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GrainGenes Reference Report: MGG-274-515

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Reference	MGG-274-515
Title	Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress.
Journal	Molecular Genetics and Genomics
Year	2005
Volume	274
Pages	515-527
Author	Rostoks N [ Show all 16 ]
Abstract	More than 2,000 genome-wide barley single nucleotide polymorphisms (SNPs) were developed by resequencing unigene fragments from eight diverse accessions. The average genome-wide SNP frequency observed in 877 unigenes was 1 SNP per 200 bp. However, SNP frequency was highly variable with the least number of SNP and SNP haplotypes observed within European cultivated germplasm reflecting effects of breeding history on genetic diversity. More than 300 SNP loci were mapped genetically in three experimental mapping populations which allowed the construction of an integrated SNP map incorporating a large number of RFLP, AFLP and SSR markers (1,237 loci in total). The genes used for SNP discovery were selected based on their transcriptional response to a variety of abiotic stresses. A set of known barley abiotic stress QTL was positioned on the linkage map, while the available sequence and gene expression information facilitated the identification of genes potentially associated with these traits. Comparison of the sequenced SNP loci to the rice genome sequence identified several regions of highly conserved gene order providing a framework for marker saturation in barley genomic regions of interest. The integration of genome-wide SNP and expression data with available genetic and phenotypic information will facilitate the identification of gene function in barley and other non-model organisms.
Locus	[ Hide all but 1 of 1441 ] BCD98 BCD454 Rh bcd907 abg471 ksuG59 psr156 abc174 bcd131 CDO99 CDO524 CDO118 phy1 RZ166 CDO1380a wx CDO17 Bmac0213 EBmac0405 Bmag0005 Bmag0211 Bmag0347 EBmac0659 HVALAAT scssr00103 EBmac0816 Bmac0063 Bmag0345 EBmac0853 Bmac0032 Bmac0154 WMC1E8 scssr02748 scssr04163 scssr08238 HVTUB scind02622 scssr10226 Bmag0692 scssr07759 scssr03381 Bmac0093 Bmac0298 EBmac0615 HVBKASI scssr00334 scssr12344 Bmag0140 Bmag0381 Bmac0216 Bmag0125 EBmac0415 EBmac0705 HvLTPPB Bmag0131 Bmac0067 Bmac0209 Bmag0006 Bmag0603 EBmac0871 scssr25691 Bmag0225 Bmag0606 Bmag0013 scind02281 EBmac0708 scssr25538 scssr20569 Bmac0084 Bmac0181 Bmag0375 EBmac0737 EBmac0906 Bmac0186 Bmag0353 scind10455 Bmac0310 EBmac0775 EBmac0658 Bmac0134 Ebmac0635 Ebmac0679 EBmac0701 Ebmac0788 scssr02306 scssr07106 Bmac0096 Bmac0113 Bmac0303 Bmag0323 Bmag0387 Bmag0394 scssr18076 Bmag0337 HVLEU Bmag0357 scssr15334 Bmag0223 scssr05939 scssr10148 EBmac0824 Bmag0222 Bmac0222 EBmac0623 scssr09041 scssr03907 scssr03906 Bmac0316 scssr09398 Bmac0018 Bmac0040 Bmag0009 