genetics of gene expression in barley material: steptoe x morex doubled haploid (dh) recombinant...
TRANSCRIPT
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
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
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
22801 contigs
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:
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
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”
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%)
10 100 1000 1e4
10
100
1000
Parent M (control)
562 genes are differentially expressed between Steptoe and Morex
after Multiple Testing Correction
SM-35DHlines562genes
DH73
DH74
Morex
Steptoe
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 …
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
eQTL for Contig 10081_at
Contig 10081_at mapped by SNP marker
cis- or trans- regulation ? 50 genes mapped by SNP markers
cis- 72%
eQTL for Contig 10984_at
Contig 10984_at mapped by SNP marker
cis- or trans- regulation ? 50 genes mapped by SNP markers
trans- 28%
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
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
Gene arrays are not just for measuring gene expression
labeled mRNA
Expression analysislabeled totalgenomic DNA
Single Feature Polymorphism(SFP) detection
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
Val
V1/n1 + V2/n2
Contigs with putative SFPs are in the 90 percentile:
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)
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
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
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
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
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
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
Thanks to :
Mike Kearsey
Zewei Luo
Robbie Waugh
Arnis Druka