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When isolates had more than one amplification peak (i.e. multiple alleles at a locus), we chose the highest peak as the main allele but also recorded alternate alleles.
Interpretation of microsatellite patterns in tetraploid species is not straightforward due to the presence of multiple alleles at each locus that can be present in more than one copy, thus the true genotype cannot be accurately resolved.
In addition, although not comparable to the scale of association mapping in diverse populations where hundreds of alleles per locus can be simultaneously tested, in JICIM multiple alleles at the order of tens can easily be tested simultaneously (Tables S1 and 1).
For each of the 120 pairs among the 16 loci, the D´ linkage disequilibrium index was plotted (using the values for each pair of alleles that had frequencies of >0.1 and taking the mean wherever there were multiple alleles at either or both loci).
We found or confirmed multiple alleles at POLLED, MC1-R, KIT, KITLG and PMEL.
Polyploidy species might not have faster pace of gene loss despite the redundancy of multiple alleles at each locus.
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For population genetic analyses, individual haplotypes were reconstructed for the nine microsatellites, when possible (single allele observed at each locus or multiple alleles observed at only one locus).
When D > 0, the average heterozygosity is more than that of segregating sites and can be considered as presence of multiple alleles; some at low and others at high frequencies [ 59, 60].
Numbers of multiple clone infections varied considerably: these were rare in Colombia and India, but > 60% of isolates carried multiple alleles in at least one locus in Thailand and Laos.
Multiple alleles may exist at single resistance loci within populations with a broad genetic base, as we observed at the Pi33 locus in our indica panel.
In cases were multiple alleles were detected at a single locus, these were interpreted as Symbiodinium populations comprised of more than a single Clade B genotype [following 22].
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