Publications by authors named "Chris Maliepaard"

48 Publications

The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit.

Plant J 2020 08 21;103(3):1189-1204. Epub 2020 Jun 21.

Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands.

Tomato (Solanum lycopersicum L.) has become a popular model for genetic studies of fruit flavor in the last two decades. In this article we present a study of tomato fruit flavor, including an analysis of the genetic, metabolic and sensorial variation of a collection of contemporary commercial glasshouse tomato cultivars, followed by a validation of the associations found by quantitative trait locus (QTL) analysis of representative biparental segregating populations. This led to the identification of the major sensorial and chemical components determining fruit flavor variation and detection of the underlying QTLs. The high representation of QTL haplotypes in the breeders' germplasm suggests that there is great potential for applying these QTLs in current breeding programs aimed at improving tomato flavor. A QTL on chromosome 4 was found to affect the levels of the phenylalanine-derived volatiles (PHEVs) 2-phenylethanol, phenylacetaldehyde and 1-nitro-2-phenylethane. Fruits of near-isogenic lines contrasting for this locus and in the composition of PHEVs significantly differed in the perception of fruity and rose-hip-like aroma. The PHEV locus was fine mapped, which allowed for the identification of FLORAL4 as a candidate gene for PHEV regulation. Using a gene-editing-based (CRISPR-CAS9) reverse-genetics approach, FLORAL4 was demonstrated to be the key factor in this QTL affecting PHEV accumulation in tomato fruit.
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http://dx.doi.org/10.1111/tpj.14795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7496274PMC
August 2020

Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads.

Front Genet 2019 16;10:335. Epub 2019 Apr 16.

Bioinformatics Group, Wageningen University & Research, Wageningen, Netherlands.

DNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information using the overlaps between the reads, the haplotypes of an individual can be obtained. Using parent-offspring relationships in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can be used to correct for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to short read lengths, low genomic variation and shallow coverage). We developed a novel method, PopPoly, to estimate polyploid haplotypes in an F1-population from short sequence data by taking into consideration the transmission of the haplotypes from the parents to the offspring. In addition, this information is employed to improve genotype dosage estimation and to call missing genotypes in the population. Through simulations, we compare PopPoly to other haplotyping methods and show its better performance. We evaluate PopPoly by applying it to a tetraploid potato cross at nine genomic regions involved in tuber formation.
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http://dx.doi.org/10.3389/fgene.2019.00335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6477055PMC
April 2019

Quantifying the Power and Precision of QTL Analysis in Autopolyploids Under Bivalent and Multivalent Genetic Models.

G3 (Bethesda) 2019 07 9;9(7):2107-2122. Epub 2019 Jul 9.

Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ Wageningen, The Netherlands

New genotyping technologies, offering the possibility of high genetic resolution at low cost, have helped fuel a surge in interest in the genetic analysis of polyploid species. Nevertheless, autopolyploid species present extra challenges not encountered in diploids and allopolyploids, such as polysomic inheritance or double reduction. Here we investigate the power and precision of quantitative trait locus (QTL) analysis in outcrossing autopolyploids, comparing the results of a model that assumes random bivalent chromosomal pairing during meiosis to one that also allows for multivalents and double reduction. Through a series of simulation studies we found that marginal gains in QTL detection power are achieved using the double reduction model when multivalent pairing occurs. However, when exploring the effect of variable genotypic information across parental homologs, we found that both QTL detection power and precision require high and uniform genotypic information contents. This effect far outweighed considerations regarding bivalent or multivalent pairing (and double reduction) during meiosis. We propose that autopolyploid QTL studies be accompanied by both marker coverage information and per-homolog genotypic information coefficients (GIC). Application of these methods to an autotetraploid potato ( L.) mapping population confirmed our ability to locate and dissect QTL in highly heterozygous outcrossing autotetraploid populations.
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http://dx.doi.org/10.1534/g3.119.400269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6643892PMC
July 2019

FitTetra 2.0 - improved genotype calling for tetraploids with multiple population and parental data support.

BMC Bioinformatics 2019 Mar 20;20(1):148. Epub 2019 Mar 20.

Wageningen University and Research - Plant Breeding, Wageningen, The Netherlands.

Background: Genetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in development of molecular techniques and computational tools facilitate new methods for automated, high-throughput genotype calling in tetraploid species. We report on the upgrade of the widely-used fitTetra software aiming to improve its accuracy, which to date is hampered by technical artefacts in the data.

Results: Our upgrade of the fitTetra package is designed for a more accurate modelling of complex collections of samples. The package fits a mixture model where some parameters of the model are estimated separately for each sub-collection. When a full-sib family is analyzed, we use parental genotypes to predict the expected segregation in terms of allele dosages in the offspring. More accurate modelling and use of parental data increases the accuracy of dosage calling. We tested the package on data obtained with an Affymetrix Axiom 60 k array and compared its performance with the original version and the recently published ClusterCall tool, showing that at least 20% more SNPs could be called with our updated.

