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12. RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

Author

Iezzoni, Amy F., McFerson, Jim, Luby, James, Gasic, Ksenija, Whitaker, Vance, Bassil, Nahla, Yue, Chengyan, Gallardo, Karina, McCracken, Vicki, Coe, Michael, Hardner, Craig, Zurn, Jason D., Hokanson, Stan, van de Weg, Eric, Jung, Sook, Main, Dorrie, da Silva Linge, Cassia, Vanderzande, Stijn, Davis, Thomas M., Mahoney, Lise L., Finn, Chad, and Peace, Cameron

Published
2020
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15. Smooth Descent : A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors

Author

Thérèse Navarro, Alejandro, Bourke, Peter M., van de Weg, Eric, Clot, Corentin R., Arens, Paul, Finkers, Richard, Maliepaard, Chris, Thérèse Navarro, Alejandro, Bourke, Peter M., van de Weg, Eric, Clot, Corentin R., Arens, Paul, Finkers, Richard, and Maliepaard, Chris

Abstract

Linkage mapping is an approach to order markers based on recombination events. Mapping algorithms cannot easily handle genotyping errors, which are common in high-throughput genotyping data. To solve this issue, strategies have been developed, aimed mostly at identifying and eliminating these errors. One such strategy is SMOOTH, an iterative algorithm to detect genotyping errors. Unlike other approaches, SMOOTH can also be used to impute the most probable alternative genotypes, but its application is limited to diploid species and to markers heterozygous in only one of the parents. In this study we adapted SMOOTH to expand its use to any marker type and to autopolyploids with the use of identity-by-descent probabilities, naming the updated algorithm Smooth Descent (SD). We applied SD to real and simulated data, showing that in the presence of genotyping errors this method produces better genetic maps in terms of marker order and map length. SD is particularly useful for error rates between 5% and 20% and when error rates are not homogeneous among markers or individuals. With a starting error rate of 10%, SD reduced it to ∼5% in diploids, ∼7% in tetraploids and ∼8.5% in hexaploids. Conversely, the correlation between true and estimated genetic maps increased by 0.03 in tetraploids and by 0.2 in hexaploids, while worsening slightly in diploids (∼0.0011). We also show that the combination of genotype curation and map re-estimation allowed us to obtain better genetic maps while correcting wrong genotypes. We have implemented this algorithm in the R package Smooth Descent.

Published
2023

16. Linkage maps and genotype data of strawberry produced with skim-sequencing data

Author

Thérèse Navarro, Alejandro, Bourke, Peter, Willemsen, Johan, van Dijk, Thijs, de Alves Freitas Guedes, Fernanda, Finkers, Richard, Arens, Paul, van de Weg, Eric, Visser, Richard, Maliepaard, Chris, Thérèse Navarro, Alejandro, Bourke, Peter, Willemsen, Johan, van Dijk, Thijs, de Alves Freitas Guedes, Fernanda, Finkers, Richard, Arens, Paul, van de Weg, Eric, Visser, Richard, and Maliepaard, Chris

Abstract

The following set of files contain the results and scripts to produce those results, described in Chapter 5 of the PhD thesis of Alejandro Thérèse Navarro, entitled "How to map a million markers: linkage mapping of skim-sequencing data in strawberry". In this study, a large dataset of markers produced by whole genome resequecning of a strawberry (Fragaria x ananassa) biparental population are used to generate linkage maps. To that end the software Smooth Descent is used, since it is oriented to obtaining linkage maps in usin low quality (error-prone) genotype data. With this methodology we were able to produce a linkage map of 27 out of 28 chromosomes of strawberry which containing 1.85M markers in ~2400 unique genetic mpositions. We also compare this map with a linkage map produced using SNP array data and with the genome sequence assembly "Camarosa".

