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Euphytica (2014) 197:109118 DOI 10.1007/s10681-013-1056-2
Detection of candidate R genes and single nucleotide polymorphisms for downy mildew resistance in maize inbred lines by association analysis
Arunee Wongkaew Chalermpol Phumichai
Julapark Chunwongse Sansern Jampatong
Pichet Grudloyma Taweesak Pulam Weerasak Doungchan
Received: 9 April 2013 / Accepted: 23 December 2013 / Published online: 16 January 2014 Springer Science+Business Media Dordrecht 2014
Abstract Downy mildew (DM) is a plant disease that strongly limits maize production. The resistance (R) genes for this disease have been identied and characterized and serve as important tools for plant disease evaluation. In this study, partial genes for PIC15, PO145579, and zmcf5 were identied and analyzed in a panel of 60 public and private maize inbred lines using bioinformatics and statistics tools. These candidate R genes exhibited an average nucleotide diversity value of 0.015. The negative Tajimas D values for these genes suggested that purifying selection has played a role in the evolution of maize DM resistance genes. In addition, linkage disequilibrium among these genes occurred across an extent
of * 200 bp. Using association analysis methods, a general linear model, and a mixed linear model, ve polymorphisms within the partial PIC15 and PO145579 genes were detected and associated with DM disease. These are new polymorphisms that have not previously been reported in association with DM disease traits. Therefore, correlations between these new polymorphisms and DM disease in these germ-plasm collections could advance the development of a functional marker for marker-assisted selection of DM disease resistance in maize breeding programs.
Keywords Downy mildew Maize disease
resistance gene Linkage disequilibrium
Association analysis General linear model
(GLM) Mixed linear model (MLM)
Electronic supplementary material The online version of this article (doi:http://dx.doi.org/10.1007/s10681-013-1056-2
Web End =10.1007/s10681-013-1056-2 ) contains supplementary material, which is available to authorized users.
A. Wongkaew C. Phumichai (&)
Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand e-mail: [email protected]; [email protected]
J. ChunwongseDepartment of Horticulture, Kasetsart University, Kamphaengsaen Campus, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
S. JampatongNational Corn and Sorghum Research Center, Inseechandrastitya Institute for Crop Research and Development, Kasetsart University, Klang Dong, Pak Chong, Nakhon Ratchasima 30320, Thailand
P. GrudloymaNakhon Sawan Field Crop Research Center, Department of Agriculture, Ministry of Agriculture and Cooperatives, Phahon Yothin, Tak Fa, Nakhon Sawan 60190, Thailand
T. PulamSweet...