Bmag0173 Bmag0219 EBmac0639 HvLOX Bmag0613 EBmac0602 EBmac0806 scssr05599 Bmag0007 Bmag0206 EBmac0603 Bmac0311 Bmac0187 Bmag0516 Bmac0031 Bmac0167 Bmac0224 Bmac0273 Bmag0011 Bmag0321 Bmag0341 Bmag0359 Bmag0369 EBmac0827 scind00149 scssr15864 Bmac0064 Bmag0384 Bmag0385 EBmac0764 Bmag0120 ABG59 Hor1 ABG74 ABG500A ABG452 CDO105B ABC257 MWG912 cMWG682 ABG358 ABG5 CDO537 ABC451 vrs1 ABG72 ABC157 ABG703A ABG377 ABG499 CDO113B WG110 MWG41 WG622 ABC303 MWG58 ABG472 WG114 ABG397 Bmy1 MWG502 ABG395 MWG2040B ABC302 ABC717 ABG712 ABG495A ABC155 ABG496 ABG453 ABG62 ABG466 Cxp3 ABG458 ABG20 MWG820 Amy1 MWG798A ABG704 ABC151A ABC158 ABC465 ABG701 WG719 ABC154B ABG461A WG380A Cat3 alm Blp Hsh Lga lks2 nud Pub rob srh ABG002 Zeo Act8A Aga6 Hor5 Hor2 MWG036A MWG837 Chs3 ABA004 ABG053 Ica1 ABG074 MWG800 ABC164 ksuF2A ABC152B BCD351C Pcr2 ABR337 Glb1 ABC160 ABG464 His3B ABC307A His4A cMWG706A MWG2028 ABC322B ABC261 MWG635C Cab2 BCD340A Aga7 ABG055 ABG387a Amy2 Bmac0029 Bmag0508A MWG938 ABA4 ABG53 ABG494 Dor2 iPgd2 AtpbA ABA2 ABG373 ABG55 ABG58 ABG8 WG516 RbcS ABG318 ABG2 MWG858 CDO64 ABG459 Pox ABC454 Adh8 MWG950 MWG557 ABG19 Bmy2 ABC468 ABC306 ABR338 ABG356 ABC162 WG996 CDO588 ABG14 MWG865 Rrn5S1 MWG503 ksuF15 ksuD22 CDO373 ABC252 Gln2 ABC153 ABC165 Pcr1 BCD410 WG645 cMWG720 ABA5 ABG460 MWG584 MWG974 ABG396 ABR334 Adh5 ABG462 ABG398 BCD828 cMWG680 ABC176 Rrn5S2 ABG315 cMWG691 ABR320 ABG389 mPub ABC161 ABA302 MWG902 MWG883 ABG654 Glb3 iBgl ABC166 MWG838 ABC172 MWG634 MWG77 Dhn6 ABR315 ABC321 ABG484 Adh4 ABA3 WG464 iAco2 iHxk2 ABG498 bAL88/2 bAP91 ABG54 ABG394 ABG366 ksuH11 ABR313 ABC483 ABG708 ABR336 Adh6 Dor5 ABG497 CDO749 Ubi2 Rrn2 Ltp1 WG541 WG530 ABA1 WG889 Ale PSR128 ABG473 ABG69 WG364 ABC168 mSrh MWG522 CDO504 WG644 iEst9 WG908 MWG877 Cab1 ABC482 ABG391 ABG707 ABG390 CDO484 ABG463 ABC309 Lth MWG620 Nar1 ABR331 Ubi4 Ubi5 Rrn1 ABA6 CDO497 ABR335 ABG474 ksuD17 ABG379 ABC163 ABG388 ABC175 Nar7 Nir MWG934 PSR154 MWG2018 ABA301 Plc ABG312 dRpg1 ABG75 ABR303 ABG320 BCD129 iEst5 WG834 CDO475 MWG89 ABG380 MWG836 Brz ABC255 ABC254 ABR329 Adh7 ABG476 ABC308 ABC455 ABG11 CDO673 MWG808 CDO464 MWG3 Ubi1 PSR129 ABC305 ABG652 WG420 Chi1 p75homd barep16y GMS021 Bmac0399 barep22j Bmag0105 HVM64 Bmag0113c EBmac0656 Bmag0344c Bmag0103b Bmac0144a Bmag0228a p22homd barep20A4 EBmac0783 HVM36 e41m32A3 Bmac0218 Bmag0518 Bmag0115 Bmag0378 EBmac0850 EBmac0854 EBmac0715 GMS003 EBmac0640 HVM63 HVM26 Bmac0132 Bmac0175c HVM23 Bmag0015 Bmac0144g Bmag0003c Bmac0144b p61m48A1 HVM54 e41m32B e46m42B8 p61homf f1p61y f1p61h barep22A3 Bmag0136 Bmac0043 Bmag0010c HVM27 HVM44 Bmag0121b Bmag0122 Bmag0138a Bmag0318a HVM33 Bmac0127b Bmag0112 HVM60 GMS116 Bmag0010b e38m50t Bmag0306b r1p34a HVM62 p22homf e46m42A9 e32m34C1 HVM40 EBmac0691 Bmag0110b Bmag0014 Bmag0350d Bmac0175a HVM13 Bmac0144d HVM3 HVM68 Bmac0030 Bmac0299 Bmac0577 