Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties

Rostoks, N and Ramsay, L and MacKenzie, K and Cardle, L and Bhat, P R and Roose, M L and Svensson, J T and Stein, N and Varshney, R K and Marshall, D F and Graner, A and Close, T J and Waugh, R (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proceedings of the National Academy of Sciences, 103 (49). pp. 18656-18661. ISSN 1091-6490

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Abstract

Genomewide association studies depend on the extent of linkage disequilibrium (LD), the number and distribution of markers, and the underlying structure in populations under study. Outbreeding species generally exhibit limited LD, and consequently, a very large number of markers are required for effective whole-genome association genetic scans. In contrast, several of the world’s major food crops are self-fertilizing inbreeding species with narrow genetic bases and theoretically extensive LD. Together these are predicted to result in a combination of low resolution and a high frequency of spurious associations in LD-based studies. However, inbred elite plant varieties represent a unique human-induced pseudooutbreeding population that has been subjected to strong selection for advantageous alleles. By assaying 1,524 genomewide SNPs we demonstrate that, after accounting for population substructure, the level of LD exhibited in elite northwest European barley, a typical inbred cereal crop, can be effectively exploited to map traits by using whole-genome association scans with several hundred to thousands of biallelic SNPs.

Item Type: Article
Divisions: UNSPECIFIED
CRP: UNSPECIFIED
Subjects: Others > Genetics and Genomics
Others > Agriculture-Farming, Production, Technology, Economics
Depositing User: Library ICRISAT
Date Deposited: 25 Oct 2011 13:21
Last Modified: 16 Sep 2013 12:41
URI: http://oar.icrisat.org/id/eprint/3024
Official URL: http://dx.doi.org/10.1073/pnas.0606133103
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: UNSPECIFIED
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