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3. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

Author

Hibrand Saint-Oyant, L., Ruttink, T., Hamama, L., Kirov, I., Lakhwani, D., Zhou, N. N., Bourke, P. M., Daccord, N., Leus, L., Schulz, D., Van de Geest, H., Hesselink, T., Van Laere, K., Debray, K., Balzergue, S., Thouroude, T., Chastellier, A., Jeauffre, J., Voisine, L., Gaillard, S., Borm, T. J. A., Arens, P., Voorrips, R. E., Maliepaard, C., Neu, E., Linde, M., Le Paslier, M. C., Bérard, A., Bounon, R., Clotault, J., Choisne, N., Quesneville, H., Kawamura, K., Aubourg, S., Sakr, S., Smulders, M. J. M., Schijlen, E., Bucher, E., Debener, T., De Riek, J., and Foucher, F.

Published
2018
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4. Rosa

Author

Smulders, M. J. M., Arens, P., Koning-Boucoiran, C. F. S., Gitonga, V. W., Krens, F. A., Atanassov, A., Atanassov, I., Rusanov, K. E., Bendahmane, M., Dubois, A., Raymond, O., Caissard, J. C., Baudino, S., Crespel, L., Gudin, S., Ricci, S. C., Kovatcheva, N., Van Huylenbroeck, J., Leus, L., Wissemann, V., Zimmermann, H., Hensen, I., Werlemark, G., Nybom, H., and Kole, Chittaranjan, editor

Published
2011
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19. Bestrijden van weekhuidmijten met roofmijten

Author

Audenaert, J., Leus, L., Witters, J., Audenaert, J., Leus, L., and Witters, J.

Abstract

Van 2016 tot 2018 hebben het PCS en ILVO samengewerkt met partners uit Nederland, Zwitserland en Spanje om de bestaande kennis op het vlak van monitoren van kleine mijten en hun bestrijding te vergelijken, optimaliseren en valideren. Voor het PCS lag de focus hierbij op de bestrijding van weekhuidmijten in azalea.

Published
2019

20. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

Author

Hibrand Saint Oyant, Laurence, Ruttink, T., Hamama, Latifa, Kirov, I., Lakhwani, Deepika, Zhou, Ningning, Bourke, P. M., Daccord, Nicolas, Leus, L., Schulz, D., Van de Geest, H., Hesselink, T., Van Laere, K., Debray, Kevin, Balzergue, Sandrine, Thouroude, Tatiana, Chastellier, Annie, Jeauffre, Julien, Voisine, Linda, Gaillard, Sylvain, Borm, T. J. A., Arens, P., Voorrips, R. E., Maliepaard, C., Neu, E., Linde, M., Le Paslier, Marie-Christine, Bérard, Aurélie, Bounon, Rémi, Clotault, Jérémy, Choisne, Nathalie, Quesneville, Hadi, Kawamura, K., Aubourg, Sébastien, Sakr, Soulaiman, Smulders, M. J. M., Schijlen, E., Bucher, Etienne, Debener, T., De Riek, J., and Foucher, Fabrice

Subjects
Vegetal Biology, fungi, food and beverages, Biologie végétale
Abstract

Rose is the world’s most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line (‘HapOB’) from Rosa chinensis ‘Old Blush’ and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1–96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

Published
2018

23. monitoren en bestrijden van kleine mijten

Author

Audenaert, J., Leus, L., Witters, J., Audenaert, J., Leus, L., and Witters, J.

Abstract

De afgelopen twee jaar hebben het PCS en ILVO samengewerkt met partners uit Nederland, Zwitserland en Spanje, om de bestaande kennis op vlak van het monitoren van kleine mijten en hun bestrijding te vergelijken, optimaliseren en valideren in het kader van het C- IPM project UNIFORCE (Unification of IPM Forces to Control Mites in Berries, Soft Fruits and Woody Ornamentals). De focus lag hierbij op galmijten en weekhuidmijten, die respectievelijk op bessenstruiken en azalea's voor grote schade kunnen zorgen. Omdat de gewassen waarop deze mijten leven in de meeste landen als ‘kleine teelten’ beschouwd worden, is het onderzoek dat hiernaar gebeurt beperkt. Met het project UNIFORCE hebben we daarom, d.m.v. een Europese samenwerking, een stimulans gegeven aan dit onderzoek op het vlak van kennisuitwisseling om de detectie, monitoring en beheersing van deze mijten efficiënter en duurzamer te maken.

