J Integr Plant Biol. ›› 2015, Vol. 57 ›› Issue (12): 1046-1062.DOI: 10.1111/jipb.12361

• Functional Omics and Systems Biology • Previous Articles     Next Articles

Quantitative trait locus mapping with background control in genetic populations of clonal F1 and double cross

Luyan Zhang1, Huihui Li1, Junqiang Ding2, Jianyu Wu2 and Jiankang Wang1**   

  1. 1The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, and CIMMYT China Office, the Chinese Academy of Agricultural Sciences, Beijing, China
    2National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, China


In this study, we considered five categories of molecular markers in clonal F1 and double cross populations, based on the number of distinguishable alleles and the number of distinguishable genotypes at the marker locus. Using the completed linkage maps, incomplete and missing markers were imputed as fully informative markers in order to simplify the linkage mapping approaches of quantitative trait genes. Under the condition of fully informative markers, we demonstrated that dominance effect between the female and male parents in clonal F1 and double cross populations can cause the interactions between markers. We then developed an inclusive linear model that includes marker variables and marker interactions so as to completely control additive effects of the female and male parents, as well as the dominance effect between the female and male parents. The linear model was finally used for background control in inclusive composite interval mapping (ICIM) of quantitative trait locus (QTL). The efficiency of ICIM was demonstrated by extensive simulations and by comparisons with simple interval mapping, multiple-QTL models and composite interval mapping. Finally, ICIM was applied in one actual double cross population to identify QTL on days to silking in maize.


Zhang L, Li H, Ding J, Wu J, Wang J (2015) Quantitative trait locus mapping with background control in genetic populations of clonal F1 and double cross. J Integr Plant Biol 57: 1046–1062 doi: 10.1111/jipb.12361

Key words: Clonal F1, double cross, haploid building, imputation, quantitative trait locus mapping

Editorial Office, Journal of Integrative Plant Biology, Institute of Botany, CAS
No. 20 Nanxincun, Xiangshan, Beijing 100093, China
Tel: +86 10 6283 6133 Fax: +86 10 8259 2636 E-mail: jipb@ibcas.ac.cn
Copyright © 2022 by the Institute of Botany, the Chinese Academy of Sciences
Online ISSN: 1744-7909 Print ISSN: 1672-9072 CN: 11-5067/Q