Using this pipeline we identified two putative alternative loci for known miRNAs, and 11 new miRNAs.
Moreover, because conifer genomes are very large, the genetic linkage within our full-sib family likely extends over numerous genes that, due to the limited statistical power of the S+A-set, all could be considered as alternative loci for the QTL.
The alignment and corresponding single-gene tree characteristics (see below) served as a basis for several alternative locus selection strategies.
An alternative locus specific method with improved reliability for CNV determination is the paralogue ratio test (PRT) [ 8].
For homozygote alternative loci, SNV concordance approached 100% for SAM, UG and HC, with slightly lower concordance observed in PL.Genotype concordance was very high in both single and multi sample results; depending on software, genotype concordance for single sample results was between 99.2-99.3% and between 99.1-99.3% for multi sample methods.
The presence of alternative loci in iJN746 explains partial disagreement for argA, argE, ilvA, and argJ.
Our results indicate that the Col1a1 locus is a good alternative to the Rosa26 locus for ubiquitous gene expression, as noted by diffuse eGFP expression after tamoxifen-mediated deletion of tdTomato in Col1a1 FRT-Cre-ER-T2-FRT; Rosa26 mTmG/+ mice.
In the case of Okanagan Lake kokanee, an outlier-based approach may offer the only alternative to neutral loci for informing fisheries management.
The use of outlier loci constitutes a promising alternative to neutral loci for informing fisheries management of recently diverged stocks, particularly for enhancing stock assessment, long-term ecological monitoring, and evaluation of current management practices.
Potentially, by using this UI locus for breeding of Brassica crops, alternative efficient systems for F1 breeding could be available in the future.
