Table 3. Summary of significant single nucleotide polymorphisms (SNPs) markers for two traits: Shoot manganese concentration (SMC) and relative shoot length (RSL).
| Trait | SNP | Chr | Position | Allele | Remark | ||
|---|---|---|---|---|---|---|---|
| Major | Minor | Missing | |||||
| SMC | SNP-2.11394332. | 2 | 11394337 | A (210) | G (61) | Intergenic region | |
| SMC | SNP-2.17092835. | 2 | 17098706 | G (154) | A (76) | 41 | Intergenic region |
| SMC | SNP-2.33444628. | 2 | 33450498 | A (139) | G (119) | 13 | Intergenic region |
| SMC | SNP-12.14960076. | 12 | 14962735 | T (195) | C (35) | 41 | Intergenic region |
| SMC | SNP-12.21274465. | 12 | 21307919 | G (250) | C (14) | 6 | Intergenic region |
| RSL | SNP-2.22465867. | 2 | 22471737 | T (226) | C (15) | 31 | Gene coding, non-synonymous, Asp-Gly, LOC_Os02g37170 |
SNPs which passed the 5% FDR adjustment (rrBLUP) and -log10 (p)>5 (TASSEL) are listed together with the corresponding trait, SNP marker ID (used in HDRA SNP genotype data), chromosome (Chr) number and position. Retrotransposon genes were not considered in the analysis. SMC shoot Mn concentration, RSL relative shoot length