Use of Identity by Descent Mapping

Approaches for FHB Resistance

Jose L. GonzalezSOUTH DAKOTA STATE

UNIVERSITY2016 USWBSI Annual MeetingDecember 4-6; St Louis, MO

2016 USWBSI Annual MeetingDecember 4-6; St Louis, MO

Acknowledgements• Umesh Rosyara (now U. Wisconsin)• Jonathan Eckard (now Monsanto)• Yuba Kandel (now Iowa St U.)• Yaqoob Thurston (PhD Student graduating this spring)

• SDSU- Karl Glover, William Berzonsky (currently Bayer), Sunish Sehgal, Shaukat Ali, Jeff Stein (currently Monsanto)

• KSU-William Bockus• UMN-James Anderson • NDSU- Francois Marais & Mohamed Mergoum (currently UGA) • USDA-ARS-Guihua Bai, Paul St. Amand, Shiaoman Chao • UNL- Steve Baenziger

Funding: • US Wheat and Barley Scab Initiative• South Dakota Wheat Commission • SDSU Agricultural Experiment Station

• U.R. Rosyara, J.L. Gonzalez-Hernandez*, K.D. Glover, K.R. Gedye And J.M. Stein 2009. Family-based Mapping Of Quantitative Trait Loci In Plant Breeding Populations With Fusarium Head Blight Resistance In Wheat As An Illustration. Theoretical And Applied Genetics. 118:1617-1631

• J.T. Eckard, J.L. Gonzalez-Hernandez*, S. Chao, P. St Amand, G. Bai. 2014. Construction Of Dense Linkage Maps "On The Fly" Using Early Generation Wheat Breeding Populations. Molecular Breeding 34:1281-1300

• Yuba R. Kandel, Karl D. Glover, Lawrence E. Osborne And Jose L. Gonzalez-Hernandez*. 2014. Mapping Quantitative Resistance Loci For Bacterial Leaf Streak Disease In Hard Red Spring Wheat Using An Identity By Descent Mapping Approach. Euphytica 201:53-65

• Eckard JT, Glover KD, Mergoum M, Aderson J, Gonzalez-Hernandez JL*. 2015. Multiple FusariumHead Blight Resistance Loci Mapped And Pyramided Onto Elite Spring Wheat Fhb1 Backgrounds Using An IBD-based Linkage Approach. Euphytica. 204 (1), 63-79

• Eckard JT, Gonzalez-Hernandez JL*, Caffe M, Berzonsky, W, Bockus WW, Marais GF, BaenzigerPS. 2015. Native Fusarium Head Blight Resistance From Winter Wheat Cultivars ‘Lyman,’ ‘Overland,’ ‘Ernie,’ And ‘Freedom’ Mapped And Pyramided Onto ‘Wesley’-fhb1 Backgrounds. Molecular Breeding. 35 (1), 1-16

• SOUTH DAKOTA STATE UNIVERSITY –PHD DISSERTATIONS: UMESH ROSYARA, MUNA KADARIA, YUBA KANDEL, JONATHAN E. TYLER,

Experimental Paradigm For QTL Mapping

P2: SusceptibleP1: Resistant

F1

F2

Fn

Integrated Molecular Breeding ApproachQ

TL linkage m

appingM

arker-assisted pyram

iding

R/rR/R

R/RR/R

R/RR/RR/rR/R

R/RR/RR/RR/r

R/RR/rR/R

R/RR/rR/R

The resistant genotypes Sumai 3 derivatives (SD3851, Freyr, SD3776) crossed with other 46 susceptible wheat genotypes

82 families, average family size = 9

Test case. Fhb1

Variance component analysis (MERLIN), Pedigree-wide regression (MERLIN-Regress) and Linkage disequilibrium analysis for quantitative traits (QTDT )

LOD score

Variance component –linkage

Pedigree-wide regression

Results: Linkage Analysis

14 DAI 21 DAI 14 DAI 21 DAI

DAI: Days after inoculation

Linkage disequilibrium14 DAI 21 DAI

Marker AS* χ2TDT P-value χ2TDT P-value

Xgwm389-3B 131 0.4 >0.05 0.04 >0.05135 0.34 >0.05 0.03 >0.05

Xgwm533.1-3B 114 6.4 0.01 8.25 0.004158 15.5 8 x 10-5 25.5 4 x 10-7

155 8.5 0.003 15.1 0.0001Xbarc133-3B 88 7.3 0.06 5.3 0.02

120 11.2 0.006 11.1 0.0008118 8.0 0.0008 17.9 2 x 10-5

Xgwm493-3B 137 0.004 8.7 0.003157 10.7 0.001 14.2 0.0002192 18.6 2 x 10-5 18.6 4 x 10-7

*AS- allele size Alleles from resistant parent are labeled blue

After successfully mapping mapping two more lines we learned:

• We need to be able to make linkage maps for the materials in question

• Additional phenotyping opportunities• Computational challenges

Consensus mapping:

Plant studies, few large populations

Joint mapping:

Animal studies, many small populations

Pop. 1 (n = 150)

Pop. 2 (n = 200)

Pop. 3 (n = 100)

Map 1

Map 2

Map 3C

onsensus map

Pop. 1 (n = 3)

Pop. 2 (n = 10)

Pop. 3 (n = 6)

Pop. 4 (n = 5)

Pop. p (n = 2)

. . .

