genetics of gene expression in barley
DESCRIPTION
Genetics of gene expression in barley. Birmingham University: Elena Potokina Zewei Luo Mike J Kearsey. SCRI (Dundee) : Arnis Druka Robbie Waugh. Material : Steptoe x Morex doubled haploid (DH) recombinant inbred lines Tool : 22,801 unigene Affymetrix Barley Chip. - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/1.jpg)
Genetics of gene expression in barley
Material: Steptoe x Morex doubled haploid (DH) recombinant inbred lines
Tool: 22,801 unigene Affymetrix Barley Chip
Genetical Genomics Approach:
• Expression Data Analysis across parental lines and DH progeny
• eQTL analysis (identification of cis- and trans-acting regulators)
• Exploring the relationship between eQTL and mapped phenotypic traits
Birmingham University:
Elena PotokinaZewei Luo Mike J Kearsey
SCRI (Dundee):
Arnis DrukaRobbie Waugh
![Page 2: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/2.jpg)
Steptoe Golden PromiseMorex
Seedlings 12 days after plantingThe length of the seedling leaves of any of the segregating lines was not significantly different
at this developmental stage (data not shown)
9 seeds per pot were planted in the vermiculate• all the seedlings from each pot were counted, measured and pooled for the RNA isolation
12 days after the planting
![Page 3: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/3.jpg)
Morex at 10 cm seedling stage (12 days after planting). Leaves were collected separately from 9 seedlings.
Material:
Steptoefeed barley
Morexmalting barley
AA BBx
35 Double Haploid lines (each in 1 replication)
(3 replications) (3 replications)
Totally: 41 hybridisations onto Affymetrix Barley1 Chip
![Page 4: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/4.jpg)
22801 contigs
![Page 5: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/5.jpg)
Probe Set: Contig8450_s_atDescription: BEST BLASTX NR: 10/02/02 BAB89658.1 6e-43 (AP003262) hypothetical protein~similar to Arabidopsis thaliana chromosome 3, At3g02290 [Oryza sativa (japonica
Probe Set: Contig8450_atDescription: BEST BLASTX NR: 10/02/02 BAB89658.1 6e-43 (AP003262) hypothetical protein~similar to Arabidopsis thaliana chromosome 3, At3g02290 [Oryza sativa (japonica
Probe Start End Sequence
1 Contig8450_at_265 253 277 GCAAGAAGCCAGTGCCTTGGGATGA
2 Contig8450_at_270 258 282 AAGCCAGTGCCTTGGGATGAACCCA
3 Contig8450_at_284 272 296 GGATGAACCCAGGACGACAGCCAAT
4 Contig8450_at_288 276 300 GAACCCAGGACGACAGCCAATATTG
5 Contig8450_at_295 283 307 GGACGACAGCCAATATTGGCGACTT
6 Contig8450_at_308 296 320 TATTGGCGACTTGGAAGTAGGTCTT
7 Contig8450_at_316 304 328 ACTTGGAAGTAGGTCTTGGTGGCAT
8 Contig8450_at_354 342 366 GAGGGCAGAGTAGCCCATGCATCTC
9 Contig8450_at_360 348 372 AGAGTAGCCCATGCATCTCCAGATG
10 Contig8450_at_364 352 376 TAGCCCATGCATCTCCAGATGTTAG
11 Contig8450_at_368 356 380 CCATGCATCTCCAGATGTTAGTGGG
1 Contig8450_s_at_394 382 406 ATGAACTTTCCCTGGAGCATGTGGA
2 Contig8450_s_at_456 444 468 GATCCTAGAGCTGGAACCTCGGAGT
3 Contig8450_s_at_490 478 502 GCAATTCTGTGCAAACATCCCCTAG
4 Contig8450_s_at_530 518 542 GGGCGGCCATGTTACTACAAGCGAT
5 Contig8450_s_at_588 576 600 TGAACATTTGAGCTCTGCCTTGCAG
6 Contig8450_s_at_603 591 615 TGCCTTGCAGTGAGCCATCGATCAT
7 Contig8450_s_at_656 644 668 GGGATAAGATCCTGGCCCCGTGTAA
8 Contig8450_s_at_669 657 681 GGCCCCGTGTAATTCTGAACAGACT
9 Contig8450_s_at_710 698 722 GTGGTGCATCAGACCGGTCAAGCTT
10 Contig8450_s_at_728 716 740 CAAGCTTCTGTTGTTGCGTGTGTTT
11 Contig8450_s_at_765 753 777 AAGTGGCCTATAAGAGCTCAAGCTC
Probe set structure:
![Page 6: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/6.jpg)
Calculation of an expression value: Probe Level Analysis Method
