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This finding suggests that these alleles are markers tagging the same variant in the gene region.
Finally, RIL XC88 showed the Cornell genotype for markers tagging the Pv09 region and the Xana genotype for markers of clusters Co-2 and Co-3.
The five SNP markers tagging the associated allele show marked variation in allele frequency between populations, being high among those of African ancestry but rare in other populations.
The third complementary gene segregated independently from molecular markers tagging the Co-1, Co-5, Co-4 and Co-u regions, so contingency chi-square tests between the resistance to race 453 and the remaining 368 loci included in the XC genetic map were conducted.
First, this analysis was focused on markers tagging the main six chromosome regions which included Co genes (Co-1 on LG Pv01; Co-2 on LG Pv11; Co-3 on LG Pv04, Co-4 on LG Pv08, Co-5 on LG Pv07 and the region of LG Pv02 in which the Co-u gene was mapped).
Contingency chi-square tests corresponding to the joint segregations for each of the resistances with markers tagging the six main anthracnose resistance clusters deviated significantly from what was expected by random in the case of markers SQ4 and SCAreoli, that tagged the Co-2 resistance cluster on LG Pv11 (Table 2).
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The markers tagged the ENPP1 locus at nearly equal intervals.
On chromosome VI, the CT119 marker tagging the Rpi-blb2 R-gene was included in MQTL_1_Late_blight.
Of these, the KASP marker tagging the 5AL genetic locus first identified in the MAGIC population was by far the most significant [−log10 p-value) = 36.42].
Ppd-A1 showed a strong trend towards increased R values at latitudes lower than 40° (Southern Italy, Syria and Lebanon, Tunisia, Morocco and Mexico) while the markers tagging Ppd- B1 showed an opposite trend.
However, in a 2-loci analysis for gene-gene interaction effects, there were significant interactions between DCLK1 intron 5 markers (m5.1 and m5.2) and markers tagging BDNF and ARC on the association with verbal memory (p-value = 0.03��0.003, after Bonferroni correction, see SOM).
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