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The patterns of SNP variation and linkage disequilibrium in wheat: moving toward genome-wide association mapping

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.] | Kiani, S [coaut.] | Luo, M.C [coaut.] | Matnyazov, R [coaut.] | Rudd, J.C [coaut.] | Sims, R [coaut.] | Sorrells, M.E | Talbert, L [coaut.] | Dreisigacker, S.
Material type: materialTypeLabelBookAnalytics: Show analyticsPublisher: Beijing (China) Chinese Academy of Agricultural Sciences : 2010Description: p. 42.Online resources: Access only for CIMMYT Staff Summary: A 1536-plex Illumina OPA was used to study linkage disequilibrium (LD) and population structure in the panel of spring and winter wheat lines from various breeding populations. Population-specific patterns of genetic differentiation and LD were discovered. Significant amount of genetic variation was captured by each breeding program as indicated by a higher level of within-population genetic variance than between population variance. Analysis of population structure suggests that breeding populations shared significant proportion of genetic ancestry. Locus-specific estimates of population structure showed the high level of heterogeneity across the wheat genome. Several chromosomal regions differentiated in allelic frequencies were detected between the spring and winter wheat populations. Some of these regions overlapped with known flowering time QTL suggesting that they harbor candidate genes involved in the regulation of growth habit. The variation of population-specific LD suggests that breeding and selection had a different impact on the wheat genomes in different populations highlighting the significance of allopolyploidy in wheat for the development of adapted cultivars. We hypothesized that the higher extent of LD in the wheat D genome than in the A and B genomes is the consequence of recent introgressions and a population bottleneck occurred during the origin of hexaploid wheat. The patterns of LD and population structure were assessed for designing genome-wide association mapping experiments in wheat.
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Conference proceedings CIMMYT Knowledge Center: John Woolston Library

Lic. Jose Juan Caballero Flores

 

CIMMYT Staff Publications Collection CIS-6270 (Browse shelf) Available
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Abstract only

A 1536-plex Illumina OPA was used to study linkage disequilibrium (LD) and population structure in the panel of spring and winter wheat lines from various breeding populations. Population-specific patterns of genetic differentiation and LD were discovered. Significant amount of genetic variation was captured by each breeding program as indicated by a higher level of within-population genetic variance than between population variance. Analysis of population structure suggests that breeding populations shared significant proportion of genetic ancestry. Locus-specific estimates of population structure showed the high level of heterogeneity across the wheat genome. Several chromosomal regions differentiated in allelic frequencies were detected between the spring and winter wheat populations. Some of these regions overlapped with known flowering time QTL suggesting that they harbor candidate genes involved in the regulation of growth habit. The variation of population-specific LD suggests that breeding and selection had a different impact on the wheat genomes in different populations highlighting the significance of allopolyploidy in wheat for the development of adapted cultivars. We hypothesized that the higher extent of LD in the wheat D genome than in the A and B genomes is the consequence of recent introgressions and a population bottleneck occurred during the origin of hexaploid wheat. The patterns of LD and population structure were assessed for designing genome-wide association mapping experiments in wheat.

Global Wheat Program

English

Lucia Segura

INT2692

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