Expression value is calculated by taking the difference between the PM and MM of every probe pair and averaging the differences over the probe set
![Page 7: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/7.jpg)
M1 M2 M3 S1 S2 S3
Contig10146_at P P P P P P
Contig10147_s_at P P P P P P
Contig10149_at P P P P P P
Contig10156_s_at P P P P P P
Contig10157_at P P P P P P
Contig10158_at P P P P P P
…… …
Contig9734_at P P P A A P
Contig976_at P P P P A A
Contig9823_at P P P A M P
EBca01_SQ004_P03_at P P P P M A
EBma03_SQ003_L14_s_at P P P A P A
Contig2885_at P P P A A A
Contig3237_at P P P A A A
…… …
HVSMEk0012K02r2_at P M P P P P
HVSMEk0021N05r2_s_at P A P P P P
HVSMEl0008P20r2_s_at P M P P P P
HVSMEl0011A04f_at P P M P P P
HVSMEl0014D05r2_at P A P P P P
HVSMEm0008F11r2_at P M P P P P
HVSMEn0001D07r2_at A P P P P P
Filtering of genes before eOTL analysis: from 22,801 to 13,720P – “present”, A – “absent”, M – “marginal”
![Page 8: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/8.jpg)
Chi-Square test = 999.16744, df = 30 (adjusted) , p = 0.00000
0.0 0.6 1.3 1.9 2.5 3.2 3.8 4.4 5.1 5.7 6.3
Standard Error of Mean (upper limits)
0
5000
10000
15000
20000
25000
No
. o
f co
ntig
sDifference in gene expression between parental genotypes ?
22 801 contigs on the chip
Filtering based on presence-absence score of parents
13 720 contigs
2 124 genes are differentially expressed (15.5%)
10 623 genes are constantly expressed (77.4%)
972 genes cannot be classified because of high standard error (7.1%)
![Page 9: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/9.jpg)
10 100 1000 1e4
10
100
1000
Parent M (control)
562 genes are differentially expressed between Steptoe and Morex
after Multiple Testing Correction
![Page 10: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/10.jpg)
SM-35DHlines562genes
DH73
DH74
Morex
Steptoe
![Page 11: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/11.jpg)
Contig4366_at MWG9380Contig5312_at6MWG83712Contig13454_at ABA00415
BCD09828Contig7167_at31Contig7301_at Ica134
Contig4647_at46JS07453Contig3640_at56Contig12550_at Caf162HS08B03u_s_at Pcr265Contig7861_at71Contig3479_at74HU14A02u_at Glb177HS06J22u_s_at83Contig4569_at89DAK123B92Contig1512_at96
Contig4564_at PSR330Contig6571_at108
Contig9006_at114
cMWG706A124Contig3100_at130BCD1930 Contig7742_at136Contig9673_s_at139
Contig8542_at148Contig10050_s_at ABC261151Contig5059_s_at157
1
MWG844A0
ABG703B13MWG878A16Contig5128_s_at19Contig1216_s_at21ABG31827
ABG35845Pox46Bgq6053Contig4775_at56ABC46858Contig5800_at61ABC45163MWG86565Contig4928_at68Contig10081_at69Contig2867_at72Contig2970_s_at75MWG50377ksuD2290Contig2043_s_at98ABC252106Contig2168_s_at109
ABC165128Contig5135_s_at134Contig2764_s_at137MWG844B140Contig5555_at143bBE54C146
1
ABG3210MWG798B1Contig1630_at4Contig10771_at Contig3379_atBCD153212
Contig4768_s_at18KO1 ABG462Contig12473_at ABG39631
Contig12356_at Contig3098_at34Contig7001_at Contig4158_at36Contig18717_at39MWG571B Contig3834_at45Contig1747_at Contig13107_atContig3880_s_at Contig2753_atHVSMEi0006K11r2_at Contig3345_at
48
ABG37753ABG453 Contig4610_s_atContig2371_at62
HVSMEm0014A16r2_s_at68CDO34571Contig3836_at Contig1916_s_at74Contig3660_at93Contig7199_at Contig13753_at96Contig3413_s_at ABG004106Contig270_at109Contig7009_at115Contig13678_at Contig5986_s_atHM01J06w_s_at Contig2281_atABC161 ABC174
124
HVSMEf0021H03r2_s_at Contig6115_at130Contig13413_at136ABC166 Contig1561_atContig15099_s_at139
Contig12390_at142
ABC172 Contig1676_at155
1
MWG6340Contig2943_s_at3Contig14522_at6JS103.313Contig7388_at21scsnp0301724Ole127BCD402B30scsnp01650 scsnp0164831scsnp0535134scsnp0008939BCD808B40Contig4147_at42Contig7061_s_at48Contig4336_at50ABG48451scind0643552Contig12508_s_at56scsnp0164658bBE54A60Contig5861_at64Contig4844_s_at70BCD453B73scsnp0359176Contig5200_at79Contig9154_at ABG319A82Contig5603_s_at89KFP22192Contig8173_at95Contig7893_at98rbah53f17_s_at101ABG397107ABG319C Contig12417_at118
