Table 3.
Genetic map locations of SNP markers flanking PHS QTL on chromosomes 3B, 4A, 7B.1 and 7D.2 in a wheat DH population of a RL4452/‘AC Domain’ cross and their corresponding physical locations/candidate regions in Brachypodium distachyon and rice
| SNP marker | Map | Survey sequence | BLASTN hits to Brachypodium genes | BLASTN hits to Rice genes |
|---|---|---|---|---|
| (cM) | Contig no. | (genomic regions in parenthesis) | (genomic regions in parenthesis) | |
| Chromosome 3B | ||||
| wsnp_Ku_c6825_11858665 | 63.0 | 10469056 | Bradi2g46510 (46,936,013-46,952,333) | LOC_Os01g48680 (27,906,608-27,920,980) |
| wsnp_Ex_c4769_8510104 | 63.0 | 10613849 | Bradi2g46590 (47,003,547-47,009,237) | LOC_Os01g48790 (27,983,688-27,990,383) |
| RAC875_rep_c113906_294 | 64.0 | 10557485 | Bradi2g51030 (50,699,047-50,702,962) | LOC_Os01g56200 (32,367,683-32,371,816) |
| BobWhite_c46650_260 | 64.0 | 10441023 | Bradi2g51017 (50,685,769-50,695,622) | LOC_Os01g56190 (32,350,513-32,360,765) |
| Kukri_c4310_489 | 64.6 | 10759762 | Bradi2g51040 (50,703,620-50,708,573) | LOC_Os02g13910 (7,558,777-7,568,835) |
| TA002966-0294 | 65.1 | 10635317 | Bradi2g46710 (47,135,003-47,136,451) | LOC_Os01g56580 (32,615,694-32,622,894) |
| 10712014 | Bradi2g49590 (49,632,703-49,638,684) | LOC_Os01g54100 (31,111,291-31,116,151) | ||
| BS00078127_51 | 65.7 | 10754454 | Bradi2g51530 (51,119,031-51,123,083) | LOC_Os01g56810 (32,788,487-32,792,751) |
| Kukri_c21818_519 | 66.2 | 10455881 | Bradi2g51620 (51,191,828-51,198,372) | LOC_Os01g56910 (32,869,293-32,878,216) |
| wsnp_Ra_rep_c74606_72470419 | 66.8 | 10523702 | Bradi2g51710 (51,287,497-51,313,181 | LOC_Os01g57082 (32,984,982-32,994,519) |
| IACX3871 | 66.8 | 10521243 | Bradi2g51890 (51,441,692-51,446,044) | LOC_Os01g57450 (33,200,667-33,201,485) |
| Excalibur_c73633_120 | 67.3 | 10673653 | Bradi2g48430 (48,731,037-48,732,308) | LOC_Os01g52260 (30,042,527-30,043,938) |
| wsnp_Ex_c5547_9774195 | 68.4 | 10770075 | Bradi2g53020 (52,250,581-52,257,598) | LOC_Os01g59670 (34,514,117-34,520,887) |
| wsnp_Ex_rep_c69664_68618163 | 68.4 | 10477393 | Bradi2g52540 (51,883,735-51,889,623) | LOC_Os01g58680 (33,919,393-33,924,664) |
| wsnp_Ku_rep_c72700_72370664 | 69.0 | 10484009 | Bradi2g53340 (52,475,967-52,481,992) | LOC_Os01g60180 (34,803,492-34,804,046) |
| RAC875_rep_c116515_181 | 69.0 | 1068363 | Bradi2g53130 (52,329,608-52,334,764) | LOC_Os01g59880 (34,629,359-34,635,205) |
| BobWhite_rep_c64944_264 | 69.6 | 1040995 | Bradi2g53970 (52,969,054-52,973,550) | LOC_Os01g61400 (35,505,448-35,508,543) |
| Tdurum_contig38427_237 | 70.2 | 10658322 | Bradi2g55100 (53,817,575-53,821,406) | LOC_Os01g63250 (36,656,340-36,660,768) |
| Tdurum_contig27495_111 | 70.2 | 10538814 | Bradi2g53450 (52,567,117-52,569,109) | LOC_Os01g60430 (34,946,618-34,949,027) |
| Kasp3B(survey)_17 | 70.8 | 10495803 | Bradi2g55230 (53,904,697-53,906,640) | LOC_Os03g60200 (34,238,474-34,241,647) |
| Chromosome 4A | ||||
| BS00068243_51 | 53.8 | 7023446 | Bradi2g12660 (11,006,410-11,009,518) | LOC_Os01g28244 (15,823,709-15,829,849) |
| CD920298 | 58.6 | 7174272 | Bradi1g00600 (481,247-482,062) | LOC_Os03g64290 (36,320,679-36,333,253) |
| Kukri_c12563_52 | 59.3 | 7128338 | Bradi1g51817 (50,293,482-50,308,189) | LOC_Os05g37500 (21,943,044-21,959,786) |
