To identify heterogeneous populations, alignment results were screened using MapView software (Fig. 3B).
Within the impact approximation, collisional line broadening parameters and depolarizing and polarization transfer (population, orientation, alignment transfer) rates are complementary: both include the effect of collisional transitions between the Zeeman sublevels of a given level, or between fine or hyperfine structure levels of a given term.
SAGA [ 15] evolves a population of alignments in a quasi evolutionary manner to gradually improve their fitness.
Inter-population homoeologue alignment using allele size (Table 3) was, therefore, derived from identifying the homoeologue pairing that maximised the number of joining loci in agreement with the alignment (matches) while minimising the number of joining loci at variance with the alignment (mismatches).
The allele size-based inter-population homoeologue alignments were made before analysis of the SL-HS markers, and in all cases SL-HS data corroborated the pairings indicated by maximised allele size agreement data.
The 406 sequence pair average was included as a control indicating the diversity within the 29 sequence population along the alignment.
A new LEA genetic resource was found in the natural B. rapa population using sequence alignment.
An unbiased estimation of diversity of a population requires the alignment of homologous sequences.
The 223 discontinuously mapped scaffolds could indicate incorrect assembly or other factors including reference errors, population differences or alignment artifacts.
Merged maps are attractive since their integration allows for an increase in marker density without the need of additional genotyping, increased marker portability (i.e., polymorphic markers can be used in more than one population), improved marker alignment precision (i.e., congruent anchor maker position), and broader inferential capabilities (i.e., cross-population prognostication).