scind02282144scsnp15094146Contig4105_s_at Bmy1147Tel4M154
1
S/M map for eQTLs: 34 lines, 220 markers - 7 chromosomes (RFLP and SNP markers)
1H 2H 3H 4H …
![Page 12: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/12.jpg)
13 720 genes subjected to eQTL analysis
1 609 genes with at least one significant QTL
eQTL analysis criteria: 1) Composite Interval Mapping (CIM) , LOD > 3.0 2) Single Marker Analysis (SMA) p-value < 0.001
1589 genes 98.7% one QTL
20 genes 0.01% two QTLs
different QTLs = QTLs on different chromosomes
13 720 genes subjected to QTL analysis
![Page 13: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/13.jpg)
eQTL for Contig 10081_at
Contig 10081_at mapped by SNP marker
cis- or trans- regulation ? 50 genes mapped by SNP markers
cis- 72%
![Page 14: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/14.jpg)
eQTL for Contig 10984_at
Contig 10984_at mapped by SNP marker
cis- or trans- regulation ? 50 genes mapped by SNP markers
trans- 28%
![Page 15: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/15.jpg)
1H2H 4H
5H6H
7H3H
0
70
140
210
280
261 eQTLs are assigned to MWG503 (2H)
121 eQTLs are assigned to MWG865 (2H)
How many eQTLs are linked to each of 222 markers:hotspot on chromosome 2H ?
Markers - Chromosomes
![Page 16: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/16.jpg)
To perform genetical genomics approach we need:
• Segregation population (DH lines, RILs, F2...)
• Set of molecular markers polymorphic between parental lines
• Information about alleles of the markers in each of progeny lines (progeny lines genotypes)
• Genetic map as a linear arrangement of the markers from recombination values
• RNA profiling data for each of progeny lines
![Page 17: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/17.jpg)
Gene arrays are not just for measuring gene expression
labeled mRNA
Expression analysislabeled totalgenomic DNA
Single Feature Polymorphism(SFP) detection
![Page 18: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/18.jpg)
pm M1 M2 M3 S1 S2 S3DH116
DH12
DH13
DH130
DH141
DH135
DH177
DH136
DH..167
Contig5061_at1 586 474 586 472 392 476 438 410 502 492 380 634 484 485 651
Contig5061_at2 519 653 769 642 645 873 463 519 730 767 626 806 680 1012 689
Contig5061_at3 354 253 330 342 267 327 352 339 452 298 306 492 345 435 376
Contig5061_at4 316 190 324 387 283 312 199 183 449 254 347 346 274 270 178
Contig5061_at5 952 830 861 590 427 638 763 643 697 632 346 1052 662 530 639
Contig5061_at6 928 823 1080 730 725 551 1096 796 909 931 664 1335 871 1219 1020
Contig5061_at7 514 176 452 56 62 56 445 58 413 324 68 505 36 268 48
Contig5061_at8 1184 1445 1224 1124 1026 1228 1031 931 1191 1205 1017 1289 822 1485 1387
Contig5061_at9 520 342 576 459 386 450 510 381 511 481 488 652 542 666 632
Contig5061_at10 664 375 642 641 426 591 577 579 706 589 498 674 509 746 685
Contig5061_at11 854 522 806 982 694 815 679 691 853 759 779 770 631 554 660
How to define Single Feature Polymorphism (SFP markers) from RNA profiling data?
Contig5061_at7:two groups from k-mean clustering
Contig5061_at3:two groups from k-mean clusteringVariance across all 40 chips
Var Group1 + Var Group 2
Val
V1/n1 + V2/n2
![Page 19: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/19.jpg)
Val
V1/n1 + V2/n2
Contigs with putative SFPs are in the 90 percentile:
![Page 20: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/20.jpg)
t-test: p=10-3 t-test: p=10-20
AA aa AA aa
DHi = aaDHi = ?
