SNP chip-based genomewide scans for germplasm evaluation, marker-trait association analysis and development of a molecular breeding platform in maize
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TextLanguage: English Publication details: Australia : 2009.Description: 16 pagesSubject(s):
In:
Proceedings of the Australian Plant Breeding, 14 and Sabrao Conference, 11; Cairns Convention Centre, Tropical North Queensland, Australia; 10-14 Aug, 2009Summary: A highly efficient molecular breeding platform requires several important components including efficient marker-trait identification, high throughput low cost DNA extraction, rapid and cost effective large-scale genotyping and semi-automated data management, analysis and interpretation. We have validated several strategies for improving the molecular breeding platform for maize including combining selective genotyping and pooled DNA analysis for more efficient identification of marker-trait associations (even for QTL with relative small effects and/or with high epistatic effects), seed DNA-based genotyping, SNP-based whole genome scans and powerful data management and analysis systems. CIMMYT scientists have recently obtained over 3,000 maize lines from genetics and breeding programs worldwide, which represent phenotypic extremes for many traits that are important in tropical maize breeding. These lines have been genotyped using a 1536-SNP chip developed through collaborations with Illumina Inc. and Cornell University. This has allowed us for the first time to test the feasibility of a one-step simultaneous marker-trait association analysis for a large number of agronomic traits. In addition, genetic diversity analysis has been carried out using a subset of 730 inbred lines screened with 849 informative SNP markers. We have also successfully applied SNP marker analysis to pooled DNA samples for genetic mapping using Illumina?s Golden Gate/Bead Station platform. We report here on the mapping of kernel hardness and tryptophan content using this method. In addition, we have used selective genotyping for genetic mapping of resistance to head smut and mosaic virus disease, and drought tolerance using 235 BILs. Finally, a subset of 554 inbred lines were evaluated under irrigated and drought stress conditions, identifying significant levels of drought tolerance at both vegetative and reproductive stages. The results of conventional linkage mapping and linkage disequilibrium-based marker-trait association analysis for drought tolerance and its component traits will be discussed.
| Item type | Current library | Collection | Call number | Status | Date due | Barcode | Item holds | |
|---|---|---|---|---|---|---|---|---|
| Conference paper | CIMMYT Knowledge Center: John Woolston Library | CIMMYT Staff Publications Collection | CIS-5623 (Browse shelf(Opens below)) | Available |
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A highly efficient molecular breeding platform requires several important components including efficient marker-trait identification, high throughput low cost DNA extraction, rapid and cost effective large-scale genotyping and semi-automated data management, analysis and interpretation. We have validated several strategies for improving the molecular breeding platform for maize including combining selective genotyping and pooled DNA analysis for more efficient identification of marker-trait associations (even for QTL with relative small effects and/or with high epistatic effects), seed DNA-based genotyping, SNP-based whole genome scans and powerful data management and analysis systems. CIMMYT scientists have recently obtained over 3,000 maize lines from genetics and breeding programs worldwide, which represent phenotypic extremes for many traits that are important in tropical maize breeding. These lines have been genotyped using a 1536-SNP chip developed through collaborations with Illumina Inc. and Cornell University. This has allowed us for the first time to test the feasibility of a one-step simultaneous marker-trait association analysis for a large number of agronomic traits. In addition, genetic diversity analysis has been carried out using a subset of 730 inbred lines screened with 849 informative SNP markers. We have also successfully applied SNP marker analysis to pooled DNA samples for genetic mapping using Illumina?s Golden Gate/Bead Station platform. We report here on the mapping of kernel hardness and tryptophan content using this method. In addition, we have used selective genotyping for genetic mapping of resistance to head smut and mosaic virus disease, and drought tolerance using 235 BILs. Finally, a subset of 554 inbred lines were evaluated under irrigated and drought stress conditions, identifying significant levels of drought tolerance at both vegetative and reproductive stages. The results of conventional linkage mapping and linkage disequilibrium-based marker-trait association analysis for drought tolerance and its component traits will be discussed.
Genetic Resources Program|Global Maize Program
Text in English
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