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Following linkage group construction by R/qtl, we used the physical linkage known from the S. rosetta genome assembly to manually link markers on the same supercontig into a single linkage group.
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Refer to Figure 1 figure supplement 1 to link marker expression to cell type localization within slug or culminant.
q FETOX-4-1 covering four linked markers was mapped at 7.4-12.0 Mb on chromosome 4.
The recombination between the target gene and linked markers would affect the selection accuracy through MAS.
Additive effect, linked markers, LOD score value and PVE are summarized in Table 2.
There was a sharp decline in LD decay for the linked markers at 5 20 cM.
Hence, these markers were considered as tightly linked markers and used for introgressing BPH31 in the background of Jaya.
M1, M2, M5 and M6 are linked markers for negative selection of linked segments of target genes.
Two or more closely linked markers that showed significant association were assumed to identify the same QTL.
Another QTL, q FETOX-1-2 was highly associated with two linked markers at the position of 36.8-38.2 Mb.
The putatively linked markers were then used for genotyping of the individual F2 plants to study linkage relationship.
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