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BreakSeq Lite version 1.0 [ 81] was used for junction mapping.
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This method was also used for junction flows.
Mapped reads were then assembled into complete transcripts by using the splice junction mapping tool Cufflinks [ 36] with option –G, which uses the Ensembl reference gene track to improve mapping.
The previously described genetic map was used for QTL mapping.
Haldane mapping function was used for all mapping calculations.
Sex-averaged linkage map distances were used for QTL mapping.
Composite Interval mapping (model 6) was used for mapping QTLs.
The Kosambi mapping function was used for map length estimations.
The regression mapping algorithm was used for map construction.
Electron (hole) mobility in p/i/n region for top junction is 4.6/4.6/100 (50/0.92/0.92) × 10−6 m2/V/s[17] and carrier mobility 100 times over those in top junction are used for the μc-Si H junction.
As TEs are largely enriched in the recombination-low heterochromatic regions or other gene-poor regions, where few genetic markers are generally mapped, the integration of TE distribution and genetic map can help users to develop unique repeat-junction markers [ 30] that can be used for construction of finer genetic map or mapping of genes of interest.
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