Comparison of different methods for mapping QTL of maize plant height with R/qtl

R/qtl%interval mapping%Composite interval mapping%Two-dimension scan%Multiple-QTL fitness

R/qtl which implemented by R language is a software specially for QTL analysis. In order to study the difference among interval mapping (IM), composite interval mapping (CIM), two-dimension scan and multiple-QTL fitness in mapping QTL, plant height data of an F2:3 maize population was used to perform QTL mapping and compare the analyzing results of difference methods. The results showed that a total of eight QTL were detected by all methods. In IM method, seven QTL were detected,and the total contribution to phenotype variation reached 54.7%, which five QTL were detected by difference algorithms, and their locations, LOD values, confidence intervals and contribution of each QTL were almost the same. In CIM mapping, four QTL were detected, which accounted for about 27.66% of phenotype variation, wherein two QTL located at 158 cM and 222cM in chromosome 3 respectively could be detected by all four algorithms. The parameters estimated by CIM and IM for four common QTL were consistent. A total of seven QTL were detected using two-dimension scan, and they explained 54.97% of phenotype variation. No interacted QTL were found. Except one QTL located at 33.5cM in chromosome 6, other QTL were consistent with those detected in IM method. Only three QTL were found by multiple-QTL fitness, and their total contribution to phenotype variation was up to 21.52%. No interacting QTL were found by multiple-QTL fitness method. These results demonstrated that the number and contribution estimated by different methods showed subtle difference to certain extent, but the major QTL could be found by all methods.In addition, there were only major QTL controlling plant height, and no epistatic QTL was found.