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6. Development and mapping of DArT markers within the Festuca - Lolium complex

Author

Kopecký, David, Bartoš, Jan, Lukaszewski, Adam J, Baird, James H, Černoch, Vladimír, Kölliker, Roland, Rognli, Odd, Blois, Helene, Caig, Vanessa, Lübberstedt, Thomas, Studer, Bruno, Shaw, Paul, Doležel, Jaroslav, and Kilian, Andrzej

Abstract

Abstract Background Grasses are among the most important and widely cultivated plants on Earth. They provide high quality fodder for livestock, are used for turf and amenity purposes, and play a fundamental role in environment protection. Among cultivated grasses, species within the Festuca-Lolium complex predominate, especially in temperate regions. To facilitate high-throughput genome profiling and genetic mapping within the complex, we have developed a Diversity Arrays Technology (DArT) array for five grass species: F. pratensis, F. arundinacea, F. glaucescens, L. perenne and L. multiflorum. Results The DArTFest array contains 7680 probes derived from methyl-filtered genomic representations. In a first marker discovery experiment performed on 40 genotypes from each species (with the exception of F. glaucescens for which only 7 genotypes were used), we identified 3884 polymorphic markers. The number of DArT markers identified in every single genotype varied from 821 to 1852. To test the usefulness of DArTFest array for physical mapping, DArT markers were assigned to each of the seven chromosomes of F. pratensis using single chromosome substitution lines while recombinants of F. pratensis chromosome 3 were used to allocate the markers to seven chromosome bins. Conclusion The resources developed in this project will facilitate the development of genetic maps in Festuca and Lolium, the analysis on genetic diversity, and the monitoring of the genomic constitution of the Festuca × Lolium hybrids. They will also enable marker-assisted selection for multiple traits or for specific genome regions.

Published
2009

7. Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

Author

Sansaloni, Carolina, Franco, Jorge, Santos, Bruno, Percival-Alwyn, Lawrence, Singh, Sukhwinder, Petroli, Cesar, Campos, Jaime, Dreher, Kate, Payne, Thomas, Marshall, David, Kilian, Benjamin, Milne, Iain, Raubach, Sebastian, Shaw, Paul, Stephen, Gordon, Carling, Jason, Pierre, Carolina Saint, Burgueño, Juan, Crosa, José, Li, HuiHui, Guzman, Carlos, Kehel, Zakaria, Amri, Ahmed, Kilian, Andrzej, Wenzl, Peter, Uauy, Cristobal, Banziger, Marianne, Caccamo, Mario, and Pixley, Kevin

Published
2020
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11. A Mid-Density Single-Nucleotide Polymorphism Panel for Molecular Applications in Cowpea (Vigna unguiculata (L.) Walp).

Author

Ongom, Patrick Obia, Fatokun, Christian, Togola, Abou, Garcia-Oliveira, Ana Luisa, Ng, Eng Hwa, Kilian, Andrzej, Lonardi, Stefano, Close, Timothy J., and Boukar, Ousmane

Subjects
COWPEA, SINGLE nucleotide polymorphisms, LINKAGE disequilibrium, CROPS, GENE frequency, ANIMAL coloration
Abstract

Molecular markers are increasingly being deployed to accelerate genetic gain in crop plants. The objective of this study was to assess the potential of a mid-density genotyping panel for molecular applications in cowpea breeding. A core set of 2,602 targeted diversity array technology (DArTag) single-nucleotide polymorphisms (SNPs) was designed from an existing 51,128 Cowpea iSelect Consortium Array. The panel's usefulness was assessed using 376 genotypes from different populations of known genetic backgrounds. The panel was informative, with over 78% of SNPs exceeding a minor allele frequency of 0.20. The panel decoded three stratifications in the constituted population, as was expected. Linkage disequilibrium (LD) decay was correctly depicted as slower in a biparental subset than in other populations. A known flower and seed coat color gene region was located on chromosome Vu07, suggesting that the mid-density panel may be used to hypothesize genomic regions underlying target traits in cowpea. Unexpected heterozygosity was detected in some lines and highly among F1 progenies, divulging the panel's potential application in germplasm purity and hybridity verification. The study unveils the potential of an excellent genomic resource that can be tapped to enhance the development of improved cowpea cultivars. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Identification of Single Nucleotide Polymorphisms Associated with Brown Rust Resistance, α-Amylase Activity and Pre-harvest Sprouting in Rye (Secale cereale L.)

Author

Rakoczy-Trojanowska, Monika, Krajewski, Paweł, Bocianowski, Jan, Schollenberger, Małgorzata, Wakuliński, Wojciech, Milczarski, Paweł, Masojć, Piotr, Targońska-Karasek, Małgorzata, Banaszak, Zofia, Banaszak, Katarzyna, Brukwiński, Waldemar, Orczyk, Wacław, and Kilian, Andrzej

Published
2017
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23. Construction of a genetic linkage map and QTL analysis in bambara groundnut

Author

Ahmad, Nariman Salih, Redjeki, Endah Sri, Ho, Wai Kuan, Aliyu, Siise, Mayes, Katie, Massawe, Festo, Kilian, Andrzej, and Mayes, Sean

Subjects
Nucleotide sequencing -- Methods, Mimosaceae -- Genetic aspects, Quantitative trait loci -- Observations, Legumes -- Genetic aspects, DNA sequencing -- Methods, Beans -- Genetic aspects, Biological sciences
Abstract

Abstract: Bambara groundnut (Vigna subterranea (L.) Verdc.) is an indigenous underutilized legume that has the potential to improve food security in semi-arid Africa. So far, there are a lack of [...]