Conclusion: Our updated software package shows clearly improved performance in genotype calling accuracy. Estimation of mixing proportions of the underlying dosage distributions is separated for full-sib families (where mixture proportions can be estimated from the parental dosages and inheritance model) and unstructured populations (where they are based on the assumption of Hardy-Weinberg equilibrium). Additionally, as the distributions of signal ratios of the dosage classes can be assumed to be the same for all populations, including parental data for some subpopulations helps to improve fitting other populations as well. The R package fitTetra 2.0 is freely available under the GNU Public License as Additional file with this article.
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http://dx.doi.org/10.1186/s12859-019-2703-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425654PMC
March 2019

Multi-allelic QTL analysis of protein content in a bi-parental population of cultivated tetraploid potato.

Euphytica 2019 8;215(2):14. Epub 2019 Jan 8.

1Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.

Protein content is a key quality trait for the potato starch industry. The objective of this study was to identify allele-specific quantitative trait loci (QTLs) for tuber protein content in cultivated potato ( L.) at the tetraploid level. We analysed 496 full-sib F clones in a 3-year field trial to dissect the complex genetic architecture of soluble tuber protein content. Genotypic data from a 60K single nucleotide polymorphism (SNP) array was used for SNP dosage scoring, constructing homologue specific linkage maps and assembly of a dense integrated chromosomal linkage map. From the integrated map, probabilistic multi-locus identity-by-descent (IBD) haplotypes (alleles) were estimated and used to detect associations between the IBD haplotypes and the phenotypic trait values. Moderate levels of trait heritability were estimated between 40 and 74% that correspond with previous studies. Our contemporary naive analysis identified potential additive QTLs on chromosomes , , (top arm) and across the years. Moreover, cofactor QTL analysis identified two masked QTLs on chromosomes and (lower arm). The QTLs on chromosomes , (lower arm) and are reported here for the first time. The QTLs that we identified on chromosomes , and (top arm) show overlap with previous studies for protein content in potato. Collectively the naive QTLs explained 12 to 17% of the phenotypic variance. The underlying alleles of the QTLs provided both positive and negative effects on the phenotype. Our work uncovers the complex genetic architecture of this trait and describes potential breeding strategies for improvement. As protein has emerged as a high-value component from industrial potato starch production, the dissection of the genetic architecture and subsequent improvement of this trait by breeding has great economic and environmental relevance.
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http://dx.doi.org/10.1007/s10681-018-2331-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390886PMC
January 2019

The effect of isolation methods of tomato pollen on the results of metabolic profiling.

Metabolomics 2019 01 8;15(1):11. Epub 2019 Jan 8.

Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ, Wageningen, The Netherlands.

Introduction: Untargeted metabolomics is a powerful tool to detect hundreds of metabolites within a given tissue and to compare the metabolite composition of samples in a comprehensive manner. However, with regard to pollen research such comprehensive metabolomics approaches are yet not well developed. To enable isolation of pollen that is tightly enclosed within the anthers of the flower, such as immature pollen, the current pollen isolation protocols require the use of a watery solution. These protocols raise a number of concerns for their suitability in metabolomics analyses, in view of possible metabolic activities in the pollen and contamination with anther metabolites.

Objectives: We assessed the effect of different sample preparation procedures currently used for pollen isolation for their suitability to perform metabolomics of tomato pollen.

Methods: Pollen were isolated using different methods and the metabolic profiles were analysed by liquid chromatography-mass spectrometry (LC-MS).

Results: Our results demonstrated that pollen isolation in a watery solution led to (i) rehydration of the pollen grains, inducing marked metabolic changes in flavonoids, phenylpropanoids and amino acids and thus resulting in a metabolite profile that did not reflect the one of mature dry pollen, (ii) hydrolysis of sucrose into glucose and fructose during subsequent metabolite extraction, unless the isolated and rehydrated pollen were lyophilized prior to extraction, and (iii) contamination with anther-specific metabolites, such as alkaloids, thus compromising the metabolic purity of the pollen fraction.

Conclusion: We conclude that the current practices used to isolate pollen are suboptimal for metabolomics analyses and provide recommendations on how to improve the pollen isolation protocol, in order to obtain the most reliable metabolic profile from pollen tissue.
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http://dx.doi.org/10.1007/s11306-018-1471-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326007PMC
January 2019

Multi-environment QTL analysis of plant and flower morphological traits in tetraploid rose.

Theor Appl Genet 2018 Oct 30;131(10):2055-2069. Epub 2018 Jun 30.

Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.