Published
2018

25. A high-quality sequence ofRosa chinensisto elucidate genome structure and ornamental traits

Author

Hibrand Saint-Oyant, L., primary, Ruttink, T., additional, Hamama, L., additional, Kirov, I., additional, Lakwani, D., additional, Zhou, N.-N., additional, Bourke, P.M., additional, Daccord, N., additional, Leus, L., additional, Schulz, D., additional, Van de Geest, H., additional, Hesselink, T., additional, Van Laere, K., additional, Balzergue, S., additional, Thouroude, T., additional, Chastellier, A., additional, Jeauffre, J., additional, Voisine, L., additional, Gaillard, S., additional, Borm, T.J.A., additional, Arens, P., additional, Voorrips, R.E., additional, Maliepaard, C., additional, Neu, E., additional, Linde, M., additional, Le Paslier, M.C., additional, Bérard, A., additional, Bounon, R., additional, Clotault, J., additional, Choisne, N., additional, Quesneville, H., additional, Kawamura, K., additional, Aubourg, S., additional, Sakr, S., additional, Smulders, M.J.M., additional, Schijlen, E., additional, Bucher, E., additional, Debener, T., additional, De Riek, J., additional, and Foucher, F., additional

Published
2018
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26. Toepassen van IPM-strategieën om plaagmijten te bestrijden in azalea

Author

Audenaert, J., Witters, J., Leus, L., Audenaert, J., Witters, J., and Leus, L.

Abstract

Zowel bessenstruiken (braambes, framboos, aardbei,…) als azalea’s worden aangetast door diverse soorten plaagmijten, met spintmijten, weekhuidmijten en galmijten als belangrijkste groepen. De galmijten en weekhuidmijten hebben daarenboven een vergelijkbare levenswijze, zijn klein, verstoppen zich en zijn moeilijk waar te nemen voor er zichtbare schade is. Omdat de gewassen waarop de mijten leven in de meeste landen als ‘kleine teelten’ beschouwd worden, is het onderzoek dat hiernaar gebeurt vrij beperkt. Door middel van het Europees project UNIFORCE willen we een stimulans geven aan kennisuitwisseling om de monitoring en beheersing van deze mijten efficiënter en duurzamer te maken.

Published
2017

29. Rosa

Author

Arens, P., Smulders, M. J. M., Koning-Boucoiran, C. F. S., Gitonga, V. W., Krens, F. A., Atanassov, A., Atanassov, I., Rusanov, K. E., Bendahmane, M., Dubois, A., Raymond, O., Caissard, J. C., Baudino, S., Crespel, L., Gudin, S., Ricci, S. C., Kovatcheva, N., Van Huylenbroeck, J., Leus, L., Wissemann, V., Zimmermann, Heike, Hensen, Isabell, Werlemark, G., Nybom, H., and Kole, C.

Subjects
Ecosystems Research, Amplify Fragment Length Polymorphism, Amplify Fragment Length Polymorphism Marker, food and beverages, Biology, Powdery Mildew, Double Flower, Quantitative Trait Locus
Abstract

Presently, about 100–250 species are usually recognized in the genus Rosa. The low levels of DNA sequence divergence found across the genus suggest that it is a young genus with much speciation taking place after the last glaciation. Poor phylogenetic resolution and commonly occurring contradictions between chloroplast and nuclear gene phylogenies suggest that hybridization has been a strong driving force in the evolution of roses, often accompanied by polyploidization. In addition, extensive anthropogenic impact has led to the development of many new semi-wild and/or cultivated rose varieties. Some wild species have become invasive.This chapter describes the taxonomy of roses. It presents examples of interesting traits in wild species that may valuable to broaden the genetic base of cultivated roses, such as thornlessness, winter hardiness, drought resistance, and improved shelf-life. Also fragrance and compounds with possible health effects are discussed. The highest priority in rose breeding research is the development of disease resistant roses. Different resistance mechanisms have been found for black spot and powdery mildew in various wild rose species. We describe how resistance genes are being mapped using crosses between wild, diploid rose species, and how other genes for traits of interest are being identified.We proceed with a discussion of various ways to overcome the taxonomic and ploidy level barriers for introgression of traits into cultivated hybrid rose or garden rose germplasm, including dihaploidization, polyploidization, and transgenics. Even so, breeding programs with wild species are usually time-consuming. For garden roses, the genetic and morphological distance between modern cultivars and the wild species is smaller, which makes the use of wild species easier than in the case of cut roses.

Published
2011

33. A high-quality genome sequence of Rosa chinensisto elucidate ornamental traits

Author

Hibrand Saint-Oyant, L., Ruttink, T., Hamama, L., Kirov, I., Lakhwani, D., Zhou, N. N., Bourke, P. M., Daccord, N., Leus, L., Schulz, D., Van de Geest, H., Hesselink, T., Van Laere, K., Debray, K., Balzergue, S., Thouroude, T., Chastellier, A., Jeauffre, J., Voisine, L., Gaillard, S., Borm, T. J. A., Arens, P., Voorrips, R. E., Maliepaard, C., Neu, E., Linde, M., Le Paslier, M. C., Bérard, A., Bounon, R., Clotault, J., Choisne, N., Quesneville, H., Kawamura, K., Aubourg, S., Sakr, S., Smulders, M. J. M., Schijlen, E., Bucher, E., Debener, T., De Riek, J., and Foucher, F.

Abstract

Rose is the world’s most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosaby sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line (‘HapOB’) from Rosa chinensis‘Old Blush’ and generated a rose genome assembly anchored to seven pseudo-chromosomes (512?Mb with N50 of 3.4?Mb and 564 contigs). The length of 512?Mb represents 90.1–96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vescagenome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosaspecies selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOEhomologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

Published
2018
Full Text
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