Open Access Highly Accessed Research article

Combined linkage and association mapping reveals candidates for Scmv1, a major locus involved in resistance to sugarcane mosaic virus (SCMV) in maize

Yongfu Tao1, Lu Jiang1, Qingqing Liu1, Yan Zhang1, Rui Zhang1, Christina Roenn Ingvardsen3, Ursula Karoline Frei2, Baobao Wang1, Jinsheng Lai1, Thomas Lübberstedt2 and Mingliang Xu1*

  • * Corresponding author: Mingliang Xu

  • † Equal contributors

Author Affiliations

1 National Maize Improvement Center, China Agricultural University, 2 West Yuanmingyuan Road, Beijing 100193, People’s Republic of China

2 Department of Agronomy, Iowa State University, 1204 Agronomy Hall, Ames, Iowa 50011, USA

3 Research Center Flakkebjerg, University of Aarhus, 4200, Slagelse, Denmark

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BMC Plant Biology 2013, 13:162  doi:10.1186/1471-2229-13-162

Published: 18 October 2013



Sugarcane mosaic virus (SCMV) disease causes substantial losses of grain yield and forage biomass in susceptible maize cultivars. Maize resistance to SCMV is associated with two dominant genes, Scmv1 and Scmv2, which are located on the short arm of chromosome 6 and near the centromere region of chromosome 3, respectively. We combined both linkage and association mapping to identify positional candidate genes for Scmv1.


Scmv1 was fine-mapped in a segregating population derived from near-isogenic lines and further validated and fine-mapped using two recombinant inbred line populations. The combined results assigned the Scmv1 locus to a 59.21-kb interval, and candidate genes within this region were predicted based on the publicly available B73 sequence. None of three predicted genes that are possibly involved in the disease resistance response are similar to receptor-like resistance genes. Candidate gene–based association mapping was conducted using a panel of 94 inbred lines with variable resistance to SCMV. A presence/absence variation (PAV) in the Scmv1 region and two polymorphic sites around the Zmtrx-h gene were significantly associated with SCMV resistance.


Combined linkage and association mapping pinpoints Zmtrx-h as the most likely positional candidate gene for Scmv1. These results pave the way towards cloning of Scmv1 and facilitate marker-assisted selection for potyvirus resistance in maize.

Maize; SCMV; QTL; Fine-mapping; Association mapping