Key Message: Rose morphological traits such as prickles or petal number are influenced by a few key QTL which were detected across different growing environments-necessary for genomics-assisted selection in non-target environments. Rose, one of the world's most-loved and commercially important ornamental plants, is predominantly tetraploid, possessing four rather than two copies of each chromosome. This condition complicates genetic analysis, and so the majority of previous genetic studies in rose have been performed at the diploid level. However, there may be advantages to performing genetic analyses at the tetraploid level, not least because this is the ploidy level of most breeding germplasm. Here, we apply recently developed methods for quantitative trait loci (QTL) detection in a segregating tetraploid rose population (F = 151) to unravel the genetic control of a number of key morphological traits. These traits were measured both in the Netherlands and Kenya. Since ornamental plant breeding and selection are increasingly being performed at locations other than the production sites, environment-neutral QTL are required to maximise the effectiveness of breeding programmes. We detected a number of robust, multi-environment QTL for such traits as stem and petiole prickles, petal number and stem length that were localised on the recently developed high-density SNP linkage map for rose. Our work explores the complex genetic architecture of these important morphological traits at the tetraploid level, while helping to advance the methods for marker-trait exploration in polyploid species.
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http://dx.doi.org/10.1007/s00122-018-3132-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6154034PMC
October 2018

TriPoly: haplotype estimation for polyploids using sequencing data of related individuals.

Bioinformatics 2018 11;34(22):3864-3872

Wageningen UR Plant Breeding, Postbus 386, AJ, Wageningen, The Netherlands.

Motivation: Knowledge of haplotypes, i.e. phased and ordered marker alleles on a chromosome, is essential to answer many questions in genetics and genomics. By generating short pieces of DNA sequence, high-throughput modern sequencing technologies make estimation of haplotypes possible for single individuals. In polyploids, however, haplotype estimation methods usually require deep coverage to achieve sufficient accuracy. This often renders sequencing-based approaches too costly to be applied to large populations needed in studies of Quantitative Trait Loci.

Results: We propose a novel haplotype estimation method for polyploids, TriPoly, that combines sequencing data with Mendelian inheritance rules to infer haplotypes in parent-offspring trios. Using realistic simulations of both short and long-read sequencing data for banana (Musa acuminata) and potato (Solanum tuberosum) trios, we show that TriPoly yields more accurate progeny haplotypes at low coverages compared to existing methods that work on single individuals. We also apply TriPoly to phase Single Nucleotide Polymorphisms on chromosome 5 for a family of tetraploid potato with 2 parents and 37 offspring sequenced with an RNA capture approach. We show that TriPoly haplotype estimates differ from those of the other methods mainly in regions with imperfect sequencing or mapping difficulties, as it does not rely solely on sequence reads and aims to avoid phasings that are not likely to have been passed from the parents to the offspring.

Availability And Implementation: TriPoly has been implemented in Python 3.5.2 (also compatible with Python 2.7.3 and higher) and can be freely downloaded at https://github.com/EhsanMotazedi/TriPoly.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty442DOI Listing
November 2018

polymapR-linkage analysis and genetic map construction from F1 populations of outcrossing polyploids.

Bioinformatics 2018 10;34(20):3496-3502

Plant Breeding, Wageningen University & Research, Wageningen, PB, The Netherlands.

Motivation: Polyploid species carry more than two copies of each chromosome, a condition found in many of the world's most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realize all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.

Results: polymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.

Availability And Implementation: polymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polymapR.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6184683PMC
October 2018

Tools for Genetic Studies in Experimental Populations of Polyploids.

Front Plant Sci 2018 18;9:513. Epub 2018 Apr 18.

Plant Breeding, Wageningen University & Research, Wageningen, Netherlands.

Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies also offer the promise of understanding polyploid genomes at a level which hitherto has remained elusive.
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http://dx.doi.org/10.3389/fpls.2018.00513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5915555PMC
April 2018

Genetical genomics of quality related traits in potato tubers using proteomics.

BMC Plant Biol 2018 01 23;18(1):20. Epub 2018 Jan 23.

Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, The Netherlands.

Background: Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. To get more insight into the genetic factors underlying variation in quality traits related to carbohydrate and starch metabolism and cold sweetening, we determined the protein content and composition in potato tubers using 2D-gel electrophoresis in a diploid potato mapping population. Upon analyzing we made sure that the proteins from the patatin family were excluded to ensure a better representation of the other proteins.

Results: We subsequently performed pQTL analyses for all other proteins with a sufficient representation in the population and established a relationship between proteins and 26 potato tuber quality traits (e.g. flesh colour, enzymatic discoloration) by co-localization on the genetic map and a direct correlation study of protein abundances and phenotypic traits. Over 1643 unique protein spots were detected in total over the two harvests. We were able to map pQTLs for over 300 different protein spots some of which co-localized with traits such as starch content and cold sweetening. pQTLs were observed on every chromosome although not evenly distributed over the chromosomes. The largest number of pQTLs was found for chromosome 8 and the lowest for chromosome number 10. For some 20 protein spots multiple QTLs were observed.

Conclusions: From this analysis, hotspot areas for protein QTLs were identified on chromosomes three, five, eight and nine. The hotspot on chromosome 3 coincided with a QTL previously identified for total protein content and had more than 23 pQTLs in the region from 70 to 80 cM. Some of the co-localizing protein spots associated with some of the most interesting tuber quality traits were identified, albeit far less than we had anticipated at the onset of the experiments.
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http://dx.doi.org/10.1186/s12870-018-1229-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5781343PMC
January 2018

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

Theor Appl Genet 2017 Dec 29;130(12):2527-2541. Epub 2017 Aug 29.

Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, The Netherlands.

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. Construction 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.
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http://dx.doi.org/10.1007/s00122-017-2974-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668331PMC
December 2017

Genetic complexity of miscanthus cell wall composition and biomass quality for biofuels.

BMC Genomics 2017 05 25;18(1):406. Epub 2017 May 25.

Wageningen UR Plant Breeding, Wageningen University and Research, PO Box 386, 6700 AJ, Wageningen, Netherlands.

Background: Miscanthus sinensis is a high yielding perennial grass species with great potential as a bioenergy feedstock. One of the challenges that currently impedes commercial cellulosic biofuel production is the technical difficulty to efficiently convert lignocellulosic biomass into biofuel. The development of feedstocks with better biomass quality will improve conversion efficiency and the sustainability of the value-chain. Progress in the genetic improvement of biomass quality may be substantially expedited by the development of genetic markers associated to quality traits, which can be used in a marker-assisted selection program.

Results: To this end, a mapping population was developed by crossing two parents of contrasting cell wall composition. The performance of 182 F1 offspring individuals along with the parents was evaluated in a field trial with a randomized block design with three replicates. Plants were phenotyped for cell wall composition and conversion efficiency characters in the second and third growth season after establishment. A new SNP-based genetic map for M. sinensis was built using a genotyping-by-sequencing (GBS) approach, which resulted in 464 short-sequence uniparental markers that formed 16 linkage groups in the male map and 17 linkage groups in the female map. A total of 86 QTLs for a variety of biomass quality characteristics were identified, 20 of which were detected in both growth seasons. Twenty QTLs were directly associated to different conversion efficiency characters. Marker sequences were aligned to the sorghum reference genome to facilitate cross-species comparisons. Analyses revealed that for some traits previously identified QTLs in sorghum occurred in homologous regions on the same chromosome.

Conclusion: In this work we report for the first time the genetic mapping of cell wall composition and bioconversion traits in the bioenergy crop miscanthus. These results are a first step towards the development of marker-assisted selection programs in miscanthus to improve biomass quality and facilitate its use as feedstock for biofuel production.
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http://dx.doi.org/10.1186/s12864-017-3802-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445440PMC
May 2017

Partial preferential chromosome pairing is genotype dependent in tetraploid rose.

Plant J 2017 Apr 20;90(2):330-343. Epub 2017 Mar 20.

Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.

It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or allopolyploid, leading to the term 'segmental allopolyploid' to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra-high-density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re-mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion-phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra-dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co-linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.
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http://dx.doi.org/10.1111/tpj.13496DOI Listing
April 2017

Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study.

Brief Bioinform 2018 05;19(3):387-403

Bioinformatics Group, Wageningen University and Research, The Netherlands.

Haplotypes are the units of inheritance in an organism, and many genetic analyses depend on their precise determination. Methods for haplotyping single individuals use the phasing information available in next-generation sequencing reads, by matching overlapping single-nucleotide polymorphisms while penalizing post hoc nucleotide corrections made. Haplotyping diploids is relatively easy, but the complexity of the problem increases drastically for polyploid genomes, which are found in both model organisms and in economically relevant plant and animal species. Although a number of tools are available for haplotyping polyploids, the effects of the genomic makeup and the sequencing strategy followed on the accuracy of these methods have hitherto not been thoroughly evaluated.We developed the simulation pipeline haplosim to evaluate the performance of three haplotype estimation algorithms for polyploids: HapCompass, HapTree and SDhaP, in settings varying in sequencing approach, ploidy levels and genomic diversity, using tetraploid potato as the model. Our results show that sequencing depth is the major determinant of haplotype estimation quality, that 1 kb PacBio circular consensus sequencing reads and Illumina reads with large insert-sizes are competitive and that all methods fail to produce good haplotypes when ploidy levels increase. Comparing the three methods, HapTree produces the most accurate estimates, but also consumes the most resources. There is clearly room for improvement in polyploid haplotyping algorithms.
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http://dx.doi.org/10.1093/bib/bbw126DOI Listing
May 2018

High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array.

Hortic Res 2016 26;3:16052. Epub 2016 Oct 26.

Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.

