Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses
Abstract
:1. Introduction
2. Materials and Methods
Construction of a Consensus Linkage Map
3. Results
3.1. Distribution of QTLs and MQTLs
3.2. Overlap of QTLs in Meta-QTLs
3.3. Major MQTLs
3.4. Candidate Genes
3.5. Evaluation of MQTLs in Geneinvestigator Software
4. Discussion
4.1. Mega MQTLs
4.1.1. Mega MQTL6.3
4.1.2. Mega MQTL4.8
4.1.3. Mega MQTL3.5
4.2. Gene Ontology
4.3. Markers Selection
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Reference | Marker | Population | Parents | Population Size | No. of Marker |
---|---|---|---|---|---|
[6] | SSR, ISSR, iPBS, Scot, IRAP, CAAT | RIL | Badia × Kavir | 106 | 392 |
[7] | SSR, ISSR, iPBS | F3 | Badia × Comino | 100 | 128 |
[17] | SNP, SSR | RILs | Maresi × Cam/B1/CI08887//CI05761 | 100 | 819 |
[19] | AFLP, SSAP, SSR, | DH | Derkado × B83-12/21/5 | 156 | 241 |
[20] | DArT, SSR | DH | Yuyaoxiangtian Erleng × Franklin | 172 | 858 |
[22] | SSR, ISSR, iPBS | F3 | Badia × Comino | 100 | 128 |
[23] | SSR, DArT | DH | CM72 × Gairdner | 93 | 332 |
[24] | SSR, SNP, DArT, STS, CAPS, dCAPS, | DH | Nure × Tremois | 118 | 162 |
[25] | SSR, DArT | DH | TX9425 × Naso Nijo | 188 | 626 |
[26] | SSR, DArT, CAPS | DH | Barque-73 × CPI-71284-48 | 72 | 1180 |
[27] | SSR, ISSR, iPBS, Scot, CAAT, IRAP, | RILs | Badia × Kavir | 106 | 302 |
[28] | SSR | DH | Steptoe × Morex, Harrington × TR306 | 149 146 | 103 |
[29] | DArT, SSR | DH | CM72 × Gairdner | 108 | 886 |
[30] | DArT, AFLP, SSR | DH | TX9425 ×Franklin | 72 | 520 |
[33] | SSR, DArT, gene-specific marker | DH | Scarlett × ISR42-8 | 76 | 371 |
[34] | RFLP | RILs | Tadmor × Er/Apm | 167 | 77 |
[35] | SSR, DArT | DH | Scarlett × ISR42-8 | 301 | 371 |
[36] | SSR, DArT, gene-specific marker | DH | Scarlett × ISR42-8 | 76 | 371 |
[37] | SSR, DArT | DH | Yerong × Franklin TX9425 ×Naso Nijo | 177 188 | 2500 524 |
[38] | AFLP | RILs | Prisma × Apex R | 94 | 191 |
[39] | EST, BR, GBM, GBS, RFLP, SSR, SNP | DH | OWBDOM × OWBREC | 94 | 650 |
[40] | SSR | DH | ISR42-8 × Scarlett | 301 | 98 |
[41] | SSR | RIL | Lewis(CI15856) × Karl(CI15487) | 146 | 104 |
[42] | SSR, AFLP, DArT | DH | TX9425 × Franklin, Yerong × Franklin | 92 177 | 520 524 |
[43] | DArT, AFLP, microsatellite markers | DH | Yerong × Franklin | 156 | 604 |
[44] | SSR, DArT | DH | YuYaoXiangTian Erleng × Franklin | 172 | 2223 |
[45] | DArT, SSR | DH | Franklin × YuYaoXiangTian Erleng | 126 | 858 |
[46] | SSR, RAPD, RFLP, CAPS, AFLP, STS, | DH | Nure × Tremois | 136 | 127 |
