Molecular characterization of Asian maize inbred lines by multiple laboratories

George, M L C and Regalado, E and Li, W and Cao, M and Dahlan, M and Pabendon, M and Warburton, M L and Xianchun, X and Hoisington, D A (2003) Molecular characterization of Asian maize inbred lines by multiple laboratories. TAG Theoretical and Applied Genetics, 109 (1). pp. 80-91. ISSN 1432-2242

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Abstract

This study focuses on the standardization of techniques across laboratories to enable multiple datasets to be compared and combined in order to obtain reliable and robust wide-scale patterns of diversity. A set of protocols using a core collection of simple sequence repeat (SSR) markers, reference lines and standard alleles, plus a common system of allele nomenclature, was adopted in the study of maize genetic diversity in a network of laboratories in Asia. Pair-wise allele comparisons of the reference lines, done to assess the general agreement between datasets from four laboratories, showed error rates (raw) ranging from 5.8% to 9.7%, which were reduced to less than 8% after adjustments of correctable errors, and further reduced to less than 6% after the exclusion of all markers with greater than 10% individual error rates. Overall, 45% of the total mismatches were due to frameshift errors, 39% to wrong allele size, 15% to failed amplification and 1% to extra alleles. Higher genetic similarity values of the reference lines were achieved using fewer markers with data of higher quality rather than with more markers of questionable quality. Cluster analysis of the merged datasets showed the lines from southern China to be highly diverse, falling into six of the seven clusters observed and all well represented by tester lines. The lines from Indonesia fell into five of six groups, with two main groups represented by tester lines. The CIMMYT lines developed for the Asian region showed a relatively narrow genetic base, falling in two out of seven and in three out of six clusters in China and Indonesia, respectively. In contrast to the case in southern China where 95% of the lines clustered separately from the CIMMYT lines, lines in the Indonesian breeding program show a closer relationship with the CIMMYT lines, reflecting a long history of germplasm exchange

Item Type: Article
Divisions: UNSPECIFIED
CRP: UNSPECIFIED
Subjects: Others > Genetics and Genomics
Others > Maize
Depositing User: Mr Sanat Kumar Behera
Date Deposited: 16 Mar 2012 13:52
Last Modified: 16 Mar 2012 13:52
URI: http://oar.icrisat.org/id/eprint/5751
Official URL: http://dx.doi.org/10.1007/s00122-004-1626-8
Projects: UNSPECIFIED
Funders: Asian Development Bank, Sichuan Agricultural University, The Indonesia Agency for Agricultural Research and Development
Acknowledgement: D. A. Hoisington is presently with ICRISAT (Patancheru)
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