| Bradi1g00760 (565,638-570,467)! | LOC_Os03g63370 (35,809,964-35,814,672)! | |||
| BS00072025_51 | 59.3 | 7168762 | Bradi1g00730 (555,714-559,377) | LOC_Os03g64210 (36,281,400-36,283,271) |
| RAC875_c21369_425 | 59.8 | 7070429 | Bradi1g00820 (594,037-597,877) | LOC_Os03g64190 (36,265,672-36,271,489) |
| IAAV3132 | 59.8 | 7114346 | Bradi1g01007 (695,876-702,209) | LOC_Os03g63920 (36,110,059-36,119,639) |
| wsnp_Ex_c5470_9657856 | 60.4 | 7174581 | Bradi1g01070 (731,493-733,959) | LOC_Os03g51390 (29,401,950-29,403,115) |
| RAC875_c25124_182 | 61.6 | 7061368 | Bradi1g01227 (825,624-828,017) | LOC_Os03g63680 (35,968,492-35,970,517) |
| wsnp_Ku_c4924_8816643 | 62.7 | 501046 | Bradi1g52230 (50,605,616-50,611,584) | LOC_Os02g29140 (17,257,940-17,266,066) |
| 3540051 | Bradi1G00720 (552,185-555,346)! | - | ||
| 864232 | - | LOC_Os03g60710 (34,502,945-34,508,158)! | ||
| Excalibur_c24511_1196 | 63.2 | 7119833 | Bradi1g49910 (48,564,700-48,565,690) | LOC_Os06g16640 (9,564,124-9,566,967) |
| 7139864 | Bradi1g00820 (594,037-597,877)! | - | ||
| 5949088 | - | LOC_Os03g53500 (30,679,685-30,689,230)! | ||
| Tdurum_contig13489_292 | 63.8 | 7124315 | Bradi1g01500 (976,919-979,161) | LOC_Os03g63470 (35,855,445-35,860,549) |
| wsnp_JD_c38619_27992279 | 66.0 | 7098863 | Bradi1g01580 (1,030,837-1,034,525) | LOC_Os03g63410 (35,826,263-35,830,205) |
| Chromosome 7B.1 | ||||
| CAP7_c10566_170 | 55.3 | 3116911 | Bradi1G46150 (44,420,413-44,423,001)! | LOC_Os06g10710 (5,588,196-5,594,757) |
| BobWhite_rep_c64768_264 | 55.3 | 3032904 | Bradi1G46137 (44,416,953-44,419,121) | LOC_Os06g10760 (5,619,105-5,621,750) |
| Tdurum_contig84962_256 | 55.3 | 3032904 | Bradi1G46137 (44,416,953-44,419,121) | LOC_Os06g10760 (5,619,105-5,621,750) |
| BS00022498_51 | 55.3 | 3115694 | Bradi1G46060 (44,341,065-44,348,362) | LOC_Os06g10880 (5,677,080-5,682,126) |
| wsnp_Ex_c908_1754208 | 56.4 | 3153345 | Bradi1g45210 (43,434,039-43,436,397) | LOC_Os06g12270 (6,603,975-6,604,635) |
| Tdurum_contig68347_605 | 56.4 | 3153345 | Bradi1G45210 (43,434,039-43,436,397) | LOC_Os06g12270 (6,603,975-6,604,635) |
| LOC_Os06g12280 (6,605,479-6,608,454) | ||||
| RFL_Contig124_558 | 57 | 3126436 | Bradi1g44967 (43,073,188-43,080,744)! | - |
| BobWhite_c46772_564 | 57 | 3109791 | Bradi1G44860 (42,951,596-42,953,323) | LOC_Os06g12990 (7,118,829-7,120,448) |
| Bradi1G44850 (42,949,245-42,951,551) | - | |||
| GENE-4333_211 | 57 | 3153554 | Bradi1G44790 (42,899,346-42,900,477) | - |
| Tdurum_contig51087_573 | 57 | 3165147 | Bradi1G44440 (42,620,688-42,629,717) | LOC_Os06g13820 (7,661,691-7,670,035) |
| Chromosome 7D.2 | ||||
| RAC875_c1829_321 | 14.3 | 3849095 | Bradi1g48660 (47,326,685-47,327,292) | LOC_Os06g06460 (3,040,092-3,041,121) |
| Kukri_c32845_116 | 14.3 | 3964075 | Bradi1g50860 (49,335,697-49,339,907) | LOC_Os06g05660 (2,558,015-2,562,242) |
| TA002473-0717 | 14.3 | 3929478 | Bradi1g49140 (47,871,489-47,874,424) | LOC_Os06g05700 (2,579,088-2,581,726) |
| wsnp_CAP8_rep_c9647_4198594 | 22.0 | 3945994 | Bradi1g48610 (47,249,027-47,255,499)! | LOC_Os06g06560 (3,079,059-3,086,808) |
!Weak hit to genomic regions in Brachpodium or rice that is orthologous to the QTL interval for PHS resistance in wheat.
Best hits that do not correspond to the candidate region in Brachpodium or rice are in italics.