[47] | SSR | DH | Dicktoo × Morex | 91 | 94 |
[51] | DArT, SSR, RFLP, STS | DH, RIL | Barque73 × CPI71284-48, Clipper × Sahara, Dayton × Zhepi2, Foster × CI4196, Steptoe × Morex, TX9425 × Franklin, Yerong × Franklin | 707 | 2935 |
[57] | AFLP, SSR, RFLP | DH | Clipper × Sahara 3771 | 150 | 211 |
[58] | RFLP, SSR | F8–9, RIL | Foster × CIho 4196 | 250 | 206 |
[59] | SSR | F4–6, RIL | Fredrickson × Stander | 116 | 143 |
[60] | RFLP, RAPD, SAP | DH | Steptoe × Morex | 150 | 295 |
[61] | DArT, AFLP, SSR | DH | TX9425 × Franklin | 92 | 520 |
[62] | SSR | DH | Steptoe × Morex, Igri × Franka | 133 | 133 |
[63] | RFLP | DH, F2/F3 | IGRI × FRANKA, VADA × H. spontaneum | 206 | 251 |
[64] | RFLP | DH | PB1 × PB11 | 111 | 136 |
[65] | SSR | DH | Lina × H. spontaneum Canada Park | 86 | 325 |
[66] | SSR, SNP | RILs | ZGMLEL × Schooner | 190 | 1011 |
[67] | DArT, SNP | RIL | Pompadour × Biosaline-19 | 98 | 8610 |
[68] | RFLP, AFLP, SSR | DH RIL | Steptoe × Morex, Dom × Rec Igri × Franka, L94 ×Vada | 317 | 3258 |
[69] | SNP, SSR | DH | Huadamai 6 × Huaai 11 | 122 | 1962 |
[70] | SSR | RIL DH | Igri × Franka, Steptoe × Morex, OWBRec × OWBDom, Lina × Canada Park, L94 × Vada, SusPtrit × Vada | 645 | 775 |
[71] | EST, CAPS, STS, SNP, SSR | DH | Haruna Nijo × H602 | 93 | 2948 |
[72] | RFLP, SSR, AFLP, RGA | DH | Foster × ND9712 × Zhedar | 75 | 214 |
[73] | RFLP, RAPD, STS, IFLP, SSR, AFLP | DH | Oregon Wolfe Barley | 94 | 830 725 |
[74] | SNP | RIL | Morex × Barke | 81 | 195 |
Stress | Traits |
---|---|
Drought | Root–shoot ratio, Root dry weight, Plant height, Harvest Index, Leaf weight, Pm.SEVAD, Stomata number, Thousand kernel weight, Leaf wilting score, Leaf osmotic potential, Free proline content, Ethylene content, Light absorption flux (ABS) per PSII reaction center, Water content, Trapped energy flux per PSII reaction center, Root Length, Drought tolerance score, Relative water content, Pm.AUDPCAD, Plant number, No. of Kernels/spike, Number of spikes/plant, Shoot dry weight, Water-soluble carbohydrate concentration at full turgor, Drought water-soluble carbohydrate concentration, Grain yield, Electron transport flux per PSII reaction center (RC), Osmotic adjustment, Osmotic potential under irrigation, Flag leaf weight, Leaf number, Plumule weight, Peduncle length, Flag leaf width, Water loss rate, The average fraction of open RC during the time needed to complete the closure of all RCs, Flag leaf length, Peduncle diameter, Internode length, Water-soluble carbohydrate concentration, REo/RC, DIo/CSm, TRo/RC, ABS/CSo, Fo, TRo/CSo, ABS/CSm, Fm, Sm, DIo/RC, DIo/CSo, ABS/RC |
