Genes Under QTL for QHDEX10.3 (v3.0)


QTL Info

Version QTL Name Linkage Group bp_start bp_end Description
3.0 QHDEX10.3 10 41745111 45820776 Panicle exsertion

 

Genes Under QTL (total genes found: 93)

Selection signature information is provided based on Mace et al 2013 and Mace et al 2014, which identified signatures of purifying and balancing selection based on whole genome resequencing of 47 individuals categorised into three groups (1. Wild and Weedy genotypes, 2. Landraces, 3. Improved Inbreds).

Regions of the genome under purifying and balancing selection were identified using the population genetics summary statistics (θπ, θw, Tajima’s D and FST) in the following three population pairwise comparisons: (i) wild and weedy versus landraces to identify domestication events, (ii) landraces versus improved inbreds to identify improvement events, (iii) wild and weedy versus improved inbreds to identify both domestication and improvement events.

Version Gene Name LG bp_start bp_end Annotation Selection Signature Browse gene at JGI
3.0 Sobic.010G146500 10 41743477 41746939 RGH1A, putative, expressed Balancing (improvement/domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G146500
3.0 Sobic.010G146600 10 41891234 41896820 cyclin-dependent kinase F-1, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G146600
3.0 Sobic.010G146700 10 41902661 41909970 transmembrane amino acid transporter protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G146700
3.0 Sobic.010G146800 10 41914699 41916632 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G146800
3.0 Sobic.010G146900 10 41917056 41917364 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G146900
3.0 Sobic.010G147000 10 41921555 41927514 tesmin/TSO1-like CXC domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147000
3.0 Sobic.010G147100 10 42005494 42012857 VHS and GAT domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147100
3.0 Sobic.010G147200 10 42040799 42043406 aluminum-activated malate transporter, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147200
3.0 Sobic.010G147250 10 42208651 42209207 CAF1 family ribonuclease containing protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147250
3.0 Sobic.010G147300 10 42217039 42219620 CAF1 family ribonuclease containing protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147300
3.0 Sobic.010G147350 10 42220358 42221810 CAF1 family ribonuclease containing protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147350
3.0 Sobic.010G147400 10 42245661 42246485 CAF1 family ribonuclease containing protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147400
3.0 Sobic.010G147500 10 42254853 42257063 tryptophan biosynthesis protein trpCF, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147500
3.0 Sobic.010G147600 10 42282829 42286943 reticulon domain containing protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147600
3.0 Sobic.010G147700 10 42293817 42299857 WD domain, G-beta repeat domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147700
3.0 Sobic.010G147833 10 42331511 42374634 transducin family protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147833
3.0 Sobic.010G147966 10 42371882 42372991 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G147966
3.0 Sobic.010G148100 10 42374651 42375455 OsMADS75 - MADS-box family gene with M-alpha type-box, expressed Invariant: cultivated https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G148100
3.0 Sobic.010G148200 10 42377237 42377661 OsCML31 - Calmodulin-related calcium sensor protein, expressed Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G148200
3.0 Sobic.010G148400 10 42383359 42384352 OsMADS75 - MADS-box family gene with M-alpha type-box, expressed Invariant: cultivated https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G148400
3.0 Sobic.010G148501 10 42432435 42437197 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G148501
3.0 Sobic.010G148600 10 42567454 42569300 WRKY31, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G148600
3.0 Sobic.010G148700 10 42591903 42595057 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G148700
3.0 Sobic.010G148750 10 42788559 42789294 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G148750
3.0 Sobic.010G148800 10 42829856 42831874 WRKY31, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G148800
3.0 Sobic.010G148866 10 42867187 42870476 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G148866
3.0 Sobic.010G148932 10 42870988 42944868 HEAT repeat family protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G148932
3.0 Sobic.010G149000 10 42902409 42903531 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G149000
3.0 Sobic.010G149200 10 42972457 42976966 CAAX amino terminal protease family protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G149200
3.0 Sobic.010G149300 10 42980290 42982321 ubiquitin-conjugating enzyme, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G149300
3.0 Sobic.010G149500 10 43024057 43031942 E1-BTB2 - Bric-a-Brac, Tramtrack, and Broad Complex domain with E1 subfamily conserved sequence, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G149500
3.0 Sobic.010G149600 10 43036399 43042747 intracellular protein transport protein USO1-related, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G149600
3.0 Sobic.010G149700 10 43190204 43191671 peroxidase precursor, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G149700
3.0 Sobic.010G149800 10 43192092 43195746 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G149800
3.0 Sobic.010G149900 10 43248861 43249490 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G149900
3.0 Sobic.010G150000 10 43252118 43254510 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150000
3.0 Sobic.010G150100 10 43260824 43266663 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150100
3.0 Sobic.010G150200 10 43268793 43270786 OsFBX209 - F-box domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150200
3.0 Sobic.010G150325 10 43371492 43382976 OsFBX101 - F-box domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150325
3.0 Sobic.010G150450 10 43373664 43376946 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150450
3.0 Sobic.010G150575 10 43378469 43381792 ribosomal protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150575