Published
2023

17. Strawberry volatile organic compounds metabolomic data and QTL study

Author

Thérèse Navarro, Alejandro, Zafra, Olga, Tikunov, Yury, Peeters, Carel, Willemsen, Johan, van Dijk, Thijs, Bourke, Peter, van de Weg, Eric, Visser, Richard, Maliepaard, Chris, Thérèse Navarro, Alejandro, Zafra, Olga, Tikunov, Yury, Peeters, Carel, Willemsen, Johan, van Dijk, Thijs, Bourke, Peter, van de Weg, Eric, Visser, Richard, and Maliepaard, Chris

Abstract

This dataset contains the supplementary materials of the publication "Multivariate QTL approach reveals a major regulator of terpenoid production and other volatiles in strawberry" of the same authors. In this study we extracted volatile organic compounds from several strawberry samples and analysed their identity and abundance. We used this volatile data to perform an extensive multivariate QTL study, the results of which can be found in this dataset. All analysis, results and figures can be reproduced using the folder included in the supplementary data 1. If you want to reproduce part or all of our analysis, only download sup data 1. If you only need one of our results or data table you can download them individually: Sup data 2: abundances of volatile organic compounds from a biparental and diverse panel (GWAS) population. Sup data 3 and 4: p-value tables for several models and all metabolites as well as multivariate traits (see publication for more information). Sup tables 1 and 2: significant QTL signals for each trait individually and summarised per QTL locus. Sup table 3: previously reported VOC QTLs in strawberry, with positions imputed in the Royal Royce genome. Sup table 4: metadata about all the identified compounds on this and previous studies. Sup table 5: SNP array positions imputed in the "Royal Royce" genome assembly.

Published
2023

19. Apple whole genome sequences: recent advances and new prospects

Author

Peace, Cameron P., Bianco, Luca, Troggio, Michela, van de Weg, Eric, Howard, Nicholas P., Cornille, Amandine, Durel, Charles-Eric, Myles, Sean, Migicovsky, Zoë, Schaffer, Robert J., Costes, Evelyne, Fazio, Gennaro, Yamane, Hisayo, van Nocker, Steve, Gottschalk, Chris, Costa, Fabrizio, Chagné, David, Zhang, Xinzhong, Patocchi, Andrea, Gardiner, Susan E., Hardner, Craig, Kumar, Satish, Laurens, Francois, Bucher, Etienne, Main, Dorrie, Jung, Sook, and Vanderzande, Stijn

Published
2019
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22. Parametric mapping of QTL for resistance to European canker in apple in 'Aroma' x 'Discovery'

Author

Skytte af Sätra, Jonas, Odilbekov, Firuz, Ingvarsson, Pär, van de Weg, Eric, and Gustavsson, Larisa

Subjects
Agricultural Science
Abstract

Resistance to European canker (Neonectria ditissima) in apple is currently one of the most important breeding targets for commercial production in Sweden. Previous research has identified significant genetic variation in susceptibility to the disease, with the local Swedish cultivar 'Aroma' considered as one of the most resistant cultivars. Identification of genetic regions underlying the resistance of this cultivar would be a valuable tool for future breeding. Thus, we performed Bayesian quantitative trait loci (QTL) mapping for resistance to European canker in a full-sib family of 'Aroma' x 'Discovery'. Mapping was performed with the area under the disease progression curves (AUDPCs) from all seven (AUDPC_All7) and the first four assessments (AUDPC_First4), and three parameters of a sigmoid growth model for lesion length. As a scale for the effect of the different parameters, historic phenotypic data from screenings of a genetically diverse germplasm was compiled and re-analyzed. The parametrization of the data on lesion growth increased the number of QTL that could be identified with high statistical power, and provided some insight into their roles during different stages of disease development in the current experimental setup. Five QTL regions with strong or decisive evidence were identified on linkage groups 1, 8, 15, and 16. The QTL regions could be assigned to either of the parameters lesion length at the first assessment ('LL_A1'), the maximal lesion growth rate (lesion length doubling time, 't_gen'), and the lesion length at girdling ('LL_G'). Three of these QTL were traced along the pedigrees of some known relatives of the FS family, and discussed in relation to future crosses for breeding and genetic research.

