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In genetic mapping studies PCR-based SSR and CAPS markers are used routinely and generation of such molecular markers becomes easier if one of the two parents of mapping population has sequence information available.
In contrast to biparental mapping populations, in which the pattern of LD and the allele frequency distribution are known and are independent of population genetic parameters, every association mapping population has a unique population history (both recent and ancient) that shapes its patterns of genetic variation and may determine which mapping method works best.
The negative correlation between recombination and residual heterozygosity observed in recombinant inbred lines of the maize nested association mapping population has been attributed to the inefficiency of selection against deleterious alleles in low recombination regions of the genome (McMullen et al. 2009; Gore et al. 2009).
The work of genotyping a mapping population has long been laborious and time-consuming, including tedious and expensive processes for marker discovery and genotyping of hundreds of lines with hundreds of markers.
The development and use of this mapping population has been described previously [ 26].
In situations where two or three clusters are observed in the GoldenGate, consistent with a biallelic SNP, the double haploids are either A/A or B/B homozygotes while the mapping population has all three allelic states, as expected.
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Approximately one-fourth of the mapping population had florets that developed a deep red color at maturity.
A total of 6,000 Infinium II type SNPs evenly distributed along the walnut physical map were selected for the construction of an Infinium BeadChip, which was used to genotype a walnut mapping population having 'Chandler' as one of the parents.
The female parent of the mapping population had white flowers and red colour in the fruit, while the male parent carried white flowers and no evidence of red flesh in male line siblings.
A subset of six plants of the T×E mapping population having a high number of recombination breakpoints and a uniform distribution across the Prunus genome was selected by Howad et al. [ 15].
Signal intensity plots from our A genome diploid mapping population had high average genotyping quality (GenTrain) scores, and the signal intensity plots were generally easy to interpret, with good separation between genotype calls.
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