Dense genetic maps create a base for QTL analysis of important traits and future implementation of marker-assisted breeding. In tetraploid rose, the existing linkage maps include <300 markers to cover 28 linkage groups (4 homologous sets of 7 chromosomes). Here we used the 68k WagRhSNP Axiom single-nucleotide polymorphism (SNP) array for rose, in combination with SNP dosage calling at the tetraploid level, to genotype offspring from the garden rose cultivar 'Red New Dawn'. The offspring proved to be not from a single bi-parental cross. In rose breeding, crosses with unintended parents occur regularly. We developed a strategy to separate progeny into putative populations, even while one of the parents was unknown, using principle component analysis on pairwise genetic distances based on sets of selected SNP markers that were homozygous, and therefore uninformative for one parent. One of the inferred populations was consistent with self-fertilization of 'Red New Dawn'. Subsequently, linkage maps were generated for a bi-parental and a self-pollinated population with 'Red New Dawn' as the common maternal parent. The densest map, for the selfed parent, had 1929 SNP markers on 25 linkage groups, covering 1765.5 cM at an average marker distance of 0.9 cM. Synteny with the strawberry () genome was extensive. Rose ICM1 corresponded to pseudochromosome 7 (Fv7), ICM4 to Fv4, ICM5 to Fv3, ICM6 to Fv2 and ICM7 to Fv5. Rose ICM2 corresponded to parts of pseudochromosomes 1 and 6, whereas ICM3 is syntenic to the remainder of Fv6.
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http://dx.doi.org/10.1038/hortres.2016.52DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080978PMC
October 2016

Inheritance and QTL analysis of the determinants of flower color in tetraploid cut roses.

Mol Breed 2016 7;36(10):143. Epub 2016 Oct 7.

Wageningen UR Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.

The success of cut rose cultivars is a direct result of their aesthetic value. The rose industry thrives on novelty, and the production of novel flower color has been extensively studied. The most popular color is red, and it is, therefore, important for breeders to produce a good red cultivar. The final visible color of the flower is a combination of a number of factors including the type of anthocyanin accumulating, modifications to the anthocyanidin molecule, co-pigmentation and vacuolar pH. Here, we analyze the quantitative variation of the biochemical constituents of flower color in a tetraploid rose population and combine this with marker information in the segregating rose population to map the chromosomal locations of putative QTLs for flower color traits. Within our tetraploid population, we found a number of QTLs that were mapped on ICM 1, 2, 6 and 7. We were able to show the effect of the different QTLs on the final visible color of the flower from salmon to dark red.
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http://dx.doi.org/10.1007/s11032-016-0565-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055553PMC
October 2016

Integrating haplotype-specific linkage maps in tetraploid species using SNP markers.

Theor Appl Genet 2016 Nov 25;129(11):2211-2226. Epub 2016 Aug 25.

Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, P.O. Box 386, 6708 PB, Wageningen, The Netherlands.

Key Message: Linkage mapping can help unravel the complexities of polyploid genomes. Here, we integrate haplotype-specific linkage maps in autotetraploid potato and explore the possibilities for mapping in other polyploid species. High-density linkage mapping in autopolyploid species has become possible in recent years given the increasing number of molecular markers now available through modern genotyping platforms. Such maps along with larger experimental populations are needed before we can obtain sufficient accuracy to make marker-trait association studies useful in practice. Here, we describe a method to create genetic linkage maps for an autotetraploid species with large numbers of markers and apply it to an F1 population of tetraploid potato (Solanum tuberosum L.) of 235 individuals genotyped using a 20K SNP array. SNP intensity values were converted to allele dosages after which we calculated pairwise maximum likelihood estimates of recombination frequencies between all marker segregation types under the assumption of random bivalent pairing. These estimates were used in the clustering of markers into linkage groups and their subsequent ordering into 96 homologue maps. The homologue maps were integrated per chromosome, resulting in a total map length of 1061 cM from 6910 markers covering all 12 potato chromosomes. We examined the questions of marker phasing and binning and propose optimal strategies for both. We also investigated the effect of quadrivalent formation and preferential pairing on recombination frequency estimation and marker phasing, which is of great relevance not only for potato but also for genetic studies in other tetraploid species for which the meiotic pairing behaviour is less well understood.
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http://dx.doi.org/10.1007/s00122-016-2768-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069339PMC
November 2016

Multi-trait QTL analysis for agronomic and quality characters of Agaricus bisporus (button mushrooms).

AMB Express 2016 Dec 8;6(1):67. Epub 2016 Sep 8.

Wageningen UR Plant Breeding, Wageningen University & Research Centre, Droevendaalsestaag 1, 6700 AA, Wageningen, The Netherlands.

The demand for button mushrooms of high quality is increasing. Superior button mushroom varieties require the combination of multiple traits to maximize productivity and quality. Very often these traits are correlated and should, therefore, be evaluated together rather than as single traits. In order to unravel the genetic architecture of multiple traits of Agaricus bisporus and the genetic correlations among traits, we have investigated a total of six agronomic and quality traits through multi-trait QTL analyses in a mixed-model. Traits were evaluated in three heterokaryon sets. Significant phenotypic correlations were observed among traits. For instance, earliness (ER) correlated to firmness (FM), cap color, and compost colonization, and FM correlated to scales (SC). QTLs of different traits located on the same chromosomes genetically explains the phenotypic correlations. QTL detected on chromosome 10 mainly affects three traits, i.e., ER, FM and SC. It explained 31.4 % phenotypic variation of SC on mushroom cap (heterokaryon Set 1), 14.9 % that of the FM (heterokaryon Set 3), and 14.2 % that of ER (heterokaryon Set 3). High value alleles from the wild parental line showed beneficial effects for several traits, suggesting that the wild germplasm is a valuable donor in terms of those traits. Due to the limitations of recombination pattern, we only made a start at understanding the genetic base for several agronomic and quality traits in button mushrooms.
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http://dx.doi.org/10.1186/s13568-016-0239-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5016490PMC
December 2016

Systems genetics reveals key genetic elements of drought induced gene regulation in diploid potato.

