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Communication dans un congrès

Development of ryegrass allele-specific markers for sustainable grassland improvement (GRASP): SNP discovery

Abstract : GRASP was an EU framework V project involving eight public institutions and one commercial partner. The major target of GRASP was the development of "functional" gene-derived and allele-specific single nucleotide polymorphism markers associated with relevant traits in Lolium perenne such as forage quality, nitrogen use efficiency, disease resistance, and abiotic stress tolerance. For each of the candidate genes, allele sequences (minimum length 1000 bp per allele) of 20 diverse genotypes ( Lolium test set=LTS) were sequenced in order to derive allele-specific SNP markers. For a total of 104 genes, allele sequencing was initiated. Allele sequencing was completed for 91 genes and have been used to derive informative SNP markers for selection experiments. At University of Arhus, 11 expressed resistance candidate genes were analysed in detail, including 6 nucleotide binding site and leucine rich repeat (NBS-LRR) like genes and 5 non-NBS-LRR resistance gene analogues. The number of haplotypes per gene ranged from 9 to 27. On average one single nucleotide polymorphism (SNP) was present per 33 bp between two randomly sampled sequences for the 11 genes. NBS-LRR like gene fragments showed higher degree of nucleotide diversity, with one SNP every 22 bp between two sampled sequences. NBS-LRR like gene fragments showed very high nonsynonymous mutation rates, leading to altered amino acid sequences. Particularly LRR regions showed very high diversity with one SNP every 10 bp between two sequences on average. In contrast, non-NBS LRR resistance gene candidates showed lower degree of nucleotide diversity, with one SNP every 112 bp. 78% of haplotypes occurred at low frequency (<5%) within the collection of 20 genotypes. Low intragenic LD was detected for most R genes, and rapid LD decay within 500 bp was detected. Comparative analyses with regard to SNP density, heterozygosity, linkage disequilibrium, etc. across different gene families will be presented.
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Communication dans un congrès
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https://hal.inrae.fr/hal-02756656
Déposant : Migration Prodinra <>
Soumis le : mercredi 3 juin 2020 - 23:13:12
Dernière modification le : vendredi 11 septembre 2020 - 15:12:02

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  • HAL Id : hal-02756656, version 1
  • PRODINRA : 267091

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Thomas Lübberstedt, Y. Xing, Ursula Frei, B. Wollenweber, B. Schejbel, et al.. Development of ryegrass allele-specific markers for sustainable grassland improvement (GRASP): SNP discovery. 27. Eucarpia Symposium on Improvement of Fodder Crops and Amenity Grasses, European Association for Research on Plant Breeding (EUCARPIA). FRA., Aug 2007, Copenhagen, Denmark. 230 p. ⟨hal-02756656⟩

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