Transmissions of information across generations which does not involve traditional inheritance of DNA-sequence alleles is often referred to as soft inheritance [15] or "Lamarckian inheritance".
While choosing a representative gene for loci containing 2 fully sequenced alleles is straightforward, in many cases 1 or both alleles were not fully sequenced and thus the genes exist in pieces on separate contigs (i.e. no contiguous sequence for the complete gene).
All of the differences between the sequenced alleles were caused by addition, removal and rearrangement of repeat units as expected if strand slippage and recombination are the predominant mechanisms that generate new alleles [1].
Introns 1, 2 and 3 for each of the fully sequenced alleles were discarded and reconstructed using the remaining alleles, considering only exon 2 and 3 sequences for nearest neighbor identification.
Numbering of the sequence in all alleles is given relative to the translation start.
The question remains whether the sequence divergence between alleles is a better functional predictor for immunocompetence than the plain number of alleles.
A new solution to separating sequences from two alleles is using the next-generation sequencing.
The distribution of the frequency of cattle-specific mtDNA sequences and microsatellite alleles is shown in Fig. 1b.
There are four allelic variants of the wild-type allele, and sequence numbering in all alleles is relative to the translation start codon.
The DNA sequence identity of hordein alleles is frequently higher than 95%, therefore designing specific primers for families, subfamilies and individual members is challenging.
Genomic sequences of alleles were very similar to each other (0.08 - 2.42% sequence divergence) and we detected only five amino acid substitutions and no premature stop codons in the coding region (Table 1).
