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Table 4 Marker–trait associations with –LogP value ≥ 3.0, their equivalent false discovery rate (FDR), proportion of phenotypic variance explained (PVE), and the average allele effects (AAE) across five environments for GT (ASS), GC and AC traits

From: Favorable alleles mining for gelatinization temperature, gel consistency and amylose content in Oryza sativa by association mapping

Traits No. SSR marker Chr. position (bp)a Environment -LogP FDR PVE(%) AAEb
GT 1 RM232 3 8409404-8410886 E4 3.48 0.0022 9.74 0.80
2 RM267 5 21881317-21881455 E3 3.48 0.0023 7.04 0.66
3 RM264 8 27926632-27926652 E1 3.60 0.0024 7.43 1.16
4 RM3600 9 17107752-17107843 E2 4.92 0.0029 10.12 1.38
GC 1 RM6712 3 35020004-35020027 E2 3.30 0.0042 7.46 16.60
2 RM5753 6 30452023-30452067 E4 3.20 0.0028 10.54 20.52
AC 1 RM6712 3 35020004-35020027 E1 4.27 0.0022 8.83 -3.57
E2 3.66 0.0022 7.89 -4.56
E3 3.22 0.0019 7.17 -4.87
E5 3.17 0.0020 7.17 -4.76
2 RM5753 6 30452023-30452067 E2 3.08 0.0065 10.48 -3.66
3 RM258 10 17570591-17570612 E1 3.04 0.0043 5.69 -5.28
4 RM6327 11 364257-364310 E2 3.09 0.0043 12.87 -2.66
E3 3.19 0.0038 11.39 -2.75
  1. Bold markers represent that they were associated with two traits
  2. aThe estimated physical position (bp) was inferred from the Gremene (http://www.gramene.org/markers) and NCBI (https://www.ncbi.nlm.nih.gov/Blast.cgi)
  3. bAverage positive allele effects of SSR loci associated significantly with GT and GC traits, average negative allele effects of SSR loci associated significantly with AC trait