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Power from joint linkage mapping, despite being low, was slightly higher than that from individual family mapping.
Thus joint linkage mapping provides us with a promising approach to study the genetics of flowering time.
These results indicated that for joint linkage mapping, rare QTL are more difficult to detect than common QTL.
For small-effect QTL, the power of individual family mapping was slightly lower than the power of joint linkage mapping.
Joint linkage mapping of NAM populations better avoids the confounding effect of population structure, and identified most genetic variation of flowering time (Tables S1 and 1).
But the LOD scores (Fig. 1) are much higher than those from individual family mapping [21], which empirically demonstrated the higher mapping power of joint linkage analysis.
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Additionally, joint linkage-association mapping strategies were proposed to evaluate the false association in soybean [ 28].
It contained five joint-linkage markers each with a RMIP >0.10 for PHT.
This marker set was then employed in joint-linkage-assisted GWAS of the RIL families.
To identify QTL, bootstrapped joint-linkage mapping was performed across RIL families (Table 2, Table S3).
To check the effect of the higher density linkage map on joint-linkage analysis, we also conducted one fivefold cross-validation analysis of joint-linkage mapping of CL with the 0.2 cM resolution map.
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