Bmac0047b EBmac0669 Bmag0344b GMS089 e42m47f WMS6 Bmag0138b HVM67 e42m47v barep20A2 Bmac0163 Bmac0306 Bmac0284 Bmac0282a EBmac0970 Bmac0144e EBmac0684 Bmag0113a HVM30 e46m42A8 GMS061 e35m42z GMS001 e45m48B8 barep34v e46m42C5 e38m50A6 p75homf Bmag0103a Bmag0174a Bmag0344a EBmac0674 EBmac0874 Bmac0047a Bmac0127a Bmac0144c Bmac0297c HVM31 Bmac0175b HVM14 HVM65 Bmgtttttt0001 Bmac0251 Bmag0571a EBmac0713 Bmag0021 HVM4 AF022725A Bmac0282b HVCMA Bmac0047c Bmag0121a Bmac0579 Bmac0162 Bmac0582 Bmac0297a Bmag0010a Bmag0228b EBmac0785 Bmag0109 Bmag0183 Bmag0189 Bmag0110a Bmag0217 Bmag0571b Bmag0174b HvAMY2 HvID bcd349 bcd808b bcd926 cdo122 cdo202 cdo244 cdo400 cdo534 cdo57b ABA005 ABG070 ABA001 ABG075 MWG058 ABG064 ABC253 ABG058 ABG014 MWG089 MWG635b MWG583 Gsp Hvex1 MWG844a ABG703b Chs1b MWG520a BG123a MWG14 MWG844b MWG555b MWG571a ABG495b MWG635a ABG500b MWG618 BG123b BCD351e ABG3a MWG813a MWG851b cMWG652a ABG387b HVM74 cMWG684c MWG851a Ris45a MWG555a ABC167a ABC156d ABC310b Ris44 BCD442 cdo1435 HVM5 HVM6 HVM11 HVM22 HVM43 ABA002 ABA003 ABA006 ABA303 ABC152A ABC152D ABC154A ABC156A ABC156C ABC167B ABC169A ABC169B ABC170A ABC170B ABC307B ABC310A ABC322A ABC323 ABC622 ABG3b ABG001A ABG004 ABG005 ABG008 ABG010 ABG011 ABG019 ABG022A ABG022B ABG054 ABG059 ABG062 ABG069 ABG077 ABG313A ABG313B ABG314A ABG314B ABG316A ABG316B ABG316C ABG316D ABG316E ABG317A ABG317B ABG319A ABG319B ABG319C ABG601 ABG610 ABG705A B12DA B12DB B15C bBE54A bBE54B bBE54C bBE54D bBE54E BCD135 BCD265B BCD298B BCD340C BCD340D BCD340E BCD351D BCD351F BCD402B BCD453B CDO36 CDO099 CDO345 CDO348B CDO542 CDO669B CDO1380b Chs1A cMWG652B Crg3A Crg3B Dor4B F3hA His3A His3C His3D His4B iPgd1A ksuA1A ksuA1B ksuA3A ksuA3B ksuA3C ksuA3D ksuD14C ksuF2B MWG35 MWG003 MWG010B MWG036B MWG041 MWG077 MWG514B MWG520B MWG571B MWG571C MWG798B MWG813B MWG851C MWG851D MWG878A Pgk2A Pgk2B Prx1A PSR106B PSR167B RZ143 RZ242 RZ323 RZ444 RZ508 RZ567 RZ590 RZ612 RZ740 WG223b WG380B WG789A WG789B WG1026B ABC324 ASE1C cMWG733A KFP190 MWG652A MWG835A TLM1 TLM3 VAtp57A MWG36B ABG77 ABG22A MWG10B MWG36A ABG1A HvKNOX3 GMS046 GMS056 End1 BCD265c ABG702a DAK605 MWG882A ABC325 HVM70a ABC805 CDO669a JS074 DAK123B PSR330 BCD1930 Bgq60 Tel3S JS195F BCD1532 JS103.3 Ole1 KFP221 Tel4M DAK133 Tel7L Tel6S DD1.1C Ldh1 Tef1 DAK213C Tel5P DAK152.1 MWG920.1B DD1.1A BCD098 Caf1 Ris17C PSR626A MWG837B Tel2S DAK595A Tef4 R1690 CDO064 DAK213A JS187C JS195B JS188A p40fA pKABA1 KG004.2 KG004.1 CDO036 cMWG663A Prx2/7 MWG949B Hot1 cnx1 MWG949A ABG655A JS195C ABC171A ABG321 ABG057A MWG014 ABG399A Dfr DAK160B DAK202 PSR626B BCD1145 DD1.1B JS068D PSR078B Y617RB ABG655B TLM2 CDO059 ABG003A Tef2 Hsp25 Caf2 ksuC2A Mta9 JS018B MWG920.1A MWG835B FBA232 DAK123C ABC706A S6F FBA332 Tef3 R3226 FBA351 C606 R273 FBB213A DAK156 DAK049 PBI7B R1925 PSR167A cMWG663B B071B PSR325B