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Table 5 Top three favorable marker alleles on each locus detected GT, GC and AC across five environments and typical varieties carrying the allele

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

Traits No. Locus-allele Chr. MAF Environment PEV Typical carrier variety
GT (grade) 1 RM232-155 3 0.071 E4 0.63 Feilaifeng
2 RM232-145 3 0.192 E4 0.67 Wanyedao
3 RM232-150 3 0.279 E4 0.03 Laowusi
4 RM267-95 5 0.086 E3 1.11 Xiangnuodao
5 RM267-125 5 0.106 E3 0.61 Feilaifeng
6 RM267-120 5 0.104 E3 0.39 Kuobanzhong
7 RM3600-90 9 0.186 E2 2.00 Longdun105
8 RM3600-85 9 0.368 E2 1.02 Ligengqing
9 RM3600-80 9 0.149 E2 0.29 Songjing12
10 RM264-195 8 0.128 E1 0.97 Shiluqing
11 RM264-160 8 0.132 E1 0.85 Kunnong8
12 RM264-130 8 0.091 E1 0.74 Yebaidao
GC (mm) 1 RM6712-95 3 0.190 E2 13.12 Dongnongjingnuo418
2 RM6712-115 3 0.223 E2 11.12 Baikenuo
3 RM5753-195 6 0.108 E4 24.02 Shenlenuo
4 RM5753-115 6 0.071 E4 28.57 Hongnong5
5 RM5753-130 6 0.069 E4 3.06 Haonuopie
AC (%) 1 RM6712-115 3 0.223 E1 -4.32 Molingjing
E2 -1.97 Xudao3
E3 -0.45 Wujing15
E5 -2.04 Baoxintaihuqing
2 RM6712-95 3 0.190 E1 -0.68 Dongnongjingnuo418
E2 -3.11 Munian4
E3 -1.67 Hangzhounuo
E5 -1.24 Munian4
3 RM5753-195 6 0.108 E2 -3.21 Guozinuo
4 RM5753-115 6 0.071 E2 -2.21 Suyunuo
5 RM5753-205 6 0.970 E2 -1.13 Suzhouqing
6 RM258-125 10 0.392 E1 -1.74 Yue109
7 RM258-140 10 0.247 E1 -0.76 Wandao68
8 RM258-135 10 0.307 E1 -0.70 Shenlenuo
9 RM6327-230 11 0.104 E2 -3.78 Jinggunuo
E3 -0.85 Hangzhounuo
10 RM6327-175 11 0.149 E2 -2.53 Baimangnuo
E3 -1.31 Baimangnuo
  1. Note: Fo r GT and GC trait, alleles with positive phenotypic effect value (PEV) are defined favorable alleles, whereas alleles with negative phenotypic effect value are considered as favorable alleles for AC trait