruction of haplotype inheritance by estimating probabilities of identity-by-descent (IBD) in tetraploid bi-parental populations have been developed (Hackett et al 2013 ; Bourke 2014 ; Zheng et al 2016 ). Although all methods are theoretically extendible to hexaploids, the method developed by Bourke ( 2014 ) is ploidy level independent and is, therefore, directly applicable to hexaploids.…”

Section: Introductionmentioning

confidence: 99%

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An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis

et al. 2017

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Key message We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL. AbstractConstruction and use of linkage maps are challenging in hexaploids with polysomic inheritance. Full map integration requires calculations of recombination frequency between markers with complex segregation types. In addition, detection of QTL in hexaploids requires information on all six alleles at one locus for each individual. We describe a method that we used to construct a fully integrated linkage map for chrysanthemum (Chrysanthemum × morifolium, 2n = 6x = 54). A bi-parental F1 population of 406 individuals was genotyped with an 183,000 SNP genotyping array. The resulting linkage map consisted of 30,312 segregating SNP markers of all possible marker dosage types, representing nine chromosomal linkage groups and 107 out of 108 expected homologues. Synteny with lettuce (Lactuca sativa) showed local colinearity. Overall, it was high enough to number the chrysanthemum chromosomal linkage groups according to those in lettuce. We used the integrated and phased linkage map to reconstruct inheritance of parental haplotypes in the F1 population. Estimated probabilities for the parental haplotypes were used for multi-allelic QTL analyses on four traits with different underlying genetic architectures. This resulted in the identification of major QTL that were affected by multiple alleles having a differential effect on the phenotype. The presented linkage map sets a standard for future genetic mapping analyses in chrysanthemum and closely related species. Moreover, the described methods are a major step forward for linkage mapping and QTL analysis in hexaploids.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-017-2974-5) contains supplementary material, which is available to authorized users.

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“…To estimate the presence of parental haplotypes in the offspring, we calculated IBD probabilities as described by Bourke ( 2014 ). A schematic overview of the method is shown in Fig.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis

et al. 2017

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“…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). Later, the availability of the first potato reference genome of Solanum tuberosum L. group phureja DM1-3 (PGSC 2011), single-nucleotide polymorphism (SNP) marker arrays (Felcher et al 2012;Hamilton et al 2011;Uitdewilligen et al 2013) and statistical methods (Bourke et al 2018;Preedy and Hackett 2016), have enabled the construction of high-density SNP-based chromosome linkage maps in tetraploid potato (e.g. Bourke et al 2016;Hackett et al 2014;Hackett et al 2013) and the subsequent reconstruction of multi-locus haplotypes (Zheng et al 2016).…”

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

confidence: 99%

“…Bourke et al 2016;Hackett et al 2014;Hackett et al 2013) and the subsequent reconstruction of multi-locus haplotypes (Zheng et al 2016). Publicly available software packages are currently used for routine genetic analyses in tetraploid potato (Bourke et al 2018;Rosyara et al 2016). The availability of new tools, that include an optimized reference genome of the self-compatible diploid potato line Solyntus™ (SGSC 2019), are expected to further enhance the genetic analysis of traits in potato.…”

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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The identification of allelic variation in potato

Willemsen¹

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Tuber shape is an intriguing morphological trait, which displays continuous trait variation ranging from flat, round to oval and long. Initially a single locus model was proposed to explain tuber shape, where multiple alleles rather than multiple loci were proposed to explain quantitative variation (van Eck et al. 1994). Besides this major-effect QTL on chromosome 10 another minor effect QTL has been published on chromosome 2, explaining 8% of the variance (Prashar et al. 2014). To obtain a better overview on the loci contributing to variation in tuber shape a comprehensive genome wide association study (GWAS) was performed in a panel of 537 commercial potato cultivars. This confirmed that the Ro locus is the major-effect QTL, but also the minor effect QTL on chromosome 2 was found. In addition, on chromosome 10, colocalization of the major effect QTL for tuber shape and a major QTL for eye depth was observed. For the Ro locus, most significant associations were found to localize on superscaffold PGSC0003DMB000000385 on chromosome 10. To refine this region we performed a recombinant screening in a diploid population (C×E). Recombinant analysis resulted in the identification of 104 recombinants originating from the female meiosis and 27 recombinants from the male meiosis. Recombinant analysis with additional SNPs within the selected region allowed us to confine the Ro locus to a 280 kb region, located on superscaffold DMB546 (323kb). Within this region a cluster of cell wall III peroxidase genes is found. Based on the putative role of peroxidases, this gene family cluster of repeats is likely to be implicated in mediating differences in tuber shape. Keywords Solanum tuberosum, organ morphology, high resolution mapping, GWAS, haplotypes Conclusion: We present a scalable approach that accurately reconstructs haplotypes in polyploid crops. The resulting haplotypes are instrumental for analysing the haplotype composition of the potato gene pool, and haplotype based QTL discovery.

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Genetic mapping in polyploids

Cited by 5 publications

References 375 publications

An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis

An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis

Genetic and molecular approaches to valorise protein and fibre in potato

The identification of allelic variation in potato

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