Pr { DHi AA AA, σAA , aa, σaa }
Pr > 0.90
Genotyping of DH lines across the population based on SFPs:
genotyping success: 60% genotyping success: 100%
(genotyping success: percentage of DH lines successfully genotyped)
![Page 21: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/21.jpg)
t-test: p=10-3 t-test: p=10-20
AA aa AA aa
Sequencing data were available for 129 probes to test the accuracy of SFPs prediction
p-value False positive rate Percentage of DH lines genotyped
Number of SFPs
<10-20 3% 100% 256
<10-15 6% 93% 1012
<10-10 10% 85% 2050
<10-5 16% 75% 2892
![Page 22: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/22.jpg)
Mapping of the predicted SFPs:
1012
648
• only one SFP/probe per contig was mapped• contigs predicting less than 31 DH line out of 34-DHset were removed
567
• 81 were removed from analysis by mapping software as identical
548 SFPs/contigs
• 19 did not join to any of linkage group by LOD=3 and higher
successfully formed 7 linkage groups corresponding to 7 barley chromosomes
Chromosome 1H 2H 3H 4H 5H 6H 7H
Number of SFP markers 57 114 82 39 109 69 77
Number of anchor RFLP markers
5 6 5 6 4 6 5
Total 62 120 87 45 113 75 82
![Page 23: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/23.jpg)
Contig21640_at5Contig2337_at100Contig4887_s_at1112MWG83713Contig5857_at715Contig5859_at719Contig22516_at921Contig21247_at727HV05F11u_x_at5Contig3217_s_at633Contig14013_s_at435ABG500A41Contig14742_x_at743Contig12283_at1049Contig6251_at356Contig2947_at10HK04F07r_at557Contig5576_at2Contig10724_at1159HK04G05r_at5HVSMEg0015I15r2_at7Contig15811_at8rbags10j11_s_at3Contig6997_at11
60
Contig17095_at861HVSMEb0014F22f_s_a1064HK05M22r_at967Contig3479_at368Contig4121_at3
70Contig12839_at1Glb1Contig14005_at971
Contig10681_at672Contig20245_at873Contig12759_at1075Contig20070_at980HV_CEa0009C07r2_at1081Contig10249_at1183Contig4450_at388Contig200_at590Contig15928_at691Contig22762_at897Contig7574_at9100Contig7898_at5102Contig3246_s_at7103Contig3532_at6105Contig10829_at7108cMWG706A115Contig9336_at4121Contig12420_at6122rbaal30e02_s_at3129Contig2449_at5133Contig14682_at8Contig2951_at6136Contig4250_s_at6138ABG387A139Contig5061_at7Contig14709_at8Contig17218_at7141
Contig14590_at10143Contig6092_at5145Contig1079_x_at7150
MWG835A0MWG9382MWG036A7MWG83712Hor114
ABA00422
BCD9830
ABG05336Ica141
ABG500A48ABC16455WG789B57ABR33761Glb165
ABC16073
ABG46486His3B93ABC307A95cMWG706A104ABC257109cMWG733114AtpbA120ABG702122ABC322B126ABC261128Cab2131Aga7133MWG912136ABG387A138
Comparison of SFP map and base RFLP map of barley: chromosome 1H
SFP map RFLP map
![Page 24: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/24.jpg)
85 DH85 88 DH88 89 DH89 116 DH116 130 DH130 135 DH135 136 DH136 140 DH140 141 DH141 146 DH146 152 DH152 155 DH155 160 DH160 167 DH167
Contig21640_at5 a A a A - A - B a A - B - B b B b B a A b B a A a A a AContig2337_at10 a A a A a A - B a A b B b B b B b B a A b B a A a A a AContig4887_s_at11 a A a A a A b B a A b B b B b - b B a A b B a A a A a AMWG837 a A a A a A b B a A b B b B b - b B a A b B a A a A a AContig5857_at7 a A a A a A b B a A b B b B b A b B a A b B a A a A a AContig5859_at7 A A A A A A B B A A B B B B 19 B B B B A A B B A A A A A -Contig22516_at9 A A 21 A A A A B B A A 21 B B B A 21 B - B B A A B B A A A A A AContig21247_at7 a B 27 a A a A b B a B 27 b B b A b B b B a A b B a A a A 