Published
2023

25. An integrated approach for increasing breeding efficiency in apple and peach in Europe

Author

Laurens, Francois, Aranzana, Maria José, Arus, Pere, Bassi, Daniele, Bink, Marco, Bonany, Joan, Caprera, Andrea, Corelli-Grappadelli, Luca, Costes, Evelyne, Durel, Charles-Eric, Mauroux, Jehan-Baptiste, Muranty, Hélène, Nazzicari, Nelson, Pascal, Thierry, Patocchi, Andrea, Peil, Andreas, Quilot-Turion, Bénédicte, Rossini, Laura, Stella, Alessandra, Troggio, Michela, Velasco, Riccardo, and van de Weg, Eric

Published
2018
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28. A new method to reconstruct the direction of parent-offspring duo relationships using SNP array data and its demonstration on ancient and modern cultivars in the outcrossing species Malus × domestica

Author

Howard, Nicholas P., van de Weg, Eric, Luby, James J., Howard, Nicholas P., van de Weg, Eric, and Luby, James J.

Abstract

Unordered parent-offspring (PO) relationships are an outstanding issue in pedigree reconstruction studies. Resolution of the order of these relationships would expand the results, conclusions, and usefulness of such studies; however, no such PO order resolution (POR) tests currently exist. This study describes two such tests, demonstrated using SNP array data in the outcrossing species apple (Malus × domestica) on a PO relationship of known order (‘Keepsake’ as a parent of ‘Honeycrisp’) and two PO relationships previously ordered only via provenance information. The first test, POR-1, tests whether some of the extended haplotypes deduced from homozygous SNP calls from one individual in an unordered PO duo are composed of recombinant haplotypes from accurately phased SNP genotypes from the second individual. If so, the first individual would be the offspring of the second individual, otherwise the opposite relationship would be present. The second test, POR-2, does not require phased SNP genotypes and uses similar logic as the POR-1 test, albeit in a different approach. The POR-1 and POR-2 tests determined the correct relationship between ‘Keepsake’ and ‘Honeycrisp’. The POR-2 test confirmed ‘Reinette Franche’ as a parent of ‘Nonpareil’ and ‘Brabant Bellefleur’ as a parent of ‘Court Pendu Plat’. The latter finding conflicted with the recorded provenance information, demonstrating the need for these tests. The successful demonstration of these tests suggests they can add insights to future pedigree reconstruction studies, though caveats, like extreme inbreeding or selfing, would need to be considered where relevant.

Published
2022

35. Development and validation of the Axiom®Apple480K SNP genotyping array

Author

Bianco, Luca, Cestaro, Alessandro, Linsmith, Gareth, Muranty, Hélène, Denancé, Caroline, Théron, Anthony, Poncet, Charles, Micheletti, Diego, Kerschbamer, Emanuela, Di Pierro, Erica A., Larger, Simone, Pindo, Massimo, Van de Weg, Eric, Davassi, Alessandro, Laurens, François, Velasco, Riccardo, Durel, Charles-Eric, and Troggio, Michela

Published
2016
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36. Smooth Descent: A ploidy-aware algorithm to improve linkage mapping in the presence of genotyping errors.

Author

Navarro, Alejandro Thérèse, Bourke, Peter M., de Weg, Eric van, Clot, Corentin R., Arens, Paul, Finkers, Richard, and Maliepaard, Chris