Plant Cell Environ 2016 09 29;39(9):1895-908. Epub 2016 Jun 29.

Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.

In plants, tolerance to drought stress is a result of numerous minor effect loci in which transcriptional regulation contributes significantly to the observed phenotypes. Under severe drought conditions, a major expression quantitative trait loci hotspot was identified on chromosome five in potato. A putative Nuclear factor y subunit C4 was identified as key candidate in the regulatory cascade in response to drought. Further investigation of the eQTL hotspots suggests a role for a putative Homeobox leucine zipper protein 12 in relation to drought in potato. Genes strongly co-expressed with Homeobox leucine zipper protein 12 were plant growth regulators responsive to water deficit stress in Arabidopsis thaliana, implying a possible conserved mechanism. Integrative analysis of genetic, genomic, phenotypic and transcriptomic data provided insights in the downstream functional components of the drought response. The abscisic acid- and environmental stress-inducible protein TAS14 was highly induced by severe drought in potato and acts as a reliable biomarker for the level of stress perceived by the plant. The systems genetics approach supported a role for multiple genes responsive to severe drought stress of Solanum tuberosum. The combination of gene regulatory networks, expression quantitative trait loci mapping and phenotypic analysis proved useful for candidate gene selection.
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http://dx.doi.org/10.1111/pce.12744DOI Listing
September 2016

Integration of multi-omics data for prediction of phenotypic traits using random forest.

BMC Bioinformatics 2016 Jun 6;17 Suppl 5:180. Epub 2016 Jun 6.

Wageningen UR Plant Breeding, Wageningen University & Research Centre, PO Box 6700 AJ, Wageningen, The Netherlands.

Background: In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of tuber quality phenotypic data from a diploid segregating mapping population of potato. In this study we present an approach to integrate these ~ omics data sets for the purpose of predicting phenotypic traits. This gives us networks of relatively small sets of interrelated ~ omics variables that can predict, with higher accuracy, a quality trait of interest.

Results: We used Random Forest regression for integrating multiple ~ omics data for prediction of four quality traits of potato: tuber flesh colour, DSC onset, tuber shape and enzymatic discoloration. For tuber flesh colour beta-carotene hydroxylase and zeaxanthin epoxidase were ranked first and forty-fourth respectively both of which have previously been associated with flesh colour in potato tubers. Combining all the significant genes, LC-peaks, GC-peaks and proteins, the variation explained was 75 %, only slightly more than what gene expression or LC-MS data explain by themselves which indicates that there are correlations among the variables across data sets. For tuber shape regressed on the gene expression, LC-MS, GC-MS and proteomics data sets separately, only gene expression data was found to explain significant variation. For DSC onset, we found 12 significant gene expression, 5 metabolite levels (GC) and 2 proteins that are associated with the trait. Using those 19 significant variables, the variation explained was 45 %. Expression QTL (eQTL) analyses showed many associations with genomic regions in chromosome 2 with also the highest explained variation compared to other chromosomes. Transcriptomics and metabolomics analysis on enzymatic discoloration after 5 min resulted in 420 significant genes and 8 significant LC metabolites, among which two were putatively identified as caffeoylquinic acid methyl ester and tyrosine.

Conclusions: In this study, we made a strategy for selecting and integrating multiple ~ omics data using random forest method and selected representative individual peaks for networks based on eQTL, mQTL or pQTL information. Network analysis was done to interpret how a particular trait is associated with gene expression, metabolite and protein data.
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http://dx.doi.org/10.1186/s12859-016-1043-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905610PMC
June 2016

Genetic Control of Water and Nitrate Capture and Their Use Efficiency in Lettuce (Lactuca sativa L.).

Front Plant Sci 2016 30;7:343. Epub 2016 Mar 30.

Plant Sciences, Centre for Crop Systems Analysis, Wageningen University Wageningen, Netherlands.

