|  |  |  |  |  |  |  |  | Candidate genes based on RNA-Seqc |  |
---|---|---|---|---|---|---|---|---|---|---|
Trait | SNP | Chr | Positiona | P | Alleles | R2 (%) | Geneb | Reference | Annotation | Fold change |
Forks | PZE-104010552 | 4 | 7,929,588 | 5.0 × 10−5 | A/G | 8.9 | Zm00001d048998 | Mu et al. 2017 [21] | Chlorophyll a-b binding protein CP26 | −2.03939 |
Crossings | PZE-104092320 | 4 | 167,437,768 | 4.7 × 10−5 | A/G | 1.8 | Zm00001d051804 | Luo et al. 2015 [22] | Glutamine synthetase root isozyme 4 | 1.65671 |
Forks | PZE-104043052 | 4 | 61,411,237 | 6.5 × 10− 5 | A/C | 11 | Zm00001d049995 | Nitrate reductase [NADH] | −2.39002 | |
Crossings | PZE-104092320 | 4 | 167,437,768 | 4.7 × 10−5 | A/G | 1.8 | Zm00001d051666 | Zanin et al. 2015 [23] | Neutral/alkaline invertase | 1.83246 |
PRL | ZM005894–0463 | 4 | 31,060,531 | 5.6 × 10−5 | A/C | 9.9 | Zm00001d049380 | Putative aminotransferase superfamily protein | 0.66934 | |
CRN | PZE-104016717 | 4 | 16,500,659 | 5.2 × 10−5 | A/G | 11 | Zm00001d049059 | He et al. 2016 [24] | Alcohol dehydrogenase2 | 0.766936 |
Tips | PZE-104049074 | 4 | 75,505,829 | 5.2 × 10−5 | A/G | 8.7 | Zm00001d050195 | WRKY DNA-binding domain protein | −0.795948 | |
Forks | PZE-104010552 | 4 | 7,929,588 | 5.0 × 10−5 | A/G | 8.9 | Zm00001d048866 | (Z)-3-hexen-1-ol acetyltransferase | 1.07489 | |
Forks | PZE-104010552 | 4 | 7,929,588 | 5.0 × 10−5 | A/G | 8.9 | Zm00001d048736 | S-alkyl-thiohydroximate lyase SUR1 | −0.576864 | |
CRN | PZE-105047147 | 5 | 36,470,371 | 6.1 × 10−5 | A/G | 13 | Zm00001d014200 | Expressed protein | 0.402627 | |
Forks | PUT-163a-91,875,212-4781 | 5 | 7,724,698 | 5.9 × 10−5 | A/G | 10 | Zm00001d013263 | Expressed protein | 1.51149 | |
Forks | PZE-104043052 | 4 | 61,411,237 | 6.5 × 10−5 | A/C | 11 | Zm00001d050092 | Zhang et al. 2015 [25] | Putative subtilase family protein | 0.585778 |
Forks | PZE-104043052 | 4 | 61,411,237 | 6.5 × 10−5 | A/C | 11 | Zm00001d049990 | Putative ENTH/ANTH/VHS protein | 1.38056 | |
PRL | ZM005894–0463 | 4 | 31,060,531 | 5.6 × 10−5 | A/C | 9.9 | Zm00001d049554 | Putative glycerol-3-phosphate transporter 1 | −0.807844 | |
PRL | ZM005894–0463 | 4 | 31,060,531 | 5.6 × 10−5 | A/C | 9.9 | Zm00001d049551 | Putative cytochrome P450 protein | 2.50626 | |
PRL | ZM005894–0463 | 4 | 31,060,531 | 5.6 × 10−5 | A/C | 9.9 | Zm00001d049502 | maternal effect embryo arrest 60 | 0.542646 | |
PRL | ZM005894–0463 | 4 | 31,060,531 | 5.6 × 10−5 | A/C | 9.9 | Zm00001d049464 | B-box type zinc finger family protein | 0.980937 | |
PRL | ZM005894–0463 | 4 | 31,060,531 | 5.6 × 10−5 | A/C | 9.9 | Zm00001d049418 | Germin-like protein subfamily 1 member 8 | 1.11388 | |
