Table 1

Intra- and interspecific cross amplification rates of SNPs on the Lolium oligo pool assay (LOPA1)
Species Mapping population Average call rate of all SNPs* Number (percentage) of SNPs generating signals Number (percentage) of polymorphic SNPs referred to SNPs generating signals Number (percentage) of polymorphic SNPs referred to 768 SNPs on LOPA1
Lolium perenne L. VrnA 0.914 a 692 (90%) 509 (74%) 509 (66%)
DLF1 0.846 b 567 (74%) 241 (43%) 241 (31%)
DLF2 0.858 b 605 (79%) 235 (39%) 235 (31%)
DLF3 0.840 b 598 (78%) 201 (34%) 201 (26%)
DLF4 0.850 b 601 (78%) 250 (42%) 250 (33%)
ILGI 0.882 c 665 (87%) †192 (29%) 192 (25%)†
Lolium multiflorum Lam. Xtg-ART 0.818 d 557 (73%) 131 (24%) 131 (17%)

*Mapping populations with different letters vary significantly at P < =0.05 in their average call rates.

†Estimation from one parent only.

SNP performance of LOPA1 in VrnA was compared to different Lolium multiflorum Lam. (Xtg-ART) and Lolium perenne L. (DLF1 to 4) mapping populations, each represented with the two parental genotypes. For each mapping background, the average call rate of all SNPs is given and varies significantly at P < =0.05 if indicated with different letters. SNPs with a clear fluorescent signal detected in both mapping patents are considered as “SNPs generating signals”. The numbers and percentages of polymorphic SNPs refer to SNP markers being heterozygous either in one or both parents, indicating a segregation pattern of lmxll, nnxnp or hkxhk [53], respectively, in the corresponding mapping population. For the ILGI reference population represented with one parental genotype only, the number of SNPs being heterozygous is given. The percentages of polymorphic SNPs are refereeing to the number of SNPs generating signals and the total number of SNPs on LOPA1.

Studer et al.

Studer et al. BMC Genomics 2012 13:140   doi:10.1186/1471-2164-13-140

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