27 a -HV05F11u_x_at5 A B A A A A B B A B B B B A - - B B A A B - A A A B 33 A AContig3217_s_at6 A B A A A A B B - B B B B A B - B B A A B - A A - B A AContig14013_s_at4 29 A B A A A A B B 29 A B B B B A B B B B A A B B A A 29 A B A AABG500A 37 B B A A A A B B 37 B B B B 37 B A B B B B A A B B A A 37 B B A AContig14742_x_at7 - B A A - A B B 43 B - B B 39 A A B B B B A A B B A A - - - AContig12283_at10 b B a A a A 60 b A 49 b B b B a A b B b B a A b B a A b B a AContig6251_at3 B B A A A B 60 B A B B B B A A B B B B A A B B A A B B A AContig2947_at10 B B A A A B B A B B B B A A B B B B A A B B A A B B A AHK04F07r_at5 b B a A a B b A b B b B a A b B b B a A b B a A b B a AContig5576_at2 b B a A a B b A b B b B a A b B b B a A b B a A b B a AContig10724_at11 B B A - A B 53 B A B B B B A - B - B B A A B B A A B B A AHK04G05r_at5 b B a A a B 58 a A b B b B a A b B b B a A b B a A b B a AHVSMEg0015I15r2_at7 B B A - 59 A B A A B B B B A A B B B B A A B B A A B B A AContig15811_at8 b B a A 62 b B a A b B b B a A b B b B a A b B a A b B a Arbags10j11_s_at3 B B A A B B A A B B B B A A B B B B A A B B A A B B A AContig6997_at11 B B A A B B A A B B B B A A B B B B A A B B A A B B A AContig17095_at8 b B a A b B a A b B b B a A b B b B a A b B a - b B a AHVSMEb0014F22f_s_a10 B B A A B B A A B B B B A A B B B B A A B B A A B B A AHK05M22r_at9 b B a A b B a A b B b B a - b B 67 b B a - b B a A b B a AContig3479_at3 b B a A b B a A b B b B a A b A 68 b B a A b B a A b B a AContig4121_at3 B B A A B B A A B B B B A A B A B B A A B B A A B B A AContig12839_at1 B B A A B B A A B B B B A A B A B B A A B B A A B B A AContig14005_at9 B B A A B B A A B B B B A A B A B B A A B B A A B B A AGlb1 B B A A B B A A B B B B A A B A B B A A B B A A B B A AContig10681_at6 b B a A b B a A b B b B a A b - b B a A b B a A b B a AContig20245_at8 b B a A b B a A b B b B a A 65 b - b B a A b - a A b B a AContig12759_at10 B B A - B B A - B B B B A A 67 A A B B A A B B A A 75 B B A AContig20070_at9 B B A A B B A A B B B - A A A - B B A A B B A B 80 B B A AHV_CEa0009C07r2_at10 B B A A B - A A B B B - A A A A B B A A B B A A B B A AContig10249_at11 B B A A B B A A B B B B A A A A B B A A B B A B B B A AContig4450_at3 B B A B B B A A 88 B B B B A B A A B B 88 A A B B A B B B A AContig200_at5 B B A A B - A - 90 B B B B A A A A B A 90 A A B B A B B B A AContig15928_at6 b B a A b B a B b B b B a A a A b A a A b B 91 a B b B a AContig22762_at8 b B a A b B a - b B b B a A a B b A a A b A 97 a B b B a AContig7574_at9 b B a A b B a B b B b B a A a A b A a A b A a B b B a AContig7898_at5 b B a A b B a B b B b B a A a A b A a A b A 73 a B b B a AContig3246_s_at7 B B A A B B A B B B B B A A 103 A A B A A A B A 74 B B B B A AContig3532_at6 B B A A B B 75 A B B B B B A B 105 A A 105 B A A A B A B B B B A AContig10829_at7 b B a A b B 108 84 b B b B b B a B a - 108 83 b A a A b A b B - B a AcMWG706A B B A A B A 115 B B B B B B A B A B 84 A A A A B - B B B A A A 115Contig9336_at4 b B a A b A b B b B b B a B a B a A a A b A b B b B a B 121Contig12420_at6 b B a A b A b B b B b B a B a - a A a A b A b - b B a Brbaal30e02_s_at3 B B A A B A B B B B B B A B A B A A A B 83 B - B B 83 B B A BContig2449_at5 B B A - B A B B B B B B A - A B A A A A 133 92 A A B B 92 A B A BContig14682_at8 B B A A B A B B B B B B A B A B A A A B 136 A A B B A B A BContig2951_at6 b B a A