Salinity | GY grain yield, Phenol, Salinity score, Root length, Stomata length, Leaf number, Sugar content, Plumule length, Spike diameter, Peroxidase, Shoot dry weight, Leaf injury score, Stomatal pore area, Spikes per plant, Shoot weight, Biomass, T/C ratio, TR transpiration rate, GS stomatal conductance, Leaf weight, Flag leaf length, Grain weight, Seed dormancy, Catalase, Dry weight per plant, Grain number per plant, Flag leaf width, Plumule weight, Dry weight of roots, Green dry weight of shoots, Green fresh weight of shoots, Fresh weight of roots per plant, Pm.SEVAS, Proline content, Stomata width, Shoot diameter, Tiller number, Seedling weight, Seedling gibberellic acid response, Root dry weight, Leaf length, Flag leaf weight, Na+:K+ ratio, Awn weight, Seminal roots, Peduncle length, REo/RC, DIo/CSm, TRo/RC, ABS/CSo, Fo, TRo/CSo, ABS/CSm, Fm, Sm, DIo/RC, DIo/CSo, ABS/RC |
Waterlogging | Longest root length, Shoot dry weight, Shoot fresh weight, Root fresh weight, Leaf chlorosis, Waterlogging index, Grain yield, Spike length, Plant survival, Tiller number, Leaf yellowing proportion, Porosity, Plant biomass reduction, Grains per spike |
Cold stress | Cold score, TMC-Ap3 accumulation, Frost tolerance, Fv/Fm value, plant survival, COR14b accumulation, Vernalization requirement |
Nitrogen Deficiency | Thousand-grain weight, Plant survival, Plant height, Number of ears, Grain yield, Days until heading, Thousand kernel weight, Sheath weight, Stem weight, Straw weight, Above-ground nitrogen uptake N, Nitrogen use efficiency of biomass, Above-ground biomass, Leaf weight, CP at maturity carboxypeptidase, Leaf chlorosis, N remobilization efficiency, Grain protein content |
Aluminum toxicity | Aluminum tolerance score |
Mn toxicity | Leaf chlorosis, Plant survival |
Chr | Meta-QTL | AIC | R2 Meta | Meta-QTL Peak Position (bp) | Meta-QTL CI Range bp | Closest Markers |
---|---|---|---|---|---|---|
1 | MQTL1.1 | 546.03 | 0.07 | 120604292 | 113763968–128399829 | * Cmwg645(59.938)-bPb-0395(60.740) |
MQTL1.2 | 0.22 | 191424829 | 187288939–198521321 | E32M61-265(94.97)-SCRI_RS_113745(95.12) | ||
MQTL1.3 | 0.22 | 215895490 | 209987507–219651209 | E38M55-493(107.09)-0501A(107.11) | ||
MQTL1.4 | 0.15 | 227122225 | 224396043–241295755 | bPb-8763(113.65)-E40M32-654(113.84) | ||
MQTL1.5 | 0.11 | 274117654 | 257758192–281940383 | His3B(135.24)-ABC152F(135.81) | ||
MQTL1.6 | 0.22 | 328366571 | 317252081–331517042 | bp5019(162.71)-bPt-5002(163.17) | ||
