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Genotypes for unrelated individuals and parents were generated based on the corresponding allele frequencies with an assumption of linkage equilibrium between adjacent random markers, and genotypes for children in each family were generated according to parental genotypes with recombination rate 0.01 between the causal and the test sites.
The discrepancies could be due to use of different sets of markers and genotypes.
Markers and genotypes with more than 10% of missing data were excluded from the analysis.
The kinship matrix was obtained using ML-Relate software [ 37] with the same SSR markers and genotypes as above.
Additional file 1: Information of DArT-seq markers and genotypes of the SY-PM genetic mapping population of B. juncea.
SNPs and indels were placed in the bin map by visual inspection of the genotypes predicted by the markers and genotypes in the bin set.
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Additional file 1: Sequences of the mapped SLAF markers and genotype of the mapping samples.
However, the development of molecular markers and genotyping a mapping population is very expensive and time consuming.
Sequence related amplified polymorphism (SRAP) markers and Genotyping-by-Sequencing (GBS) technologies were successfully used for genotyping wheat germplasm, cultivars and mapping populations [ 37- 39].
These polymorphic markers were subsequently used for analysis of genetic diversity and population structure, identification of trait-associated markers and genotype characterization in Elaeis guineensis.
The molecular data retrieved comprise: QTL or gene, associated marker and genotyping data from CEREALAB project work.
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