PRL | ZM005894–0463 | 4 | 31,060,531 | 5.6 × 10−5 | A/C | 9.9 | Zm00001d049407 | Polyphenol oxidase chloroplastic | −0.61096 | |
PRL | ZM005894–0463 | 4 | 31,060,531 | 5.6 × 10−5 | A/C | 9.9 | Zm00001d049365 | Methionine aminopeptidase | 0.319478 | |
CRN | PZE-104016717 | 4 | 16,500,659 | 5.2 × 10−5 | A/G | 11 | Zm00001d049187 | Phosphogluconate dehydrogenase3 | −1.54203 | |
CRN | PZE-104016717 | 4 | 16,500,659 | 5.2 × 10−5 | A/G | 11 | Zm00001d049158 | Transcription factor bHLH62 | 1.27949 | |
CRN | PZE-104016717 | 4 | 16,500,659 | 5.2 × 10−5 | A/G | 11 | Zm00001d049127 | Putative serine/threonine protein | −0.848596 | |
Forks | PZE-104010552 | 4 | 7,929,588 | 5.0 × 10−5 | A/G | 8.9 | Zm00001d048979 | Putative sucrose-phosphate synthase protein | 2.06952 | |
Forks | PZE-104010552 | 4 | 7,929,588 | 5.0 × 10−5 | A/G | 8.9 | Zm00001d048925 | Hydroquinone glucosyltransferase | 1.25909 | |
Forks | PZE-104010552 | 4 | 7,929,588 | 5.0 × 10−5 | A/G | 8.9 | Zm00001d048901 | Transcription factor bHLH47 | 2.69849 | |
Forks | PZE-104010552 | 4 | 7,929,588 | 5.0 × 10−5 | A/G | 8.9 | Zm00001d048843 | Math-btb9 | 1.16984 | |
Forks | PZE-104010552 | 4 | 7,929,588 | 5.0 × 10−5 | A/G | 8.9 | Zm00001d048795 | SPR1 | 1.27812 | |
Forks | PZE-104010552 | 4 | 7,929,588 | 5.0 × 10−5 | A/G | 8.9 | Zm00001d048709 | benzoxazinless1 | −5.53653 | |
Forks | PZE-110109365 | 10 | 148,503,798 | 4.7 × 10−5 | A/G | 7.5 | Zm00001d026605 | Endoglucanase 5 | −5.62458 | |
Forks | PZE-110108403 | 10 | 148,106,661 | 5.4 × 10−5 | A/C | 8.9 | Zm00001d026603 | Mg chelatase subunit H 1 | 0.836012 | |
Forks | PZE-110108403 | 10 | 148,106,661 | 5.4 × 10−5 | A/C | 8.9 | Zm00001d026573 | Methylthioribose kinase | −1.75366 | |
Forks | PZE-110108403 | 10 | 148,106,661 | 5.4 × 10−5 | A/C | 8.9 | Zm00001d026542 | Myb family transcription factor PHL5 | −4.47132 | |
CRN | PZE-105047221 | 5 | 36,532,569 | 5.6 × 10−5 | A/G | 11 | Zm00001d014555 | Tyrosine-sulfated glycopeptide receptor 1 | −1.98805 | |
Forks | PUT-163a-91,875,212-4781 | 5 | 7,724,698 | 5.9 × 10−5 | A/G | 10 | Zm00001d013287 | – | 0.957732 | |
Forks | PUT-163a-91,875,212-4781 | 5 | 7,724,698 | 5.9 × 10−5 | A/G | 10 | Zm00001d013269 | Beta-glucanase3 | −0.88007 | |
Crossings | PZE-104092320 | 4 | 167,437,768 | 4.7 × 10−5 | A/G | 1.8 | Zm00001d051829 | U-box domain-containing protein 44 | 0.605786 | |
Crossings | PZE-104092320 | 4 | 167,437,768 | 4.7 × 10−5 | A/G | 1.8 | Zm00001d051692 | Aspartyl protease AED1 | 0.609318 | |
Crossings | PZE-104092320 | 4 | 167,437,768 | 4.7 × 10−5 | A/G | 1.8 | Zm00001d051664 | 2OG and Fe (II)-dependent superfamily protein | 0.924731 | |
Crossings | PZE-104092320 | 4 | 167,437,768 | 4.7 × 10−5 | A/G | 1.8 | Zm00001d051598 | Plant-specific domain TIGR01570 protein | 1.82658 |