2 | MQTL2.1 | 966.53 | 0.09 | 42367561 | 39815442–44919679 | AWBMS62(17.55)-WG516(17.79) |
MQTL2.2 | 0.2 | 68439906 | 64629701–72250111 | bPb-6235a(28.42)-bPb-6128(28.76) | ||
MQTL2.3 | 0.09 | 97387878 | 91468880–103306875 | BNL16.06(40.61)-bPb-3574(41.08) | ||
MQTL2.4 | 0.04 | 139419949 | 135909288–142930609 | P61M48h(58.13)-bPb-3575(59.69) | ||
MQTL2.5 | 0.22 | 170213114 | 166570654–173855574 | BF064492(71.03)-AWBMA33(71.19) | ||
MQTL2.6 | 0.06 | 189767373 | 187766416–191768330 | Bmag0711(49.14)-EBmac521a(80.08) | ||
MQTL2.7 | 0.1 | 263383407 | 256445958–270320855 | EBmatc0039(109.90)-AWBMA21(109.95) | ||
MQTL2.8 | 0.12 | 294464135 | 290701857–298226412 | BQ740141(122.82)-3179-497(122.96) | ||
MQTL2.9 | 0.07 | 611525900 | 608806036–614245763 | BM815937(221.69)-BM816122(257.49) | ||
3 | MQTL3.1 | 775.59 | 0.09 | 268408330 | 261707356–275109306 | E32M62-92(101.28)-E35M48-250(101.83) |
MQTL3.2 | 0.23 | 379792248 | 376613242–384250770 | E41M61-400(143.95)-E42M51-442(143.96) | ||
MQTL3.3 | 0.1 | 436460332 | 428189641–444731023 | bPb-3320(165.22)-basd27g02(165.47) | ||
MQTL3.4 | 0.17 | 473526748 | 471178768–475874727 | bPt-6567(179.18)-bPt-5150(179.52) | ||
MQTL3.5 | 0.31 | 498826884 | 495476397–502177372 | bp4025(189.03)-7241-553(189.17) | ||
MQTL3.6 | 0.07 | 573909459 | 563449078–584369838 | ABA302(217.25)-P15M47-91(217.59) | ||
4 | MQTL4.1 | 889.8 | 0.07 | 182695125 | 175965050–193845575 | SCRI_RS_180891(80.50)-SCRI_RS_119628(83.45) |
MQTL4.2 | 0.08 | 250437750 | 245089075–255786425 | BOPA2_12_10063(113.09)-E36M62-78(113.51) | ||
MQTL4.3 | 0.04 | 285624125 | 277921575–293326675 | basd13l12(128.85)-E33M60--5.5(129.43) | ||
MQTL4.4 | 0.03 | 317672025 | 304090350–331253725 | E40M32-153(143.70)-E36M59-94(143.91) | ||
MQTL4.5 | 0.12 | 339354100 | 332668250–346039950 | E33M54-416(153.49)-bPb-6872(153.58) | ||
MQTL4.6 | 0.17 | 352946825 | 348117550–357776125 | E32M62-386(158.61)-E38M55-139(158.80) | ||
MQTL4.7 | 0.17 | 403538300 | 400996575–406080025 | BF258346B(182.46)-bPb-7395(182.61) | ||
MQTL4.8 | 0.32 | 462329625 | 460130475–465799650 | mHsh(209.15)-ABC305(209.24) | ||
5 | MQTL5.1 | 710.31 | 0.03 | 11389965 | 9196970–13582960 | ABG464(10.90)-Act8A(11.32) |
MQTL5.2 | 0.12 | 121232310 | 120331310–122133305 | bp3200(106.34)-E40M40-354(107.08) | ||
MQTL5.3 | 0.09 | 135954265 | 133744270–138164260 | E42M55-350(119.80)-E37M50-70(120.07) | ||
MQTL5.4 | 0.14 | 152138215 | 149316225–154960210 | Bmac282a(134.20)-E37M62-231(134.43) | ||
