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The presence of predicted microsatellite repeat motifs and correspondence of fragment length polymorphism with repeat length expansion/contraction for each polymorphic markers were inferred among chickpea genotypes.
Unique marker segregation patterns were included in the set of map bins if they met one of two criteria: (1) at least three independent markers were inferred to have the pattern independently, or (2) the pattern was inferred from at least one marker with at least 20 SNPs such that the mean of the estimated probabilities of the inferred SNP phases was greater than 0.9.
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A The gold markers are inferred as the main convergence nodes of back-projected rays arising from the detected projection peaks.
The expected position of additional 288 COSII markers was inferred in the pepper map via pepper-tomato synteny, bringing the total orthologous markers in the pepper genome to 587.
The chromosome and distance between markers was inferred from Miller et al. (2012).
However, each of the three resolutions for the placement of those clades received concordance factors below 50% with over 95% credibility: the discordance among COSII markers was inferred to be real and strong.
Missing marker and pseudo marker genotypes were inferred from flanking marker information using the multipoint method (Jiang and Zeng 1997).
Progenitor haplotype probabilities for each marker interval were inferred using the HAPPY R package (Mott et al. 2000) and an additive model.
Regions of strongly associated markers (LD blocks) were inferred using the confidence-interval method proposed by Gabriel et al. [ 47].
For the sex-specific markers, the linkage phases were inferred automatically, while for the markers with 1 : 2 : 1 segregation type (AB × AB), the linkage phase was deduced based on the genotypes of grandparents to assist the map construction.
We evaluated the discriminative power of pathway markers, where the pathway activities were inferred using the proposed method as well as other inference methods.
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