Table 2.
SNPs, chromosomal position and candidate genes significantly associated with three husk traits identified by GWAS using MLM method
| Trait | SNP | Chr | Position (bp) | Allelea | R2(%)b | MAFc | P-value | Gene | Gene interval (bp) | Annotation | Pathwayd |
|---|---|---|---|---|---|---|---|---|---|---|---|
| HN | chr4.S_205554186 | 4 | 205554186 | A/C | 2.6 | 0.06 | 9.40E-06 | GRMZM2G016447 | 205553899-205557585 | Unknown | n.d |
| HN | SYN10582 | 5 | 17966191 | G/A | 0.2 | 0.19 | 6.43E-06 | GRMZM2G097364 | 17965846-17977924 | Unknown | n.d |
| HN | chr5.S_203403202 | 5 | 203403202 | C/A | 1.9 | 0.31 | 6.41E-06 | GRMZM2G542272 | 203402576-203403244 | Unknown | n.d |
| HN | chr9.S_123419252 | 9 | 123419252 | C/G | 4.1 | 0.18 | 2.57E-06 | GRMZM2G124239 | 123411699-123426029 | Vacuolar protein sorting-associated protein 52 | Cellular trafficking |
| HN | chr10.S_143066093 | 10 | 143066093 | C/G | 3.7 | 0.08 | 1.00E-05 | GRMZM2G396846 | 143066059-143068062 | Global transcription factor group E7 | Transcriptional regulation |
| Totale | 11.2 | ||||||||||
| HW | chr5.S_215787314 | 5 | 215787314 | T/C | 4.9 | 0.18 | 4.51E-06 | GRMZM2G056598 | 215781414-215787413 | Chromatin remodeling 4 | Transcriptional regulation |
| Totale | 4.9 | ||||||||||
| HT | chr5.S_11925326 | 5 | 11925326 | C/T | 8.2 | 0.06 | 1.06E-06 | GRMZM2G157166 | 11925082-11925880 | Oxysterol binding protein-related protein 1A | Metabolism |
| HT | chr6.S_106444300 | 6 | 106444300 | C/T | 7.2 | 0.06 | 3.37E-06 | GRMZM2G404081 | 106425279-106427173 | GDSL/SGNH-like acyl-esterase family | Metabolism |
| HT | chr8.S_145474885 | 8 | 145474885 | T/C | 11.5 | 0.09 | 2.08E-06 | GRMZM2G029077 | 145474389-145483146 | Adaptin family | Cellular trafficking |
| Totale | 21.4 |
aMajor/minor allele, underlined bases are the favorable alleles
bPercentage of phenotypic variation explained by the additive effect of the single significant SNP
c Minor allele of frequency
d n.d means not denoted
e Total percentage of phenotypic variation explained by all significant SNPs