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Segregation distortion has been previously reported in cotton populations and, not unexpectedly, a number of markers in both the intraspecific and interspecific maps showed significant distortion from expected F2 segregation ratios.
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Distortions from expected Mendelian allelic segregations were observed for all mapped parents of the segregating progenies.
One of the problems in linkage mapping of oysters is that moderate distortions from expected Mendelian segregation are common [ 5].
Distortions from expected Mendelian segregation have been observed in both inter-specific and intra-specific derivatives with different magnitudes.
Those markers with significant amounts of segregation distortion (departure from expected Mendelian segregation ratios (α ≥ 0.05)) are indicated with '*' at the end of the locus name (Additional files 1 and 2).
Distortion from the expected Mendelian genotypic ratio was observed for three markers: UNH130, UNH180 and UNH907, suggesting linkage with a QTL affecting survival.
No segregation distortion from the expected ratio was observed in the analyses for any marker.
Segregation distortion from an expected 1 1 DR1350: N2 ratio was tested by χ2 analysis for each marker with Bonferroni-corrected significance levels.
From the initial panel, only SNPs with more than 95% of detectable genotype signal (call) and SNPs with no distortion from the expected 50% inheritance of each allele on a 99% confidence interval were considered for analysis (Table S1).
Markers were examined by Chi-square analysis and those showing extreme segregation distortions (p = 0.0001) from expected 1 2 1 ratios were eliminated from the analysis.
In this study, a significant proportion of markers demonstrated a departure from expected Mendelian segregation ratios (segregation distortion; α < 0.05).
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