Genes Under QTL for QLFIR9.4 (v2.1)


QTL Info

Version QTL Name Linkage Group bp_start bp_end Description
2.1 QLFIR9.4 9 55028258 55622514 Leaf firing

 

Genes Under QTL (total genes found: 91)

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
2.1 Sobic.009G200400 9 55032680 55034197 weakly similar to Os05g0518800 protein Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G200400
2.1 Sobic.009G200700 9 55068083 55071539 similar to Os05g0519000 protein Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G200700
2.1 Sobic.009G200800 9 55075136 55079361 similar to Os05g0519200 protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G200800
2.1 Sobic.009G200900 9 55080204 55081513 similar to Putative uncharacterized protein Invariant: cultivated https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G200900
2.1 Sobic.009G201100 9 55093657 55094799 similar to Os10g0557900 protein Invariant - W&W https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G201100
2.1 Sobic.009G201200 9 55096427 55101087 similar to Os05g0519500 protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G201200
2.1 Sobic.009G201400 9 55107726 55108736 similar to Glucan endo-1,3-beta-glucosidase GV (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase GV) ((1->3)-beta-glucanase isoenzyme GV) Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G201400
2.1 Sobic.009G201500 9 55111029 55114832 similar to Heat shock protein 101 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G201500
2.1 Sobic.009G201600 9 55115583 55120505 similar to Putative uncharacterized protein P0483D07.4 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G201600
2.1 Sobic.009G201700 9 55120557 55126823 similar to Putative oligosaccharyl transferase STT3 subunit https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G201700
2.1 Sobic.009G201800 9 55130446 55133164 similar to Os05g0520100 protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G201800
2.1 Sobic.009G201900 9 55133415 55136916 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G201900
2.1 Sobic.009G202000 9 55145802 55148153 similar to Putative uncharacterized protein Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G202000
2.1 Sobic.009G202200 9 55155309 55156846 similar to Putative uncharacterized protein P0483D07.8 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G202200
2.1 Sobic.009G202400 9 55167970 55170253 weakly similar to Putative uncharacterized protein P0483D07.9 Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G202400
2.1 Sobic.009G202600 9 55177822 55179511 similar to Acyltransferase family protein Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G202600
2.1 Sobic.009G202700 9 55182153 55184930 weakly similar to Chromosome chr6 scaffold_3, whole genome shotgun sequence Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G202700
2.1 Sobic.009G202900 9 55197725 55205225 similar to Putative uncharacterized protein P0483D07.18 Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G202900
2.1 Sobic.009G203000 9 55202579 55210054 similar to Putative uncharacterized protein Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G203000
2.1 Sobic.009G203100 9 55214637 55217094 similar to Os12g0611700 protein Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G203100
2.1 Sobic.009G203200 9 55218716 55221278 similar to Putative pectin methylesterase Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G203200
2.1 Sobic.009G203400 9 55228280 55230859 similar to Os05g0521900 protein Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G203400
2.1 Sobic.009G203500 9 55237720 55243537 similar to Hexokinase Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G203500
2.1 Sobic.009G203600 9 55241964 55246851 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G203600
2.1 Sobic.009G203700 9 55255637 55260284 similar to Auxin-responsive protein IAA18 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G203700
2.1 Sobic.009G203800 9 55266681 55267934 similar to 60S ribosomal protein L8-2 Invariant: cultivated https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G203800
2.1 Sobic.009G203900 9 55270591 55271949 similar to Profilin-3 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G203900
2.1 Sobic.009G204100 9 55280712 55282032 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G204100
2.1 Sobic.009G204200 9 55282384 55286591 similar to Dual-specificity protein-like phosphatase 4 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G204200
2.1 Sobic.009G204300 9 55293687 55301536 similar to Putative receptor like protein kinase Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G204300
2.1 Sobic.009G204600 9 55315622 55321023 similar to Putative uncharacterized protein Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G204600
2.1 Sobic.009G204700 9 55321001 55325367 similar to Os05g0525600 protein Invariant - W&W https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G204700
2.1 Sobic.009G204900 9 55345337 55349539 similar to Putative receptor like protein kinase https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G204900
2.1 Sobic.009G205200 9 55363776 55369379 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G205200
2.1 Sobic.009G205300 9 55369983 55372519 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G205300
2.1 Sobic.009G205400 9 55376971 55378891 similar to Putative uncharacterized protein OJ1593_C11.14 Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G205400
2.1 Sobic.009G205500 9 55381685 55382884 similar to Putative uncharacterized protein Invariant: cultivated https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G205500
2.1 Sobic.009G205600 9 55386289 55388468 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G205600
2.1 Sobic.009G205700 9 55389151 55390578 similar to Os05g0527000 protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G205700
2.1 Sobic.009G205800 9 55395755 55397745 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G205800
2.1 Sobic.009G205900 9 55403951 55405381 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G205900
2.1 Sobic.009G206000 9 55410870 55412309 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G206000
2.1 Sobic.009G206400 9 55438949 55440379 similar to Putative flavonol glucosyltransferase https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G206400
2.1 Sobic.009G206500 9 55441630 55451540 similar to Respiratory burst oxidase-like protein C https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G206500
