Page 9 - Legume Genomics and Genetics

Legume Genomics and Genetics 2012, Vol.3, No.1, 1- 7
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with P<0.005 and LOD>3.0 as the threshold.
3.2 Materials and methods of Meta-analysis
Mapping information of soybean height QTLs, including
names, traits, chromosomes, markers LGs, marker and
population was collected from the public database
Soybase (www.soybase.org) and recent reports. QTLs of
one population for a given trait under a given
environment were integrated as one experiment, and
QTLs analyzed by the mean of several locations, were
also integrated as one experiment. Two important
parameters of QTL were the map position (most
likely position and CI) and explained proportion of
phenotypic variance, respectively. When the CI for
QTL position was not available in literature, the
formula proposed by Darvasi (1993; 1997) was used
to calculate 95% CI.
Although the QTLs from different populations had
different backgrounds and obtained by different
methods, all QTLs were projected from original maps
to the reference map, soymap2 (Song et al., 2004), by
most likely position and CI with homothetic function.
Calculations referred to reference (Chardon, 2004).
Most projected QTLs were in a cluster in the
integrated map. Based on the analysis principle of the
software BioMercator 2.1, the QTL cluster was that
the CI of original QTL covered half with each other,
or the CI of original QTL covered another, reference
to Qi (2009).
Meta-analysis was used to estimate the existence of the
real QTL and CI. The basic process of meta-analysis
was as follows. QTLs from many independent
experiments associated on the same LG at neighboring
interval were used to calculate a real QTL. This QTL
could give five models, and the minimum Akaike
Information Criteria (AIC) value was used to choose
the best model QTL, called real QTL. The formula was
estimated and described by Goffinet and Gerber (2000).
The height QTL was analyzed by software BioMercator
ver. 2.1-tools-Meta analysis. The consensus QTLs were
determined by the smallest AIC value.
Authors' contributions
Ya'nan Sun is first writer who perform this experiment,
data analysis and write manuscript; Huaihai Luan and
Chunyan Liu participated the experiment design and conducted
this experiment; Zhaoming Qi and Dapeng Shan participated
the field experiment; Guohua Hu and Qingshan Chen are the
persons who take charge of this project, including experiment
design, data analysis, writing and modifying of the manuscript,
and corresponding authors of this manuscript. All authors have
read and approved the final manuscript.
Acknowledgments
This study was partially supported by the ‘Transgenic Specific
Technology’ program (2009ZX08009-013B), the Chinese
‘Introducing International Super Agricultural Science and
Technology’ program (2006-G1(A)) and the ‘Public Agricultural
research special funds projects’ (200903003).
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