Subjects
ERROR rates, GENE mapping, ALGORITHMS
Abstract

Linkage mapping is an approach to order markers based on recombination events. Mapping algorithms cannot easily handle genotyping errors, which are common in high-throughput genotyping data. To solve this issue, strategies have been developed, aimed mostly at identifying and eliminating these errors. One such strategy is SMOOTH, an iterative algorithm to detect genotyping errors. Unlike other approaches, SMOOTH can also be used to impute the most probable alternative genotypes, but its application is limited to diploid species and to markers heterozygous in only one of the parents. In this study we adapted SMOOTH to expand its use to any marker type and to autopolyploids with the use of identity-by-descent probabilities, naming the updated algorithm Smooth Descent (SD). We applied SD to real and simulated data, showing that in the presence of genotyping errors this method produces better genetic maps in terms of marker order and map length. SD is particularly useful for error rates between 5% and 20% and when error rates are not homogeneous among markers or individuals. With a starting error rate of 10%, SD reduced it to ~5% in diploids, ~7% in tetraploids and ~8.5% in hexaploids. Conversely, the correlation between true and estimated genetic maps increased by 0.03 in tetraploids and by 0.2 in hexaploids, while worsening slightly in diploids (~0.0011). We also show that the combination of genotype curation and map re-estimation allowed us to obtain better genetic maps while correcting wrong genotypes. We have implemented this algorithm in the R package Smooth Descent. [ABSTRACT FROM AUTHOR]

Published
2023
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37. A new method to reconstruct the direction of parent-offspring duo relationships using SNP array data and its demonstration on ancient and modern cultivars in the outcrossing species malus × domestica

Author

Howard, Nicholas P., van de Weg, Eric, and Luby, James J.

Subjects
Plant Breeding, Genetics, Life Science, Plant Science, EPS, Horticulture, PE&RC, Biochemistry, Biotechnology
Abstract

Unordered parent-offspring (PO) relationships are an outstanding issue in pedigree reconstruction studies. Resolution of the order of these relationships would expand the results, conclusions, and usefulness of such studies; however, no such PO order resolution (POR) tests currently exist. This study describes two such tests, demonstrated using SNP array data in the outcrossing species apple (Malus × domestica) on a PO relationship of known order (‘Keepsake’ as a parent of ‘Honeycrisp’) and two PO relationships previously ordered only via provenance information. The first test, POR-1, tests whether some of the extended haplotypes deduced from homozygous SNP calls from one individual in an unordered PO duo are composed of recombinant haplotypes from accurately phased SNP genotypes from the second individual. If so, the first individual would be the offspring of the second individual, otherwise the opposite relationship would be present. The second test, POR-2, does not require phased SNP genotypes and uses similar logic as the POR-1 test, albeit in a different approach. The POR-1 and POR-2 tests determined the correct relationship between ‘Keepsake’ and ‘Honeycrisp’. The POR-2 test confirmed ‘Reinette Franche’ as a parent of ‘Nonpareil’ and ‘Brabant Bellefleur’ as a parent of ‘Court Pendu Plat’. The latter finding conflicted with the recorded provenance information, demonstrating the need for these tests. The successful demonstration of these tests suggests they can add insights to future pedigree reconstruction studies, though caveats, like extreme inbreeding or selfing, would need to be considered where relevant.

Published
2021

45. Apple FBo-Hi elite material mid-density genotypic data

Author

Howard, Nicholas P., van de Weg, Eric, Troggio, Michela, Muranty, Hélène, Howard, Nicholas P., van de Weg, Eric, Troggio, Michela, and Muranty, Hélène

Abstract

This dataset corresponds to the genotypic data used for the elite material in the FBo-Hi panel used by Cazenave et al (2021) "Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple" G3: Genes, Genomes, Genetics. The dataset was obtained using the 20K apple SNP array (Bianco et al, 2014). These data were obtained in the frame of the EU seventh Framework Programme project FruitBreedomics: Integrated Approach for increasing breeding efficiency in fruit tree crops (http://www.fruitbreedomics.com/).

Published
2021

48. Estimation of genetic parameters and prediction of breeding values for apple fruit-quality traits using pedigreed plant material in Europe

Author

Kouassi, Abou Bakari, Durel, Charles-Eric, Costa, Fabrizio, Tartarini, Stefano, van de Weg, Eric, Evans, Kate, Fernandez-Fernandez, Felicidad, Govan, Ceri, Boudichevskaja, Anastasia, Dunemann, Frank, Antofie, Adriana, Lateur, Marc, Stankiewicz-Kosyl, Marta, Soska, Andrzej, Tomala, Kazimierz, Lewandowski, Markus, Rutkovski, Krzysztof, Zurawicz, Edwards, Guerra, Walter, and Laurens, François

Published
2009
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