ABG378B Crg2 Apt PSR106A HVM41 JS068E DAK233 DAK595B ABG020 DAK123A G57 CDO507 JS195D JS195E JS188C JS187D MWG602B Sft C61278 pM13 MWG035 B170 B172 B071A BCD1975 B138B B024 AMP843 pM6 B156 Y617RA R560 JS068C JS068B dRcs5 DAK185.1 JS018A JS195A JS187B JS188B JS195H Bhm1B MWG911B JS187A HVM002B-2 CDO017 DAK642 dRsmMx JS068A Hsp17 JS192.1 DAK160A HVM005 B138A ABC302A scind00046 scssr10477 scssr02236 Bmag0113e Bmac0144f scsnp03343 MWG844E KFP203 scsnp06130 scssr08447 scssr10559 scsnp23255 Bmag0877 scind03751 scssr18005 scssr14079 scssr02503 Bmac0273b scind02587 scsnp04260 KFP002 scssr16991 scsnp06144 scsnp02737 Bmag0113d scsnp00177 scsnp15296 scsnp07825 scsnp02109 scsnp03683 MWG602A scssr02093 Bmac0218c scsnp21226 scind04312b scssr07970 scsnp00460 scsnp22290 scsnp00703 scssr04056 Tha1 MWG706A MWG720 MWG652B scsnp01216 scsnp02972 scsnp00940 scind05281 scsnp01648 scind04312a scind01728 scsnp03612 scsnp21640 scsnp04538 e32m36v_1H kAzmil MWG837A scsnp15164 Bmac0509 r1p61d scsnp07301 scsnp06009 P61homc scsnp00912 ABG720 scind13561 scsnp18274 E32M34v E43M38C7 ABG722 r1p61e EBmac0695 scsnp00634 Bmac0560a Bmac0501 HVM21 scind05789 scsnp03346 scsnp05122 scsnp02639 scsnp04187 scsnp02877 scind08151 scsnp03430 scsnp02590 scsnp01834 scsnp07565 scsnp08004 scsnp50108 P61M48r scsnp26333 ABG721 scsnp04545 E35M42A6 scsnp04853 scind06274 scsnp01149 e39m61u_251_1H scsnp09099 scsnp00875 r1p61a scsnp16431 p95m95_122 f1p61b e43m38A8_1H scind07753 scsnp01812 X5.4 scsnp11085 scsnp07434 p21m38_97 e39m61p_354_1H scsnp17647 scsnp02622 scsnp02329 scsnp10887 scsnp05128 scsnp00970 scsnp01327 p21m38_184 scsnp02112 scsnp02113 scsnp15492 scsnp02116 scsnp01259 scsnp01249 scsnp01257 scsnp05033 scsnp05977 scsnp01644 scind02403 scsnp06322 HVM50 scsnp06958 e40m62k_2H scsnp01222 scsnp06091 scsnp15266 Bmac0557 Bmac0558 scsnp00383 scsnp03057 scsnp03181 scsnp00953 X2.2 scsnp05995 Bmac0521 scsnp03476 scsnp03810 scsnp05236 scsnp02258 e32m34B3_166_2H scsnp01238 scsnp18641 p95m95_162 scsnp03443 scsnp04861 scsnp01242 f1p61k X2.3 scsnp14531 scsnp01075 scsnp04622 scsnp06173 ABG723 scsnp07501 scsnp26393 scsnp01335 scsnp00592 scsnp00680 scsnp02555 scsnp07096 scsnp06766 scsnp05737 scsnp07356 scsnp05814 X2.4 e35m42A3_2H X2.5 wst e38m50r_265_2H X2.6 scsnp01404 scsnp01380 X3.1 E32M34z e32m34C4_102_3H ABG724 scsnp13296 scsnp16710 p95m95_293 p95m95_307 scsnp03441 scsnp01374 scsnp03043 scsnp02294 scsnp17236 scsnp05852 scsnp06074 scsnp00495 scsnp04759 Bmag0012a scsnp04158 scind04897 scsnp04006 scsnp03835 scsnp01483 scsnp19175 scsnp01634 scsnp47832 scind15443 scsnp11642 JS68D scsnp44574 P34homb scsnp15559 scsnp05580 Aamyb scsnp06150 scsnp06150_2 e39m61A1_184_3H scsnp11661_03 scsnp07331_03 X3.2 scsnp01918_02 X3.3 scsnp07722 scsnp03814 scsnp03814_2 scind07197 scsnp14307 scsnp08046 scsnp08541 scsnp08208 scsnp19616 scsnp07681 scsnp06381 