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DArT markers: Diversity analyses and mapping in Sorghum bicolor

Mace, E.S. and Xia, L. and Jordan, D.R. and Halloran, K. and Parh, D.K. and Huttner, E. and Wenzl, P. and Kilian, A. (2008) DArT markers: Diversity analyses and mapping in Sorghum bicolor. BMC Genomics, 9 (26).

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Article Link(s): http://dx.doi.org/10.1186/1471-2164-9-26

Publisher URL: http://www.biomedcentral.com/

Abstract

The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obtain sufficient return on investment to justify the routine use of marker-assisted breeding for many traits and particularly quantitative traits. Diversity Arrays Technology (DArT™) is a cost effective hybridisation-based marker technology that offers a high multiplexing level while being independent of sequence information. This technology offers sorghum breeding programs an alternative approach to whole-genome profiling. We report on the development, application, mapping and utility of DArT™ markers for sorghum germplasm.

Results: A genotyping array was developed representing approximately 12,000 genomic clones using PstI+BanII complexity with a subset of clones obtained through the suppression subtractive hybridisation (SSH) method. The genotyping array was used to analyse a diverse set of sorghum genotypes and screening a Recombinant Inbred Lines (RIL) mapping population. Over 500 markers detected variation among 90 accessions used in a diversity analysis. Cluster analysis discriminated well between all 90 genotypes. To confirm that the sorghum DArT markers behave in a Mendelian manner, we constructed a genetic linkage map for a cross between R931945-2-2 and IS 8525 integrating DArT and other marker types. In total, 596 markers could be placed on the integrated linkage map, which spanned 1431.6 cM. The genetic linkage map had an average marker density of 1/2.39 cM, with an average DArT marker density of 1/3.9 cM.

Conclusion: We have successfully developed DArT markers for Sorghum bicolor and have demonstrated that DArT provides high quality markers that can be used for diversity analyses and to construct medium-density genetic linkage maps. The high number of DArT markers generated in a single assay not only provides a precise estimate of genetic relationships among genotypes, but also their even distribution over the genome offers real advantages for a range of molecular breeding and genomics applications.

Item Type:Article
Corporate Creators:Department of Employment, Economic Development and Innovation (DEEDI), Agri-Science, Crop and Food Science, Plant Science
Business groups:Agri-Science, Crop and Food Science
Additional Information:© Mace et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords:Cluster analysis; diversity arrays technology; DNA microarray; gene cluster; gene mapping; gene technology; genetic linkage; genetic marker; genetic variability; genotype; microarray analysis; molecular cloning; nonhuman; plant genetics; quality control; sorghum; suppression subtractive hybridization; Sorghum bicolour.
Subjects:Science > Biology > Genetics
Plant culture > Field crops > Sorghum
Deposited On:02 Feb 2009 04:36
Last Modified:25 Oct 2011 05:37

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