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For our analysis the number of parental populations was set at two.
These estimates rely on allele frequencies of AIMs in four putative un-admixed parental populations [39].
Moreover, we assumed that allele frequencies were correlated (i.e. similar across parental populations) and that the parental populations show different levels of differentiation (FST, with prior mean of 0.01 and standard deviation of 0.05).
We assumed that three parental populations (K = 3 clusters) contributed to the genome of the admixed individuals.
Indeed, when considering K = 3 unknown parental populations, each cluster could be unambiguously assigned to a breed.
This is expected to some extent as variants were selected to ensure the absence of LD in the parental populations.
Since the surrogate parental populations chosen here are unlikely to represent the genetic variability present in the true parental populations, the resulting mY values merely describe the relative contribution of the surrogate parental populations to the admixed populations, not their absolute contributions.
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Most bi-parental populations have only one opportunity for crossing over and about 34 break-up points are estimated to occur per crossing generation (Huang et al., 2009).
The genotyping by sequencing approach used previously to genotype bi-parental populations (Elshire et al. 2011); (Huang et al. 2010) was used in this study.
Relative to bi-parental populations, MAGIC populations will have greater genotypic diversity, a higher level of recombination, and reduced linkage drag.
The mapping of quantitative trait loci (QTL) using bi-parental populations identified several tolerance QTL mitigating symptom formation, grain yield losses, or the degradation of straw quality.
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