Table 2 SilicoDArT and SNP markers correlated with genes associated with different traits in pearl millet (Varshney et al.34).

From: Genotyping by sequencing provides new insights into the diversity of Napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between collections

SNP_ID Chr Pos Ref Alt Closest_gene_PM Closest_gene_function Traits Treatment P value R2 (%)
9999783 5 65917816 A G Pgl_GLEAN_10010048 AP2/ERF domain 1000-Grain Mass (g) Early stress 2.46E-11 19
8171327 3 3033078 G T Pgl_GLEAN_10005840 Ionotropic glutamate receptor Fresh Stover Yield (t/ha) Early stress 5.80E-12 12
23610697 6 184529223 C G Pgl_GLEAN_10022294 NA Fresh Stover Yield (t/ha) Early stress 4.93E-11 12
23598607 5 66047648 T C Pgl_GLEAN_10002412 Protein kinase, catalytic domain Grain Number /m2 (No.) Control 2.41E-12 20
23588862 5 66273007 T C Pgl_GLEAN_10007383 UbiA prenyltransferase family Grain Number /m2 (No.) Late stress 9.71E-12 17
9972446 5 60443354 G A Pgl_GLEAN_10009273 Fatty acid hydroxylase Grain Number /m2 (No.) Early stress 5.39E-11 16
9968140 5 59276838 C T Pgl_GLEAN_10025573 Alcohol dehydrogenase superfamily, zinc-type Grain Number /m2 (No.) Early stress 1.62E-11 17
23640298 3 5347418 T G Pgl_GLEAN_10000839 Peptidase S8/S53, subtilisin/kexin/sedolisin Grain Number /Panicle (No.) Control 6.91E-11 15
23588558 5 64510034 C T Pgl_GLEAN_10002983 Phospholipase D/Transphosphatidylase Grain Number /Panicle (No.) Control 3.09E-11 18
23602204 5 67552785 G A Pgl_GLEAN_10006368 Protein kinase, catalytic domain Panicle Number (‘000/ha) Control 1.63E-11 18
23623063 3 8675580 T A Pgl_GLEAN_10008425 Proteasome, alpha-subunit, N-terminal domain Panicle Number (‘000/ha) Control 3.48E-14 24
9967966 2 135590394 A T Pgl_GLEAN_10018209 Sodium/solute symporter Panicle Number (‘000/ha) Control 8.84E-12 18
23617275 2 72418790 G C Pgl_GLEAN_10021161 NA Panicle Number (‘000/ha) Early stress 2.99E-11 15
9966416 2 43404632 G C Pgl_GLEAN_10021658 NA Panicle Number (‘000/ha) Control 4.92E-11 16
23634420 2 2182294 C T Pgl_GLEAN_10023314 Zinc finger, RING-type Panicle Number (‘000/ha) Control 6.18E-11 16
23615392 4 162832391 G A Pgl_GLEAN_10008211 Raffinose synthase Plant Height (cm) Control 2.79E-11 17
23618303 4 119817514 G C Pgl_GLEAN_10012722 Heat shock protein DnaJ, N-terminal Plant Height (cm) Control 6.63E-11 15
9975905 4 78593371 A G Pgl_GLEAN_10019616 NA Plant Height (cm) Late stress 1.00E-11 12
23624988 4 140312557 C A Pgl_GLEAN_10031827 Protein of unknown function DUF914, eukaryotic Plant Height (cm) Late stress 1.75E-12 12
23588605 4 34598785 C T Pgl_GLEAN_10036604 Ubiquitin-associated/translation elongation factor Plant Height (cm) Control 8.23E-13 18
23603442 2 214449399 A G Pgl_GLEAN_10031324 NA Plant Population (‘000/ha) Late stress 5.38E-13 23
17974203 5 80840668 G A Pgl_GLEAN_10038503 Transcription factor, SBP-box Plant Population (‘000/ha) Late stress 2.13E-13 23
  1. Chr = chromosome; Pos = position within chromosome; Ref = reference allele; Alt = alternative allele; PM = pearl millet; NA = information not available.