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Start Over Descriptor "dispensable" Topic genotyping by sequencing
2 results on '"dispensable"'

1. Genotyping by sequencing transcriptomes in an evolutionary pre-breeding durum wheat population.

Author

David, Jacques, Holtz, Yan, Ranwez, Vincent, Santoni, Sylvain, Sarah, Gautier, Ardisson, Morgane, Poux, Gérard, Choulet, Fréderic, Genthon, Clémence, Roumet, Pierre, and Tavaud-Pirra, Muriel

Subjects
*WHEAT breeding, *SEQUENCE alignment, *PLANT RNA, *DURUM wheat, *EMMER wheat, *DOMESTICATION of plants, *GENOTYPES, *SINGLE nucleotide polymorphisms
Abstract

The genetic diversity in durum wheat, Triticum turgidum durum, has been strongly reduced since the domestication of the wild Triticum turgidum dicoccoides. Monitoring durum wheat composite crosses incorporating related tetraploid taxa, such as wild and domesticated emmer wheat, is a suitable evolutionary pre-breeding method. Transcriptome sequencing paves the way for a genomic survey of single nucleotide polymorphisms (SNPs) segregating in such populations, offering the possibility of genotyping by sequencing to use these resources in genome-wide association studies (GWAS) and genomic selection (GS) programs. Evolutionary Pre-breeding pOpulation (EPO) is an evolutionary durum wheat pre-breeding population. Sequencing the transcriptome of 179 durum wheat lines (175 from EPO) led to the detection of 103,262 SNPs on two reference transcriptomes: one from the International Wheat Genome Sequencing Consortium and one assembled de novo on durum wheat. Using strict filtering to remove dubious heterozygous SNPs, EPO genetic diversity was eventually described with 76,188 high-confidence SNPs. The percentage of missing genotyping data depended on the expression level, and 88 individuals out of 175 were genotyped per SNP on average. Using the 3B pseudo-molecule of bread wheat, the transcription and diversity levels were shown to be higher in distal regions than in proximal regions, but SNPs were available throughout the chromosomes. Assuming good synteny with Hordeum, the trend was similar on the 14 chromosomes of the durum wheat genome. EPO hosts a high level of diversity, has a number of SNPs in low linkage disequilibrium (<40 Mb) and would be well suited for GWAS and GS programs. [ABSTRACT FROM AUTHOR]

Published
2014
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2. Genotyping by sequencing transcriptomes in an evolutionary pre-breeding durum wheat population

Author

Yan Holtz, Gautier Sarah, Frédéric Choulet, Morgane Ardisson, Clémence Genthon, Jacques David, Muriel Tavaud-Pirra, Pierre Roumet, Sylvain Santoni, Gérard Poux, Vincent Ranwez, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), flagship project Agropolis Resource Center for Crop Conservation, Adaptation and Diversity (ARCAD) - Agropolis Fondation 0900-001, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, dispensable, Population, SNP, Plant Science, Biology, 01 natural sciences, DNA sequencing, diversity, 03 medical and health sciences, Genetics, genotyping by sequencing, repeatability, education, Molecular Biology, Genotyping, 030304 developmental biology, Genetic association, Synteny, 2. Zero hunger, 0303 health sciences, Genetic diversity, education.field_of_study, food and beverages, durum wheat, Marker-assisted selection, RNAseq, SNP genotyping, Agronomy and Crop Science, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 010606 plant biology & botany, Biotechnology
Abstract

The genetic diversity in durum wheat, Triticum turgidum durum, has been strongly reduced since the domestication of the wild Triticum turgidum dicoccoides. Monitoring durum wheat composite crosses incorporating related tetraploid taxa, such as wild and domesticated emmer wheat, is a suitable evolutionary pre-breeding method. Transcriptome sequencing paves the way for a genomic survey of single nucleotide polymorphisms (SNPs) segregating in such populations, offering the possibility of genotyping by sequencing to use these resources in genome-wide association studies (GWAS) and genomic selection (GS) programs. Evolutionary Pre-breeding pOpulation (EPO) is an evolutionary durum wheat pre-breeding population. Sequencing the transcriptome of 179 durum wheat lines (175 from EPO) led to the detection of 103,262 SNPs on two reference transcriptomes: one from the International Wheat Genome Sequencing Consortium and one assembled de novo on durum wheat. Using strict filtering to remove dubious heterozygous SNPs, EPO genetic diversity was eventually described with 76,188 high-confidence SNPs. The percentage of missing genotyping data depended on the expression level, and 88 individuals out of 175 were genotyped per SNP on average. Using the 3B pseudo-molecule of bread wheat, the transcription and diversity levels were shown to be higher in distal regions than in proximal regions, but SNPs were available throughout the chromosomes. Assuming good synteny with Hordeum, the trend was similar on the 14 chromosomes of the durum wheat genome. EPO hosts a high level of diversity, has a number of SNPs in low linkage disequilibrium (< 40 Mb) and would be well suited for GWAS and GS programs.

Published
2014

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