Robustness in lettuce, defined as the ability to produce stable yields across a wide range of environments, may be associated with below-ground traits such as water and nitrate capture. In lettuce, research on the role of root traits in resource acquisition has been rather limited. Exploring genetic variation for such traits and shoot performance in lettuce across environments can contribute to breeding for robustness. A population of 142 lettuce cultivars was evaluated during two seasons (spring and summer) in two different locations under organic cropping conditions, and water and nitrate capture below-ground and accumulation in the shoots were assessed at two sampling dates. Resource capture in each soil layer was measured using a volumetric method based on fresh and dry weight difference in the soil for soil moisture, and using an ion-specific electrode for nitrate. We used these results to carry out an association mapping study based on 1170 single nucleotide polymorphism markers. We demonstrated that our indirect, high-throughput phenotyping methodology was reliable and capable of quantifying genetic variation in resource capture. QTLs for below-ground traits were not detected at early sampling. Significant marker-trait associations were detected across trials for below-ground and shoot traits, in number and position varying with trial, highlighting the importance of the growing environment on the expression of the traits measured. The difficulty of identifying general patterns in the expression of the QTLs for below-ground traits across different environments calls for a more in-depth analysis of the physiological mechanisms at root level allowing sustained shoot growth.
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http://dx.doi.org/10.3389/fpls.2016.00343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4812043PMC
April 2016

Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions.

Front Plant Sci 2015 1;6:1032. Epub 2015 Dec 1.

Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen University Wageningen, Netherlands.

The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding.
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http://dx.doi.org/10.3389/fpls.2015.01032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664704PMC
December 2015

A Systems Genetics Approach Identifies Gene Regulatory Networks Associated with Fatty Acid Composition in Brassica rapa Seed.

Plant Physiol 2016 Jan 30;170(1):568-85. Epub 2015 Oct 30.

Wageningen UR Plant Breeding, Wageningen University and Research, 6708PB Wageningen, The Netherlands (R.K.B., D.P.D.C., D.X., J.B., R.G.F.V., C.M., G.B.);Centre for BioSystems Genomics, 6708PB Wageningen, The Netherlands (R.K.B., R.G.F.V., C.M.);Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, Korea (M.J.); andNational Research Council of Canada, Saskatoon, Saskatchewan, Canada SK S7N 0W9 (K.B., P.F.)

Fatty acids in seeds affect seed germination and seedling vigor, and fatty acid composition determines the quality of seed oil. In this study, quantitative trait locus (QTL) mapping of fatty acid and transcript abundance was integrated with gene network analysis to unravel the genetic regulation of seed fatty acid composition in a Brassica rapa doubled haploid population from a cross between a yellow sarson oil type and a black-seeded pak choi. The distribution of major QTLs for fatty acids showed a relationship with the fatty acid types: linkage group A03 for monounsaturated fatty acids, A04 for saturated fatty acids, and A05 for polyunsaturated fatty acids. Using a genetical genomics approach, expression quantitative trait locus (eQTL) hotspots were found at major fatty acid QTLs on linkage groups A03, A04, A05, and A09. An eQTL-guided gene coexpression network of lipid metabolism-related genes showed major hubs at the genes BrPLA2-ALPHA, BrWD-40, a number of seed storage protein genes, and the transcription factor BrMD-2, suggesting essential roles for these genes in lipid metabolism. Three subnetworks were extracted for the economically important and most abundant fatty acids erucic, oleic, linoleic, and linolenic acids. Network analysis, combined with comparison of the genome positions of cis- or trans-eQTLs with fatty acid QTLs, allowed the identification of candidate genes for genetic regulation of these fatty acids. The generated insights in the genetic architecture of fatty acid composition and the underlying complex gene regulatory networks in B. rapa seeds are discussed.
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http://dx.doi.org/10.1104/pp.15.00853DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704567PMC
January 2016

The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map.

Genetics 2015 Nov 15;201(3):853-63. Epub 2015 Sep 15.

Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen 6708 PB, The Netherlands

The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species. In this study, we produced a high-density linkage map of tetraploid potato and used it to identify regions of double reduction in a biparental mapping population. The frequency of multivalents required to produce this degree of double reduction was determined through simulation. We also determined the effect that multivalents or preferential pairing between homologous chromosomes has on linkage mapping. Low levels of multivalents or preferential pairing do not adversely affect map construction when highly informative marker types and phases are used. We reveal the double-reduction landscape in tetraploid potato, clearly showing that this phenomenon increases with distance from the centromeres.
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http://dx.doi.org/10.1534/genetics.115.181008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649655PMC
November 2015

Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.).

Front Plant Sci 2015 21;6:249. Epub 2015 Apr 21.

Wageningen UR Plant Breeding, Wageningen University and Research Centre Wageningen, Netherlands.

In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
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http://dx.doi.org/10.3389/fpls.2015.00249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404716PMC
May 2015

Genetic variation, heritability and genotype by environment interaction of morphological traits in a tetraploid rose population.

BMC Genet 2014 Dec 20;15:146. Epub 2014 Dec 20.

Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, the Netherlands.

Background: Global trade has ensured that the ornamental horticulture continues to grow worldwide, with rose hybrids being the most economically important genus (Rosa x hybrida). Due to changes in global trade and an increase in energy costs the ornamental industry has seen a shift in the production and sale of flowers from the US and Europe alone to production in Africa and Latin America. As Kenya is a major exporter of roses to Europe we studied the genetic variation and heritability of specific morphological traits in a tetraploid population grown in the Netherlands and in Kenya. The aim was to estimate genotype by environment interaction (G × E) and to investigate the implications of (G × E) for rose breeding.