b A b B b B b B a B a B a A a B a A b B a B a BContig4250_s_at6 b B a A b A b B b - b B a B 98 a - a A a B a A b B a - a BABG387A b B a A # b A b - b B b - 103 a B 103 b B a A a - a - b B a - a - 139Contig5061_at7 B B A A # A A B B B B B B 112 B B B B A A A B - A B B A - 141 112 A A 141Contig14709_at8 B B A A A A B B B B B B B B B B A A A B A - B B 118 A A 141 118 B AContig17218_at7 B B A A A A B B B B B B B B B B A A A B A A B B 123 B A B AContig14590_at10 b B a A a A b B b B b B b B - B a A a B a - b B b A b AContig6092_at5 b B a A a A b B b B 145 b B b B b B a A a B a A b B b A 145 b AContig1079_x_at7 b B a A a A b B b A 150 b B b B b B a A a B a - b B b B 150 b A
B A A B B B B B A 133 A A B B BB A A B B B B B A 137 B A B B BB A A B B B B B A B A B B BB A A B B B B B A B A B B BB A A B B B B B A B A B B Bb a a b b b b b a b a b b bB A A B B B B B A B A B B Bb a a b b b b b a b a b b 141 bb a a b b b b b a b a b b 141 ab a a b b b b b a b a b b ab a a b b b b b a b a b b ab a a b b b b b a b a b b ab a a b b b b b a b a b b aB A A B B B B B A B A B B AB A A - B - B B A - - B - -
Alignment of haplotypes from the SFP and SNP barley maps: chromosome 1H
![Page 25: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/25.jpg)
Contig21640_at50
Contig4887_s_at1112
MWG83713
Contig5857_at715
Contig5859_at719
Contig22516_at921
Contig21247_at727
HV05F11u_x_at533
Contig14013_s_at435
ABG500A41
Contig14742_x_at743
Contig12283_at1049
Contig6251_at356
Contig2947_at1057
Contig5576_at259
HK04G05r_at5
Contig15811_at8
Contig6997_at11
60
Contig17095_at861
HVSMEb0014F22f_s_a1064
HK05M22r_at967
Contig3479_at368
Contig4121_at370
Contig12839_at1
Contig14005_at971
Contig10681_at672
Contig20245_at873
Contig12759_at1075
Contig20070_at980
HV_CEa0009C07r2_at1081
Contig10249_at1183
Contig4450_at388
Contig200_at590
Contig15928_at691
Contig22762_at897
Contig7574_at9100
Contig7898_at5102
Contig3246_s_at7103
Contig3532_at6105
Contig10829_at7108
cMWG706A115
Contig9336_at4121
Contig12420_at6122
rbaal30e02_s_at3129
Contig2449_at5133
Contig14682_at8136
Contig4250_s_at6138
ABG387A139
Contig5061_at7
Contig17218_at7141
Contig14590_at10143
Contig6092_at5145
Contig1079_x_at7150
Contig11315_at90Contig13877_at72HVSMEi0018A05r2_x_53Contig11003_at110ABG703B12Contig19578_at914Contig17510_s_at517Contig12308_at1118rbah35f01_s_at419Contig589_x_at621Contig4823_at823Contig308_x_at424Contig594_x_at7Contig19241_at1125
Contig12089_at726Contig327_s_at929Contig61_s_at331ABG31833Contig2769_s_at839Contig25371_at1041HVSMEb0010F06r2_at1043Contig20626_at1145Contig3579_x_at1147HV11O16u_at348HY10B05u_x_at2Contig18594_at3Contig6254_at6
49
Contig8346_at750Pox51Contig8914_at953Contig4265_s_at955Contig25428_x_at257Contig7102_at558Contig9717_at7Contig19984_at1159
Contig26451_at560Contig14514_at8Contig20540_at461
HVSMEi0003C20r2_at1162Contig10535_at1163Contig11000_at4Contig11524_at7
64
rbags21b15_at965Contig1559_at1066Contig7293_at1167rbaak37h22_at668Contig6993_at6Contig17958_at4Contig8154_at3
70
Contig14898_at1071Contig12607_at1072Contig9258_at1173Contig14030_at876Contig24074_at179Contig2253_s_at481Contig8908_at1082Contig6198_at7Contig26114_at3
83
HV04J01r_at684Contig13835_at11HU04E13r_at9
85
