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Genome-wide patterns of SNP variation in polyploid wheat

By: Akhunov, E.
Contributor(s): Anderson, J.A | Baenziger, P.S | Bruckner, P.L [coaut.] | Campbell, K [coaut.] | Carver, B.F [coaut.] | Chao, S [coaut.] | Chen, J [coaut.] | Clark, D.R [coaut.] | Dubcovsky, J [coaut.] | Dvorak, J [coaut.] | Glover, K [coaut.] | Haley, S [coaut.] | Luo, M.C [coaut.] | Matnyazov, R [coaut.] | Rudd, J.C [coaut.] | Saintenac, C [coaut.] | Sims, R [coaut.] | Sorrells, M.E | Talbert, L [coaut.] | Dreisigacker, S.
Material type: materialTypeLabelBookAnalytics: Show analyticsPublisher: 2010Description: p. 46.Online resources: Access only for CIMMYT Staff Summary: Genome-wide set of SNPs is an essential tool for linkage and association mapping of agronomic traits and studying the genetic variation in populations of cultivated crop species and their wild ancestors. Recent advances in genomic technologies including the development of highly-multiplexed genotyping assays and next-generation sequencing technologies opened new possibilities for the analysis of plant genomes. We adopted these technologies to characterize the patterns of genetic variation in tetraploid and hexaploid wheat. A panel of 480 spring and winter US wheat cultivars was genotyped using 1536-plex Illumina OPA. The SNP genotyping data was used to infer the population structure and genome-wide patterns of genetic diversity and linkage disequilibrium in a collection of wheat cultivars and to assess the utility of an assembled hexaploid wheat panel for LD mapping. A strong effect of breeding on genetic differentiation of cultivars was demonstrated. The sequence-capture and next-generation sequencing approaches were used to resequence 1 kb fragments of 3,500 genes in tetraploid wild emmer and durum wheat. More than 3,000 SNP sites were used to investigate the distribution of mutations differentiating the genomes of wild and domesticated tetraploid wheat. Our study showed that this strategy is fast and very efficient method for the targeted analysis of the regions of interest in highly complex genomes, such as polyploid wheat. The potential impact of new genomic tools on utilization of plant genetic resources for breeding will be discussed.
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Conference proceedings CIMMYT Knowledge Center: John Woolston Library

Lic. Jose Juan Caballero Flores

 

CIMMYT Staff Publications Collection CIS-6172 (Browse shelf) Available
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Abstract only

Genome-wide set of SNPs is an essential tool for linkage and association mapping of agronomic traits and studying the genetic variation in populations of cultivated crop species and their wild ancestors. Recent advances in genomic technologies including the development of highly-multiplexed genotyping assays and next-generation sequencing technologies opened new possibilities for the analysis of plant genomes. We adopted these technologies to characterize the patterns of genetic variation in tetraploid and hexaploid wheat. A panel of 480 spring and winter US wheat cultivars was genotyped using 1536-plex Illumina OPA. The SNP genotyping data was used to infer the population structure and genome-wide patterns of genetic diversity and linkage disequilibrium in a collection of wheat cultivars and to assess the utility of an assembled hexaploid wheat panel for LD mapping. A strong effect of breeding on genetic differentiation of cultivars was demonstrated. The sequence-capture and next-generation sequencing approaches were used to resequence 1 kb fragments of 3,500 genes in tetraploid wild emmer and durum wheat. More than 3,000 SNP sites were used to investigate the distribution of mutations differentiating the genomes of wild and domesticated tetraploid wheat. Our study showed that this strategy is fast and very efficient method for the targeted analysis of the regions of interest in highly complex genomes, such as polyploid wheat. The potential impact of new genomic tools on utilization of plant genetic resources for breeding will be discussed.

Global Wheat Program

English

Lucia Segura

INT2692

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