3.0 Sobic.010G150600 10 43384079 43387095 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150600
3.0 Sobic.010G150700 10 43385894 43391519 polyadenylate-binding protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150700
3.0 Sobic.010G150701 10 43516457 43518915 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150701
3.0 Sobic.010G150800 10 43592744 43593468 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150800
3.0 Sobic.010G150900 10 43624162 43626620 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G150900
3.0 Sobic.010G151000 10 43625333 43633284 UAA transporter family domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G151000
3.0 Sobic.010G151050 10 43735854 43738126 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G151050
3.0 Sobic.010G151100 10 43738127 43740926 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G151100
3.0 Sobic.010G151200 10 43755649 43756814 GRF zinc finger family protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G151200
3.0 Sobic.010G151325 10 43771550 43774815 transposon protein, putative, unclassified, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G151325
3.0 Sobic.010G151450 10 43952504 43953492 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G151450
3.0 Sobic.010G151575 10 44006475 44012234 white-brown complex homolog protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G151575
3.0 Sobic.010G151700 10 44032883 44039100 extra-large G-protein-related, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G151700
3.0 Sobic.010G151801 10 44052483 44053926 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G151801
3.0 Sobic.010G151900 10 44071190 44078758 ribonuclease P family protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G151900
3.0 Sobic.010G152000 10 44081155 44086248 powdery mildew resistant protein 5, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152000
3.0 Sobic.010G152100 10 44086850 44089945 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152100
3.0 Sobic.010G152200 10 44095111 44095671 avr9/Cf-9 rapidly elicited protein 194, putative, expressed Invariant: cultivated https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152200
3.0 Sobic.010G152250 10 44126217 44128241 retrotransposon protein, putative, unclassified, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152250
3.0 Sobic.010G152300 10 44208442 44211133 glycosyltransferase, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152300
3.0 Sobic.010G152400 10 44214509 44218018 glycosyltransferase, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152400
3.0 Sobic.010G152500 10 44289185 44292435 glycosyltransferase, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152500
3.0 Sobic.010G152600 10 44301184 44304020 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152600
3.0 Sobic.010G152700 10 44484308 44487797 helix-loop-helix DNA-binding domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152700
3.0 Sobic.010G152800 10 44497512 44501356 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152800
3.0 Sobic.010G152850 10 44505356 44508261 acyltransferase, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152850
3.0 Sobic.010G152900 10 44512062 44515190 beta-D-xylosidase, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G152900
3.0 Sobic.010G153000 10 44516453 44523115 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153000
3.0 Sobic.010G153100 10 44529015 44538215 prefoldin, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153100
3.0 Sobic.010G153201 10 44560561 44565129 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153201
3.0 Sobic.010G153300 10 44566748 44582052 DEAD/DEAH box helicase, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153300
3.0 Sobic.010G153400 10 44586819 44592377 protein phosphatase 2C, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153400
3.0 Sobic.010G153466 10 44593519 44603097 SNF2 family N-terminal domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153466
3.0 Sobic.010G153532 10 44602117 44603499 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153532
3.0 Sobic.010G153600 10 44645471 44648856 pentatricopeptide, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153600
3.0 Sobic.010G153700 10 44648956 44671503 cyclic nucleotide-gated ion channel 1, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153700
3.0 Sobic.010G153800 10 44706218 44707631 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153800
3.0 Sobic.010G153900 10 44759504 44767453 spermidine synthase, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G153900
3.0 Sobic.010G154000 10 44772564 44783125 zinc finger protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G154000
3.0 Sobic.010G154150 10 44899318 44900415 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G154150
3.0 Sobic.010G154300 10 45530866 45531517 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G154300
3.0 Sobic.010G154400 10 45534837 45535441 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G154400
3.0 Sobic.010G154500 10 45558755 45561391 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G154500
3.0 Sobic.010G154600 10 45567297 45570549 OsSCP18 - Putative Serine Carboxypeptidase homologue, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G154600
3.0 Sobic.010G154700 10 45603891 45608569 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G154700
3.0 Sobic.010G154801 10 45606498 45607089 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G154801
3.0 Sobic.010G154900 10 45611838 45618931 Divergent PAP2 family domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G154900
3.0 Sobic.010G155000 10 45614381 45615832 NAC domain containing protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G155000
3.0 Sobic.010G155100 10 45621730 45623894 NAC domain containing protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G155100
3.0 Sobic.010G155200 10 45666073 45667270 hypothetical protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G155200
3.0 Sobic.010G155300 10 45701695 45702656 VQ domain containing protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G155300
3.0 Sobic.010G155401 10 45758087 45771362 receptor-like protein kinase 5 precursor, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.010G155401