MWG50386Contig14108_at1187Contig8616_at488Contig4350_at689Contig7630_at792Contig15767_at1097Contig19953_at898Contig6795_at10102Contig2809_at7104Contig2046_at2108Contig10730_at11110Contig2044_at4111ABC252117Contig6105_s_at1123Contig24523_at3125Contig10785_at1130Contig12574_at10133Contig1433_at1138Contig5135_s_at10140Contig11295_at11142Contig17366_at7145bBE54C147Contig4801_at4149HVSMEg0016P19f_x_a3150Contig13815_at5151HVSMEm0015J14r2_at5156
Contig125_at90
Contig12220_at36
Contig4161_at18
Contig17530_at69
Contig10114_at9
Contig8506_at710
Contig4769_at414
Contig7870_at516
HVSMEl0023I10r2_at817
Contig12833_at719
EBro04_SQ003_B10_s620
Contig11952_at821
Contig1164_at323
Contig11188_at1125Contig1786_s_at628
Contig5845_at4
Contig6681_at4
Contig12753_at7
33
MWG798B34
Contig19045_at637
Contig21913_at539
Contig6119_at1040
Contig10972_at4
HVSMEl0008I17r2_at542
Contig9352_at545
HV_CEa0003N18r2_at3
Contig8330_at1048
Contig16307_at449
Contig4997_s_at651
Contig23811_at1054
Contig21442_at465
Contig1430_at567
Contig2949_s_at973
Contig8408_at576
Contig18723_at977
Contig2613_s_at279
Contig3166_at181
CDO113B84
Contig18557_at387
Contig30_at989
Contig410_at291
Contig14467_at292
Contig6460_at593
Contig15356_at10
Contig10854_s_at1195
Contig7199_at796
Contig16567_at797
Contig7928_s_at1098
ABG004 Contig5754_at9Contig5753_at3
103
Contig18959_at10106
Contig5075_at3108
Contig21378_at9118
Contig13892_at9119
Contig5646_at7120
Contig4700_at9121
baal31g17_s_at8
Contig17946_at6125
Contig3927_s_at11126
Contig19223_at10129
HM09F12r_s_at9132Contig13352_at6135
Contig13874_at6136
Contig1159_at2137
Contig12390_at1140
HVSMEb0010A16r2_at7142
Contig1179_at8147
ABC172155
Contig7699_at80
Contig7522_at77
Contig7698_at7HVSMEl0008P20r2_at9Contig7951_at7
8
Contig16774_at1010
Contig10968_at919
MWG07725
Contig5487_s_at1132
HV_CEa0009K11r2_at1135
Contig9300_at439
rbaal1i15_s_at941
Contig12802_at842
HW03O03u_at5Contig12614_at8
45
Contig7594_at748
HC113H12_SK_at1053
Contig16020_at155
Contig4605_at257
ABG48461
Contig19630_at10Contig13173_at10
64
Contig5531_at565
Contig10310_at766
Contig11844_at969
Contig8511_at272
Contig18240_at873
Contig24154_at574
Contig16261_at781
Contig5836_s_at483
HVSMEh0095L04f_s_a590
Contig3205_s_at8
Contig19601_at10
92
HY02C09u_x_at499
Contig7474_s_at3106
Contig9190_at3Contig10095_at8
109
iHxk2112
Contig10937_at5116
Contig5903_s_at11117
ABG319C136
ASE1C157
Contig11126_at11Contig12587_at5
158
ABA307A167
Contig16318_at1
Contig9243_at50Contig7295_s_at106Contig1300_x_at88HV_CEb0001A10f2_at714Contig3947_s_at1016Contig6315_s_at824rbaak13h13_s_at827Contig9522_at1135Contig7106_at936Contig13951_at246Contig10757_at848Contig6519_at249rbaal22m22_s_at751Contig5083_at852Contig2893_at1054Contig5974_s_at1055ABG70557Contig6996_at159Contig26251_at760HVSMEi0008J09r2_x_1161Contig18379_at162Contig3237_at3Contig8209_at6EBro03_SQ005_O21_s4
63
Contig16134_at11HVSMEi0019L06r2_at964
HY07G16u_at865EBma03_SQ003_J21_s467Contig10497_at168Contig5231_at11Contig7176_at470
Contig18705_at471HVSMEm0003A13r2_at572Contig5847_at273HVSMEg0008B24r2_at974Contig13997_at1175HP01B09w_at976Contig10883_at977Contig9283_at979S78730_at386ABC30287Contig3054_at888Contig7450_at289Contig19506_at390Contig10407_at1191HVSMEn0020J05f_x_a593HU09F16u_s_at796EBro03_SQ004_E10_a997Contig7020_at8104HV_CEb0012I09r2_x_11105Contig4267_at7106Contig24438_at1111Contig12567_at7113Contig24449_at10114Contig4384_at10116Contig5182_at9117Contig6939_at9119Contig16074_at9121Contig13943_s_at3122