2.1 Sobic.009G206600 9 55457663 55461732 similar to Putative uncharacterized protein Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G206600
2.1 Sobic.009G206700 9 55463250 55465884 similar to Proteasome maturation factor-like https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G206700
2.1 Sobic.009G206800 9 55466844 55468258 weakly similar to Putative WRKY DNA binding protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G206800
2.1 Sobic.009G207000 9 55475486 55479517 similar to Putative uncharacterized protein OJ1187_E11.15 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G207000
2.1 Sobic.009G207100 9 55480154 55483760 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G207100
2.1 Sobic.009G207200 9 55485448 55488800 similar to ER lumen protein retaining receptor https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G207200
2.1 Sobic.009G207300 9 55488941 55491898 similar to Os01g0731000 protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G207300
2.1 Sobic.009G207600 9 55515530 55518680 similar to Putative uncharacterized protein OJ1187_E11.20 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G207600
2.1 Sobic.009G207700 9 55521190 55527133 similar to LEM3 family/CDC50 family protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G207700
2.1 Sobic.009G207900 9 55533139 55537039 similar to Putative uncharacterized protein P0435H01.17 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G207900
2.1 Sobic.009G208000 9 55542835 55546184 similar to Spl7 protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G208000
2.1 Sobic.009G208100 9 55546297 55550661 similar to OSK1 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G208100
2.1 Sobic.009G208300 9 55566072 55567496 similar to Putative uncharacterized protein OJ1131_E09.12 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G208300
2.1 Sobic.009G208400 9 55577148 55578063 weakly similar to Putative uncharacterized protein Invariant - W&W https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G208400
2.1 Sobic.009G208500 9 55578436 55579430 weakly similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G208500
2.1 Sobic.009G208600 9 55583182 55584390 similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G208600
2.1 Sobic.009G208700 9 55587167 55588682 similar to Os05g0531400 protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G208700
2.1 Sobic.009G208800 9 55591180 55596430 similar to Os05g0531500 protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G208800
2.1 Sobic.009G208900 9 55598918 55602083 weakly similar to Putative uncharacterized protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G208900
2.1 Sobic.009G209200 9 55610976 55613988 similar to Os05g0533500 protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G209200
2.1 Sobic.009G209300 9 55617529 55625868 similar to Starch synthase-like protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G209300
2.1 Sobic.009G200300 9 55027483 55028782 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G200300
2.1 Sobic.009G200500 9 55044802 55051819 Homeobox domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G200500
2.1 Sobic.009G200600 9 55060447 55060981 Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G200600
2.1 Sobic.009G201000 9 55085734 55090793 hydrolase, acting on carbon-nitrogen, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G201000
2.1 Sobic.009G201300 9 55101295 55107003 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G201300
2.1 Sobic.009G202100 9 55153680 55155259 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G202100
2.1 Sobic.009G202300 9 55157240 55157873 heat shock protein STI, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G202300
2.1 Sobic.009G202500 9 55173265 55174381 Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G202500
2.1 Sobic.009G202800 9 55186300 55193469 kinesin motor domain containing protein, expressed Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G202800
2.1 Sobic.009G203300 9 55221412 55223132 harpin-induced protein 1 domain containing protein, expressed Purifying (domestication) https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G203300
2.1 Sobic.009G204000 9 55272214 55275201 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G204000
2.1 Sobic.009G204400 9 55302939 55308861 M-phase phosphoprotein 10, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G204400
2.1 Sobic.009G204500 9 55309373 55313356 mitochondrial-processing peptidase subunit, mitochondrial precursor, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G204500
2.1 Sobic.009G204800 9 55339304 55344068 senescence-induced receptor-like serine/threonine-protein kinase precursor, putative, expressed Invariant - W&W https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G204800
2.1 Sobic.009G205000 9 55352265 55358136 pentatricopeptide repeat protein PPR986-12, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G205000
2.1 Sobic.009G205100 9 55358801 55360828 zinc finger/CCCH transcription factor, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G205100
2.1 Sobic.009G206100 9 55417906 55421373 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G206100
2.1 Sobic.009G206200 9 55427880 55428979 tRNA nucleotidyltransferase/polyA polymerase family protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G206200
2.1 Sobic.009G206300 9 55433767 55435223 anthocyanidin 5,3-O-glucosyltransferase, putative, expressed Invariant - W&W https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G206300
2.1 Sobic.009G206900 9 55469931 55472249 https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G206900
2.1 Sobic.009G207400 9 55497035 55503106 ATP binding protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G207400
2.1 Sobic.009G207500 9 55504325 55506939 OsFBX238 - F-box domain containing protein, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G207500
2.1 Sobic.009G207800 9 55530845 55532269 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G207800
2.1 Sobic.009G208200 9 55554920 55560938 WD repeat-containing protein 55, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G208200
2.1 Sobic.009G209000 9 55603640 55603864 expressed protein https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G209000
2.1 Sobic.009G209100 9 55605859 55610208 plasminogen activator inhibitor 1 RNA-binding protein, putative, expressed https://phytozome.jgi.doe.gov/pz/portal.html#!gene?search=1&detail=1&method=5228&searchText=locusName:Sobic.009G209100