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Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays.

Bernardo AN, Bradbury PJ, Ma H, Hu S, Bowden RL, Buckler ES, Bai G - BMC Genomics (2009)

Bottom Line: Six wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified.The Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat.The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat.

View Article: PubMed Central - HTML - PubMed

Affiliation: ARS-USDA Plant Science and Entomology Unit, Agricultural Research Service-U.S. Department of Agriculture, Manhattan, KS 66506, USA. amy8@ksu.edu

ABSTRACT

Background: Wheat (Triticum aestivum L.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (approximately 17,000 Mb) and high levels of repetitive sequences; the whole genome sequence may not be expected in the near future. Available linkage maps have low marker density due to limitation in available markers; therefore new technologies that detect genome-wide polymorphisms are still needed to discover a large number of new markers for construction of high-resolution maps. A high-resolution map is a critical tool for gene isolation, molecular breeding and genomic research. Single feature polymorphism (SFP) is a new microarray-based type of marker that is detected by hybridization of DNA or cRNA to oligonucleotide probes. This study was conducted to explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome.

Results: Six wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified. A subset of 164 unigenes was sequenced and 54% showed polymorphism within probes. Microarray analysis of 71 recombinant inbred lines from the cross Ning 7840/Clark identified 955 SFPs and 877 of them were mapped together with 269 simple sequence repeat markers. The SFPs were randomly distributed within a chromosome but were unevenly distributed among different genomes. The B genome had the most SFPs, and the D genome had the least. Map positions of a selected set of SFPs were validated by mapping single nucleotide polymorphism using SNaPshot and comparing with expressed sequence tags mapping data.

Conclusion: The Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat. The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat.

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Related in: MedlinePlus

A high-density map of wheat chromosome 5 consisting of 157 SFP and SSR markers in Ning 7840/Clark population. Numbers to the left of each chromosome are interval distances in centimorgans. On the right of each chromosome are mapped markers; markers derived from the Affymetrix 'Ta.' probe sets were abbreviated as 'Xta' and those from 'TaAffx' as 'Xaf'.
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Figure 6: A high-density map of wheat chromosome 5 consisting of 157 SFP and SSR markers in Ning 7840/Clark population. Numbers to the left of each chromosome are interval distances in centimorgans. On the right of each chromosome are mapped markers; markers derived from the Affymetrix 'Ta.' probe sets were abbreviated as 'Xta' and those from 'TaAffx' as 'Xaf'.

Mentions: To explore the possibility of directly mapping the SFPs, 71 RILs were analyzed on the Affymetix Wheat Genome Arrays. A total of 2,426 probe sets showed different intensity patterns between the parents, Ning 7840 and Clark, as evidenced by significant probe × variety interaction (p < 1e-7). Out of the 2,426 SFPs, 955 SFPs with at least 60 RIL calls were identified and 142 of these matched SFPs found in the first experiment. Nine hundred and twenty-three (97%) SFPs and 269 SSRs were mapped in 54 linkage groups and covered 1,944 cM genetic distance. Of the 53 linkage groups, 45 can be assigned to 21 chromosomes (Figures 2, 3, 4, 5, 6, 7, 8 and 9) according to previously reported SSR map information [25]. A total of 877 SFPs could be assigned to a chromosome location. About 63% of the SFP were mapped on the B genome, and only 10% were mapped in the D genome (Table 3). Chromosome 1B had the most SFPs, and 4D had the fewest. Chromosome arm 1BS had about 125 SFP markers that only spanned about 3 cM (Figure 2).


Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays.

Bernardo AN, Bradbury PJ, Ma H, Hu S, Bowden RL, Buckler ES, Bai G - BMC Genomics (2009)

A high-density map of wheat chromosome 5 consisting of 157 SFP and SSR markers in Ning 7840/Clark population. Numbers to the left of each chromosome are interval distances in centimorgans. On the right of each chromosome are mapped markers; markers derived from the Affymetrix 'Ta.' probe sets were abbreviated as 'Xta' and those from 'TaAffx' as 'Xaf'.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2698007&req=5

Figure 6: A high-density map of wheat chromosome 5 consisting of 157 SFP and SSR markers in Ning 7840/Clark population. Numbers to the left of each chromosome are interval distances in centimorgans. On the right of each chromosome are mapped markers; markers derived from the Affymetrix 'Ta.' probe sets were abbreviated as 'Xta' and those from 'TaAffx' as 'Xaf'.
Mentions: To explore the possibility of directly mapping the SFPs, 71 RILs were analyzed on the Affymetix Wheat Genome Arrays. A total of 2,426 probe sets showed different intensity patterns between the parents, Ning 7840 and Clark, as evidenced by significant probe × variety interaction (p < 1e-7). Out of the 2,426 SFPs, 955 SFPs with at least 60 RIL calls were identified and 142 of these matched SFPs found in the first experiment. Nine hundred and twenty-three (97%) SFPs and 269 SSRs were mapped in 54 linkage groups and covered 1,944 cM genetic distance. Of the 53 linkage groups, 45 can be assigned to 21 chromosomes (Figures 2, 3, 4, 5, 6, 7, 8 and 9) according to previously reported SSR map information [25]. A total of 877 SFPs could be assigned to a chromosome location. About 63% of the SFP were mapped on the B genome, and only 10% were mapped in the D genome (Table 3). Chromosome 1B had the most SFPs, and 4D had the fewest. Chromosome arm 1BS had about 125 SFP markers that only spanned about 3 cM (Figure 2).

Bottom Line: Six wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified.The Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat.The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat.

View Article: PubMed Central - HTML - PubMed

Affiliation: ARS-USDA Plant Science and Entomology Unit, Agricultural Research Service-U.S. Department of Agriculture, Manhattan, KS 66506, USA. amy8@ksu.edu

ABSTRACT

Background: Wheat (Triticum aestivum L.) is a staple food crop worldwide. The wheat genome has not yet been sequenced due to its huge genome size (approximately 17,000 Mb) and high levels of repetitive sequences; the whole genome sequence may not be expected in the near future. Available linkage maps have low marker density due to limitation in available markers; therefore new technologies that detect genome-wide polymorphisms are still needed to discover a large number of new markers for construction of high-resolution maps. A high-resolution map is a critical tool for gene isolation, molecular breeding and genomic research. Single feature polymorphism (SFP) is a new microarray-based type of marker that is detected by hybridization of DNA or cRNA to oligonucleotide probes. This study was conducted to explore the feasibility of using the Affymetrix GeneChip to discover and map SFPs in the large hexaploid wheat genome.

Results: Six wheat varieties of diverse origins (Ning 7840, Clark, Jagger, Encruzilhada, Chinese Spring, and Opata 85) were analyzed for significant probe by variety interactions and 396 probe sets with SFPs were identified. A subset of 164 unigenes was sequenced and 54% showed polymorphism within probes. Microarray analysis of 71 recombinant inbred lines from the cross Ning 7840/Clark identified 955 SFPs and 877 of them were mapped together with 269 simple sequence repeat markers. The SFPs were randomly distributed within a chromosome but were unevenly distributed among different genomes. The B genome had the most SFPs, and the D genome had the least. Map positions of a selected set of SFPs were validated by mapping single nucleotide polymorphism using SNaPshot and comparing with expressed sequence tags mapping data.

Conclusion: The Affymetrix array is a cost-effective platform for SFP discovery and SFP mapping in wheat. The new high-density map constructed in this study will be a useful tool for genetic and genomic research in wheat.

Show MeSH
Related in: MedlinePlus