MQTL5.5 | 0.07 | 177842140 | 174833150–180851130 | 1896-1435(156.80)-bags4p07(157.03) | ||
MQTL5.6 | 0.06 | 197188085 | 192853095–201523070 | Bmac0223(173.52)-CDO57B(174.12) | ||
MQTL5.7 | 0.06 | 206322725 | 204237395–208408050 | MWG923(181.91)-GBM1227(182.46) | ||
MQTL5.8 | 0.26 | 239937290 | 238061630–241812955 | bPb-4988(211.63)-7523-440(211.80) | ||
MQTL5.9 | 0.19 | 262479225 | 262054225–262904225 | dhn9(231.4)-bPb-6367(231.8) | ||
6 | MQTL6.1 | 438.51 | 0.12 | 129309961 | 120005985–138613926 | bPb- 8054(38.32)-bPb-9768(38.80) |
MQTL6.2 | 0.07 | 198777337 | 181047449–216507225 | bPb-4555(58.80)-GBM1049(58.86) | ||
MQTL6.3 | 0.55 | 256188394 | 251612394–260764394 | Bmac297(75.84)-bPb-1116(75.92) | ||
MQTL6.4 | 0.26 | 320961575 | 319965327–321957823 | 4191-268(95.03)-E45M48e(93.05) | ||
7 | MQTL7.1 | 640.38 | 0.15 | 172041612 | 165726420–178356810 | bPb- 8054(38.32)-bPb-9768(38.80) |
MQTL7.2 | 0.11 | 205841892 | 197894802–213788982 | bPb-4555(58.80)-GBM1049(58.86) | ||
MQTL7.3 | 0.07 | 224776302 | 218058726–231493884 | Bmac297(75.84)-bPb-1116(75.92) | ||
MQTL7.4 | 0.06 | 248606394 | 240290454–256922334 | 4191-268(95.03)-E45M48e(93.05) | ||
MQTL7.5 | 0.11 | 278695794 | 273308316–284083272 | GBM1030(124.47)-bPb-1039(124.83) | ||
MQTL7.6 | 0.21 | 293069850 | 289839600–296300106 | BOPA1_5480-826(131.10)-BOPA1_ABC11989-1-2-148(131.14) | ||
MQTL7.7 | 0.01 | 311177142 | 306538548–319839582 | bp8365(138.93)-SCRI_RS_122512(139.52) | ||
MQTL7.8 | 0.04 | 352488594 | 345402156–359575026 | bPb-5260(157.53)-Bmag0174b(157.88) | ||
MQTL7.9 | 0.08 | 381929706 | 374642082–389217330 | ABC305(170.76)-bPb-9269(171.07) | ||
MQTL7.10 | 0.16 | 413807478 | 411996750-415618206 | bPb-4129(185.06)-bp5141(185.26) |
Chr | Drought | Low Temperature | Water-Logging | Salinity | Mineral Toxicity and Deficiency | Total |
---|---|---|---|---|---|---|
1H | 18(4) | 2(2) | 11(4) | 21(6) | 12(4) | 64(20) |
2H | 54(6) | 1(1) | 10(4) | 43(8) | 12(4) | 120(23) |
3H | 43(6) | 0 | 8(4) | 23(5) | 25(2) | 99(17) |
4H | 32(4) | 2(1) | 8(3) | 39(8) | 15(4) | 96(20) |
5H | 16(4) | 9(1) | 3(2) | 23(6) | 7(2) | 58(15) |
6H | 21(2) | 2(1) | 2(2) | 22(4) | 12(3) | 59(12) |
7H | 26(6) | 0 | 5(4) | 35(7) | 23(4) | 89(21) |
Total | 210(32) | 16(6) | 47(23) | 206(44) | 106(23) | 585(128) |
Meta-QTL. | Stress | Meta-QTL | Stress | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Low Temperature | Mineral Toxicity and Deficiency | Waterlogging Tolerance | Salinity | Drought | Low Temperature | Mineral Toxicity and Deficiency | Waterlogging Tolerance | Salinity | Drought | ||