123Contig8979_at11126rbah38o04_s_at9130Contig6745_at4140Contig14054_at5145HVSMEm0007B06r2_s_2148Contig10941_at11151Contig9724_at11154Contig1181_x_at3157EBro02_SQ008_M09_a7158Contig21308_at6Contig24410_at6165
Contig6838_at9166HB14F21r_at10Contig2129_x_at3168
Contig6095_at6169Contig2130_at1171Contig9707_at4172Contig14157_at5173HVSMEf0003C10r2_at10174Contig15607_at8181Contig5252_at8190Contig17228_at11196Contig331_x_at3199Contig1003_at2200Contig9042_x_at2203Contig8225_at6205HV_CEa0001E19r2_at11207Contig9470_at6209Contig14544_at4214Contig8849_at11216ABG463219
Contig1568_x_at70
Contig2400_at1113
Contig1579_s_at615
Contig7192_at818
MWG62020
Contig2305_at1021
Contig24914_at224
Contig8716_at1125
HVSMEn0020P13r2_x_730
Contig8091_at733
EBem09_SQ002_H11_x535
HVSMEg0004N17r2_x_436
HA16L09r_s_at840
Contig19209_at142
Contig9927_s_at843
HV_CEb0011B08r2_at945
ABC152A46
rbags22p06_s_at1052
Contig4666_at653
Contig10126_at1160
Contig10125_s_at661
Contig9408_at1
Contig1659_x_at11
Contig14824_at11
62
Contig5948_at6
Contig23373_at1
Contig4320_at6
Contig4706_at4
63
Contig18566_at10
Contig12739_at264
Contig10706_at865
Contig1042_x_at1166
Contig6770_at869
HA04k13r_at871
Contig13806_at11
Contig4906_at1173
HV_CEb0007N06r2_at11
Contig15923_at474
Contig590_at776
Contig4108_x_at978
ksuD1780
Contig2885_at885
Contig5801_at1086
Contig477_at6
Contig8372_at787
HV11N12u_at1090
HVSMEa0009E14r2_at392
HVSMEg0011O06r2_s_1096
Contig17043_at697
Contig12824_at698
Amy1118
Contig16766_at8126
ABC170A Contig679_s_at1130
HV_CEb0009L11r2_at1
Contig12030_at11131
HVSMEc0012C08r2_at10132
HU11B09u_at11133
Contig19427_at11150
HVSMEl0003E22r2_at100
HW01O15u_at72
Contig10150_at74
Contig11996_s_at105
Contig2659_at116
Contig14594_at97
Contig18822_at38
Contig3141_at79
Contig11397_s_at1111
ABG32012
Contig6752_s_at517
Contig40_x_at321
Contig10425_at122
Contig570_s_at124
Contig11509_at728
Contig4028_x_at729
Contig5588_at1130
Contig20455_at831
Contig3024_at533
Contig15204_s_at934
Contig253_s_at538
HA11J15u_s_at1139
ksuA1A41
Contig13249_at142
Contig18524_at543
Contig13250_at1144
rbaal37j13_s_at950
HV_CEb0010H02r2_at252
Contig861_at154
Contig3840_at756
Contig18530_s_at9
HVSMEh0089C16r2_at457
Contig11942_at1158
Contig2810_at762
Contig5815_at563
Contig8756_at965
66
Contig2163_at1167
Contig24926_at1068
Contig1661_x_at369
rbaal9p16_x_at170
Contig742_at11
Contig7183_at471
Contig15402_at472
Contig20066_at973
Contig7248_at174
Contig2170_at575
Contig13416_at9
HVSMEm0003G02r2_at1176
Contig7278_at577
Contig8776_s_at1078
Contig14342_at1082
Contig4300_at1
Contig4374_s_at783
HVSMEm0001B03r2_at384
Contig6283_s_at1086
Contig13190_at7
Contig10950_at1194
Contig7157_at1195
Contig1048_at699
Contig10197_at8106
Contig3777_at8107
Contig4056_at6111
Contig25162_at1113
ABG461115
HS04A09u_s_at2122
The SFP genetic map of barley
![Page 26: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/26.jpg)
Summary
We suggest a simple algorithm to detect SFPs from RNA profiling data of any segregation population combining homozygote progeny lines
Number of detected SFP markers is sufficient to create a high densitygenetic map for any unknown cross
Construction of genetic map, measurement of gene expression and mapping of eQTL can be achieved within the same experiment
![Page 27: Genetics of gene expression in barley](https://reader036.vdocument.in/reader036/viewer/2022062301/568143b1550346895db039e6/html5/thumbnails/27.jpg)
Thanks to :
Mike Kearsey
Zewei Luo
Robbie Waugh
Arnis Druka