scsnp05754 scsnp02838 scsnp05919_2 ABG726 scsnp05919 E34M39A9 scind15434 Bmac0541 Bmag0705 scsnp03017 E45M48D3 scsnp06172 scsnp02416 scsnp03135 scsnp01650 scsnp05351 f1p61t scsnp07112 scsnp00089 scsnp06249 scind02594 Bmag0781 scsnp01247 Bmac0540 DAK595c scsnp06208 scsnp06435 E45M48D1 scsnp18109 scsnp06282 scsnp06247 scsnp03465 scsnp01198 scsnp02614 scsnp05189 scsnp06725 scsnp03097 scind05809 scsnp01646 X4.1 X4.2 scsnp03096 scsnp03591 scsnp05836 X4.3 scind07013 scsnp07359 scsnp10311 scsnp06018 X4.4 scsnp09920 scsnp02813 scsnp20989 scsnp03154 X4.5 scsnp15094 scind02282 scsnp00388 scsnp01741 e40m62j_5H Bmac0560b ABG64 scsnp04923 scsnp02771 scsnp02159 HVM2B-1 scsnp02581 scsnp03171 Bmac0518 scsnp46137 scsnp07010 scsnp05926 scsnp03250 scsnp02265 scsnp00086 e38m50u_5H scsnp05704 E46M42D3 P95M95f OPY11b scsnp03594 scsnp01204 scsnp02738 scsnp02739 scsnp06096 scsnp14689 scsnp14350 p95m95_81 E33M52s scsnp14060 scsnp14759 scsnp05508 scsnp00892 scsnp22879 e41m32A1_113_5H scsnp03900 scsnp01178 scsnp07194 scsnp03113 scsnp00314 EbmatcA3 scsnp15798 E41M32u scsnp24102 scsnp20733 scsnp00635 E41M32z scsnp03275 scsnp04240 E34M39l scsnp14544 E34M39z scsnp07305 e46m42C4_151_6H scsnp25019 84c21j33 scsnp07351 scsnp01964 scsnp00600 scsnp06204 X6.1 HVM11s X6.2 scsnp02895 scsnp14687 BAREP16f scsnp01243 scsnp01797 scsnp14681 scsnp18140 scind04992 Bmag0001 Bmag0004a scsnp04676 scsnp04320 scsnp06878 scsnp04725 e43m38d_>500_6H E46M42g E45M48D4 X6.3 scsnp05096 scsnp00917 cMWG684d scsnp05623 E45M48d E41M32q scsnp00681 X6.4 scsnp40618 X6.5 scsnp04275 scsnp03149 scsnp04273 scsnp04220 X6.6 scsnp04135 ABG725 E39M35n scsnp12121 scsnp02493 scsnp03141 scsnp14826 scsnp00823 scsnp17320 HVCABG HVM4_7H Bmag0794 scsnp06992 scsnp01868 scsnp00694 scsnp04730 scsnp06931 scsnp03646 scind10942 scsnp06154 scsnp01808 scsnp15204 scsnp01208 scsnp14397 scsnp17091 scsnp05772 scind03559 Bmac0192 scsnp05818 scind06372 scsnp08537 scsnp14052 ABG727 EbmatcB4 scsnp02786 scind04282 scsnp00610 scsnp04337 scind03212 scsnp02273 scsnp01864 scsnp01865 scsnp00091 scsnp15259 scsnp05362 HVPRP ABG22B E32M36v E39M61u-251 P95M95-122 E43M38A8 P21M38-97 E39M61p-354 E38M50r-265 E35M42A3 P21M38-184 P95M95-162 E32M34B3-166 E40M62k Bmac0525 Bmac0578 Bmag0571d E32M34C4-102 P95M95-293 P95M95-307 scind47832 E39M61A1-184 E40M62j EbmatcE6 EbmatcD4 OPR10d E38M50u EbmatcA3x OPB10a SC10-54c P95M95-81 E41M32A1-113 E43M38d->500 E46M42C4-151 Septoria ABC156Aa aCDO113 Dor4 scind01634 scsnp06150-2 scsnp11661-3 scsnp07331-3 PSR78b scsnp01918-2 scsnp0381422 scind08208 scsnp05919-2 scind06435 MWG813Aa X1.2 X1.1 X7.1 scind02771 scsnp01648-2 X2.1 scsnp01216-abc X5.3 X5.2 X5.1
Map Data	Barley, Abiotic QTL Consensus [ Show all 6 ]
Probe	ABC06204 ABC02895 ABC01719 ABC14681
QTL	QC13.LiHS-6H.2 [ Show all 14 ]

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