MQTL1.1 | 1 | 3 | 2 | 1 | 0 | MQTL4.6 | 0 | 0 | 0 | 15 | 3 |
MQTL1.2 | 0 | 0 | 5 | 5 | 4 | MQTL4.7 | 0 | 9 | 4 | 1 | 0 |
MQTL1.3 | 0 | 1 | 3 | 10 | 4 | MQTL4.8 | 2 | 3 | 3 | 10 | 18 |
MQTL1.4 | 0 | 0 | 0 | 1 | 2 | MQTL5.1 | 0 | 0 | 0 | 2 | 0 |
MQTL1.5 | 1 | 1 | 0 | 2 | 0 | MQTL5.2 | 9 | 0 | 0 | 8 | 0 |
MQTL1.6 | 0 | 7 | 1 | 2 | 8 | MQTL5.3 | 0 | 0 | 0 | 5 | 0 |
MQTL2.1 | 1 | 0 | 0 | 14 | 0 | MQTL5.4 | 0 | 5 | 0 | 2 | 2 |
MQTL2.2 | 0 | 7 | 0 | 7 | 18 | MQTL5.5 | 0 | 0 | 0 | 0 | 1 |
MQTL2.3 | 0 | 1 | 0 | 0 | 8 | MQTL5.6 | 0 | 0 | 2 | 0 | 0 |
MQTL2.4 | 0 | 2 | 2 | 1 | 1 | MQTL5.7 | 0 | 0 | 1 | 0 | 0 |
MQTL2.5 | 0 | 0 | 5 | 4 | 14 | MQTL5.8 | 0 | 0 | 0 | 1 | 11 |
MQTL2.6 | 0 | 2 | 0 | 2 | 0 | MQTL5.9 | 0 | 2 | 0 | 5 | 2 |
MQTL2.7 | 0 | 0 | 2 | 5 | 12 | MQTL6.1 | 2 | 0 | 1 | 3 | 0 |
MQTL2.8 | 0 | 0 | 1 | 4 | 1 | MQTL6.2 | 0 | 1 | 0 | 1 | 0 |
MQTL2.9 | 0 | 0 | 0 | 6 | 0 | MQTL6.3 | 0 | 9 | 1 | 9 | 19 |
MQTL3.1 | 0 | 0 | 1 | 2 | 5 | MQTL6.4 | 0 | 2 | 0 | 9 | 2 |
MQTL3.2 | 0 | 7 | 4 | 8 | 5 | MQTL7.1 | 0 | 11 | 2 | 10 | 2 |
MQTL3.3 | 0 | 0 | 2 | 3 | 8 | MQTL7.2 | 0 | 0 | 0 | 0 | 6 |
MQTL3.4 | 0 | 0 | 1 | 0 | 14 | MQTL7.3 | 0 | 0 | 1 | 2 | 0 |
MQTL3.5 | 0 | 18 | 0 | 8 | 5 | MQTL7.4 | 0 | 7 | 1 | 0 | 0 |
MQTL3.6 | 0 | 0 | 0 | 2 | 6 | MQTL7.5 | 0 | 0 | 0 | 7 | 0 |
MQTL4.1 | 0 | 0 | 0 | 5 | 0 | MQTL7.6 | 0 | 0 | 0 | 6 | 6 |
MQTL4.2 | 0 | 0 | 1 | 1 | 6 | MQTL7.7 | 0 | 3 | 0 | 0 | 0 |
MQTL4.3 | 0 | 2 | 0 | 1 | 0 | MQTL7.8 | 0 | 0 | 0 | 1 | 2 |
MQTL4.4 | 0 | 0 | 0 | 1 | 0 | MQTL7.9 | 0 | 0 | 1 | 5 | 1 |
MQTL4.5 | 0 | 1 | 0 | 5 | 5 | MQTL7.10 | 0 | 2 | 0 | 4 | 9 |
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Akbari, M.; Sabouri, H.; Sajadi, S.J.; Yarahmadi, S.; Ahangar, L.; Abedi, A.; Katouzi, M. Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses. Genes 2022, 13, 2087. https://doi.org/10.3390/genes13112087
Akbari M, Sabouri H, Sajadi SJ, Yarahmadi S, Ahangar L, Abedi A, Katouzi M. Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses. Genes. 2022; 13(11):2087. https://doi.org/10.3390/genes13112087
Chicago/Turabian StyleAkbari, Mahjoubeh, Hossein Sabouri, Sayed Javad Sajadi, Saeed Yarahmadi, Leila Ahangar, Amin Abedi, and Mahnaz Katouzi. 2022. "Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses" Genes 13, no. 11: 2087. https://doi.org/10.3390/genes13112087
APA StyleAkbari, M., Sabouri, H., Sajadi, S. J., Yarahmadi, S., Ahangar, L., Abedi, A., & Katouzi, M. (2022). Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses. Genes, 13(11), 2087. https://doi.org/10.3390/genes13112087