Linkage Maps With Multiple PopulationsJoint m

ap

Four-way Crosses To Pyramid Resistance

Founder Lines

F1 Hybrids

Fhb1 R1 R2 R3

Four-way F1 plants

Building Linkage Maps in Winter Wheat Breeding Populations

Population Pedigree SSR genotyped SNP genotyped01 Wesley-Fhb1-BC56 / NE06545 // Ernie / Overland 20 1902 Ernie / Wesley-Fhb1-BC06 // Ernie / NE06545 26 -03 Ernie / Wesley-Fhb1-BC06 // Lyman / AL-107-6106 22 1604 Ernie / Wesley-Fhb1-BC56 // Ernie / Lyman 40 3705 Ernie / Wesley-Fhb1-BC56 // NI08708 / Lyman 40 3806 Ernie / Lyman // Ernie / Wesley-Fhb1-BC06 12 -07 Ernie / Overland // Freedom / Wesley-Fhb1-BC56 5 -08 Ernie / Overland // Overland / Wesley-Fhb1-BC56 24 2309 Ernie / Overland // NI08708 / Wesley-Fhb1-BC06 33 30

10 Ernie / NE06545 // McGill / Wesley-Fhb1-BC56 28 -

11 Ernie / McGill // Lyman / Wesley-Fhb1-BC06 12 912 Freedom / Wesley-Fhb1-BC06 // Ernie / Overland 12 913 Freedom / Wesley-Fhb1-BC06 // Lyman / AL-107-6106 7 714 Freedom / Wesley-Fhb1-BC06 // Overland / Wesley-Fhb1-BC56 11 915 Freedom / Wesley-Fhb1-BC56 // Ernie / NE06545 4 -16 Freedom / Ernie // Overland / Wesley-Fhb1-BC56 34 3017 Freedom / Ernie // NI08708 / Wesley-Fhb1-BC06 29 -18 Freedom / Overland // Lyman / AL-107-6106 8 819 Freedom / NI08708 // Wesley-Fhb1-BC56 / NE06545 7 -20 AL-107-6106 / Overland // Lyman / Wesley-Fhb1-BC06 11 1021 AL-107-6106 / Overland // NI08708 / Lyman 14 1422 Lyman / Wesley-Fhb1-BC56 // Ernie / Lyman 37 3523 Lyman / Wesley-Fhb1-BC56 // NI08708 / Lyman 31 -24 Overland / Wesley-Fhb1-BC56 // Ernie / Lyman 44 4125 Overland / Wesley-Fhb1-BC56 // Ernie / NE06545 5 -26 Overland / McGill // Lyman / Wesley-Fhb1-BC06 12 927 NI08708 / Wesley-Fhb1-BC06 // Ernie / NE06545 8 -28 NI08708 / Lyman // Overland / Wesley-Fhb1-BC56 29 28

Total population 565 372Genotypic data points 15 M 3.3 MM

Methodology For Map Development

www.animalgenome.org

CRI-MAP – Provides multipoint maximum likelihood estimation in general pedigrees.

Set threshold

Extend map

Permutateorders

Ordered loci

Recombination fractions

(CRI-MAP)

Linkage grouping (JoinMap)

SNP thinning

(R)

(CRI-MAP)

Map Development

Polymorphic loci

• 4,000

Genetic bins (𝜃𝜃 < 0.001)

• 1,269

Linkage groups

• 31 (consolidated to 21)

Linkage maps

Chromosome 3B𝑟𝑟𝑆𝑆 = 0.976

Chromosome 3A𝑟𝑟𝑆𝑆 = 0.980

5443, 77710.0447, 5427, 4927, 5430, (8)0.278611.76387, 2993, 82802.52737, 27383.140667.5

8127, 85113.5

8105, 8106, 393917.9480420.2425722.0

199647.4634048.73448, 5642, 373949.088549.84334, 4335, 4333, 755253.3641354.1539956.5515156.6702256.944357.3197257.75763, 8526, 6334, 1812, (9)58.9687759.02763, 2095, 33559.35387, 5444, 9059.5161460.56306, 63760.672061.2143, 2156, 1922, 4912, (5)61.4379461.86187, 531662.12153, 215462.4202362.5701262.7625662.83071, 6923, 7010, 3069, (5)62.9516463.61487, 3156, 4397, 462, (13)63.9731964.82617, 234, 108565.54923, 2750, 2886, 3930, (13)66.53836, 6170, 678366.7407566.88580, 711467.58465, 133, 743, 512467.85315, 7541, 2801, 5994, (14)69.33250, 411069.53999, 1701, 1536, 1700, (22)69.65286, 7159, 5285, 1678, (11)70.0319870.5183173.5837474.7816278.9177880.4925, 4926, 4851, 1260, (5)80.8405381.55419, 5596, 8455, 1892, (6)86.9716987.4189187.91611, 85589.36996, 6997, 129491.47696, 3524, 545695.55980, 5213, 5982, 5212, (5)101.9524, 799, 523, 2029, (5)107.46396120.37297, 1207, 2372134.77812, 1367149.795, 94152.33559, 3560158.33493159.65111159.95112161.54258, 7835, 2949162.18000, 7999, 2396, 6716, (5)166.33949170.84407, 1457, 602, 2870171.6