Results: A tetraploid rose population (K5) from a cross between two tetraploid parents was field tested over two seasons in the Netherlands (summer and winter) and two locations in Kenya (Nairobi and Njoro). Ten traits were compared per genotype across the four environments. There were differences in trait association across the four environments showing that the traits were partially influenced by the environment. The traits that had a low ratio of σ(2) ge/σ(2) g also showed a high value for heritability. For the traits number of petals, prickles on petioles, prickles on stems the interaction is minimal. For the traits chlorophyll content, stem width and side shoots we observed a much higher interaction ratio of 0.83, 1.43 and 3.13 respectively. The trait number of petals had the highest heritability of 0.96 and the lowest σ(2) ge/σ(2) g ratio (0.08). The trait number of side shoots (SS) with the lowest heritability (0.40) also had the highest σ(2) ge/σ(2) g ratio of 3.13.

Conclusion: Attained by this experiment showed that we have different magnitudes of non-crossover G × E interactions. For the traits number of petals, prickles on stems and prickles on petioles with a low interaction and high heritability, selection can be done at any of the environments. Thus, these traits can be confirmed at the breeding site. For the traits stem width, side shoots and chlorophyll content that had a higher interaction selection for or against these traits should be done at the production location or at least be verified there.
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http://dx.doi.org/10.1186/s12863-014-0146-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4293809PMC
December 2014

Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes.

BMC Genomics 2013 Dec 1;14:840. Epub 2013 Dec 1.

Wageningen UR Plant Breeding, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.

Background: Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverse B. rapa morphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study in B. rapa seed.

Results: Seed developmental stages were similar in developing seeds of pak choi and yellow sarson of B. rapa; however, the colour of embryo and seed coat differed among these two morphotypes. In this study, most transcriptional changes occurred between 25 and 35 DAP, which shows that the timing of seed developmental processes in B. rapa is at later developmental stages than in the related species B. napus. Using a Weighted Gene Co-expression Network Analysis (WGCNA), we identified 47 "gene modules", of which 27 showed a significant association with temporal and/or genotypic variation. An additional hierarchical cluster analysis identified broad spectra of gene expression patterns during seed development. The predominant variation in gene expression was according to developmental stages rather than morphotype differences. Since lipids are the major storage compounds of Brassica seeds, we investigated in more detail the regulation of lipid metabolism. Four co-regulated gene clusters were identified with 17 putative cis-regulatory elements predicted in their 1000 bp upstream region, either specific or common to different lipid metabolic pathways.

Conclusions: This is the first study of genome-wide profiling of transcript abundance during seed development in B. rapa. The identification of key physiological events, major expression patterns, and putative cis-regulatory elements provides useful information to construct gene regulatory networks in B. rapa developing seeds and provides a starting point for a genetical genomics study of seed quality traits.
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http://dx.doi.org/10.1186/1471-2164-14-840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046715PMC
December 2013

Relation between HLA genes, human skin volatiles and attractiveness of humans to malaria mosquitoes.

Infect Genet Evol 2013 Aug 18;18:87-93. Epub 2013 May 18.

Laboratory of Entomology, Wageningen University and Research Centre, P.O. Box 8031, 6700 EH Wageningen, The Netherlands.

Chemical cues are considered to be the most important cues for mosquitoes to find their hosts and humans can be ranked for attractiveness to mosquitoes based on the chemical cues they emit. Human leukocyte antigen (HLA) genes are considered to be involved in the regulation of human body odor and may therefore affect human attractiveness to mosquitoes, and hence, affect the force of malaria transmission. In the present study the correlations between HLA profiles, human skin volatiles and human attractiveness to the malaria mosquito Anopheles gambiae Giles sensu stricto were examined. Skin emanations of 48 volunteers were collected by rubbing a foot over glass beads. Previously the attractiveness of these emanations to An. gambiae was determined. In this study, the chemical composition of these emanations was determined by gas chromatography-mass spectroscopy (GC-MS) and blood samples of all volunteers were taken for HLA analysis. Hierarchical cluster analysis (HCA), partial least squares discriminant analysis (PLS-DA), Fisher's exact test and random forest regression were used to test for correlations between individuals classified as either highly or poorly attractive to mosquitoes and their HLA profile and volatile composition. HLA profiling suggests that people carrying HLA gene Cw∗07 are more attractive to mosquitoes. GC-MS revealed that limonene, 2-phenylethanol and 2-ethyl-1-hexanol were associated with individuals that were poorly attractive to An.gambiae and lactic acid, 2-methylbutanoic acid, tetradecanoic acid and octanal with individuals that were highly attractive. Such compounds offer potential for disruption of mosquito behavior in malaria intervention programs.
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http://dx.doi.org/10.1016/j.meegid.2013.05.009DOI Listing
August 2013