Published
2016

27. A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

Author

Paux, Etienne, Sourdille, Pierre, Salse, Jérôme, Saintenac, Cyrille, Choulet, Frédéric, Leroy, Philippe, Korol, Abraham, Michalak, Monika, Kianian, Shahryar, Spielmeyer, Wolfgang, Lagudah, Evans, Somers, Daryl, Kilian, Andrzej, Alaux, Michael, Vautrin, Sonia, Bergès, Hélène, Eversole, Kellye, Appels, Rudi, Safar, Jan, Simkova, Hana, Dolezel, Jaroslav, Bernard, Michel, and Feuillet, Catherine

Published
2008
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33. Analysis of Genetic Diversity and Resistance to Foliar Pathogens Based on Genotyping-by-Sequencing of a Para Rubber Diversity Panel and Progeny of an Interspecific Cross.

Author

Roy, C. Bindu, Goonetilleke, Shashi N., Joseph, Limiya, Krishnan, Anu, Saha, Thakurdas, Kilian, Andrzej, and Mather, Diane E.

Subjects
GENETIC variation, PHYTOPHTHORA, HEVEA, SINGLE nucleotide polymorphisms, DISEASE resistance of plants, GENE mapping, RUBBER plantations
Abstract

Para rubber trees (Hevea brasiliensis) are the largest major source of natural rubber in the world. Its major pathogens are Phytophthora spp., Corynespora cassiicola, and Colletotrichum spp. A rubber diversity panel of 116 clones using over 12,000 single nucleotide polymorphisms (SNPs) from DArTSeq genotyping revealed clear phylogenetic differences in clones that originated from different geographical regions of the world. An integrated linkage map constructed with an F1 progeny of 86 from an interspecific cross between H. brasiliensis and H. benthamiana using 23,978 markers [10,323 SNPs and 13,655 SilicoDArTs] spanned 3947.83 cM with 0.83 cM average marker-interval. The genome scaffolds that were anchored to the linkage map, covering 1.44 Gb of H. brasiliensis reference genome, revealed a high level of collinearity between the genetic map and reference genome. Association analysis identified 12 SNPs significantly associated with the resistance against Phytophthora, Corynespora, and Colletotrichum in six linkage groups: 2, 6, 12, 14, 17, and 18. Kompetitive Allele-Specific PCR marker assays were developed for those 12 SNPs, screened with 178 individuals, and detected clear separation between two genotypes. Within the proximity to those SNPs, 41 potentially key genes that have previously been reported to associate with plant disease resistance were predicted with high confidence. [ABSTRACT FROM AUTHOR]

Published
2022
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48. Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map

Author

Reddy, Umesh K., Rong, Jun-kang, Nimmakayala, Padma, Vajja, Gopinath, Rahman, Mohammad A., Yu, John, Soliman, Khairy M., Heller-Uszynska, Katarzyna, Kilian, Andrzej, and Paterson, Andrew H.

Subjects
Genomes -- Analysis -- Physiological aspects -- Research, Anopheles -- Analysis -- Genetic aspects -- Research, Biological sciences
Abstract

A diversity array technology (DArT) marker platform was developed for the cotton genome, to evaluate the use of DArT markers compared with AFLP markers in mapping and transferability across the mapping populations. We used a reference genetic map of tetraploid Gossypium L. that already contained ~5000 loci, which coalesced into 26 chromosomes, to anchor newly developed DArT and AFLP markers with the aim of further improving utility and map resolution. Our results indicated that the percentage of polymorphic DArT markers that could be genetically mapped (78.15%) was much higher than that of AFLP markers (22.28%). Sequence analysis of DArT markers indicated that a majority matched known expressed sequence tag (EST) sequences from tetraploid and diploid Gossypium species. A total of 794 Arabidopsis genes were homologous with various DArT marker sequences. Chromosomes 5(A), 7(A), 19(D), 23(D), and 24(D) had more Arabidopsis syntenic DArT markers than the other chromosomes. Anchoring DArT markers from the reference map to a recombinant inbred line (RIL) map indicated that DArT markers will speed the building of maps in de novo RIL populations. Key words: diversity array technology markers, reference genetic map, AFLPs, Arabidopsis synteny. Une plate-forme de genotypage DArT a ete developpee pour le genome du cotonnier de maniere a comparer les marqueurs DArT aux marqueurs AFLP en matiere de cartographie et de transportabilite des marqueurs d'une population a une autre. Les auteurs ont employe une carte genetique de reference pour le Gossypium L. tetraploide qui comptait deja environ 5,000 locus, groupes en 26 chromosomes, pour y ajouter les marqueurs DArT et AFLP nouvellement developpes en vue d' ameliorer l' utilite et la resolution de cette carte. Les resultats obtenus ont montre que la proportion des marqueurs DArT qu' ils etaient en mesure de placer sur la carte (78,15 %) etait beaucoup plus elevee que pour les marqueurs AFLP (22,28 %). L'analyse de la sequence des marqueurs DArT a revele que la majorite d'entre eux etaient homologues a des sequences d' EST rapportees chez des especes tetraploides ou diploides du Gossypium. Au total, 794 genes d'Arabidopsis etaient homologues a une sequence de marqueur DArT. Les chromosomes 5(A), 7(A), 19 (D), 23(D) et 24(D) portaient davantage de marqueurs DArT synteniques avec le genome d'Arabidopsis que les autres chromosomes. L'ancrage des marqueurs DArT de la carte de reference sur une carte de lignees RIL a permis de constater que ces marqueurs permettent d' accelerer la production de cartes pour de nouvelles populations de lignees RIL. Mots-cles : marqueurs DArT, carte genetique de reference, AFLP, Arabidopsis syntenie. [Traduit par la Redaction], Introduction Cotton is one of the world's most important crops and sustains one of the world's largest industries (textiles), which accounts for a value of ~$500 billion/year worldwide. The value [...]

Published
2011
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