3Agwm389, 1950.066513.6barc1335.854269.8529910.62908, 75812.0gwm49316.0288, 289, 249320.61187, 71635.5830339.7663, 280, 4625, 5618, (5)46.7734246.8398352.86632, 3425, 342656.54235 2662, 2663, 4054, 378759.45325, 3117, 3716, 347, (5)59.9390461.46192, 3150, 3149, 691961.6584362.3748, 74763.56482, 3731, 3732, 726764.51458, 4838, 3390, 145964.92409, 2408, 484365.12074, 2119, 7748, 1416, (7)66.14040, 4310, 7860, 4039, (5)66.24755, 7294, 6165, 6243, (14)66.4380, 376, 5351, 729, (6)69.3210, 377, 563869.66017, 9170.6gwm285, 299071.73021, 6814, 6655, 249472.0262272.1120672.31383, 1607, 7247, 4193, (10)73.06793, 2329, 6677, 4452, (15)73.1300073.4537, 5613, 629774.02782, 3710, 3711, 5101, (10)75.3443975.5751075.7577075.95880, 5677, 249277.4629, 628, 638178.0579278.25775, 4653, 5710, 4218, (8)81.8586983.23245, 461383.6408584.9735385.2barc164, 4156, 707885.6571185.8450786.2615787.16221, 6222, 1148, 713187.33305, 3306, 649387.46254, 1467, 7225, 1196, (8)87.56223, 5805, 6158, 330487.7301888.2472188.3649288.56104, 610588.77946, 343989.8212491.71598, 2399, 2510, 133192.21332, 2361, 3833, 383592.36552, 7870, 813692.48137, 1333, 133492.52204, 3244, 3834, 445792.63046, 3402, 360192.72720, 2721, 2661, 722192.9455394.92862, 7889, 2620, 3455, (11)96.5216796.6168296.7206396.84906, 654296.9154197.0168397.17561, 859497.25646102.7714, 5941, 6375, 6299, (6)102.92951, 3592, 1095, 3591, (6)104.31731, 3170, 6002, 4498, (10)115.33332, 3331117.63667118.45013, 5014, 5015, 4778, (5)119.14600125.01094133.1barc84133.37542134.6784139.5787, 785, 8628139.9786140.25594, 8058141.0939141.56930149.04312, 4311152.66273, 8185156.9

3B

3250.0

5469, 7468, 5695, 1321, (5)26.3767228.8464731.1229331.5

648556.2

7526, 408160.66777, 4683, 179660.98059, 1715, 7274, 8578, (7)65.0153, 1624, 4877, 3012, (7)65.6

523078.3

3D3A 3B 3D

Summary of Linkage Maps

Chrom Mapped loci Geneticbins

Total cM distance

Mean interval

Rank-ordercorrelation

Observedcrossovers

1A 350 88 174 2.0 0.953 1,0741B 193 59 160 2.8 0.990 9191D 110 30 92 3.2 - 4642A 214 92 225 2.5 0.992 1,4502B 364 72 142 2.0 0.640 9172D 50 25 103 4.3 - 5963A 231 76 171 2.3 0.980 1,1073B 288 116 156 1.4 0.976 1,2453D 30 11 78 7.8 - 2054A 104 56 151 2.8 0.992 9944B 104 47 140 3.1 0.969 9014D 9 7 39 6.6 - 585A 296 104 255 2.5 0.997 1,7505B 335 113 212 1.9 0.986 1,2845D 39 22 190 9.1 - 7476A 242 72 176 2.5 0.976 9266B 338 85 133 1.6 0.519 8406D 44 16 45 3.0 - 1047A 316 105 206 1.9 0.993 1,2637B 189 58 186 3.3 0.928 1,1617D 29 15 36 2.7 - 189Overall 3,875 1,269 3,080 2.5 0.921 18,194

Founders of Spring Wheat Breeding PopulationsFounder Pedigree Class Xumn10 Resistance lociAZ10-1859 SD3934 / Granger // Granger HRSW 238 Fhb1AZ10-1876 SD3934 / SD4101 // HW010 HRSW 238 Fhb1AZ10-1913 SD3934 / SD4027 // Sonalika HRSW 238 Fhb1AZ10-1941 SD3934 / SD4101 // SD3997 HRSW 238 Fhb1AZ10-1973 SD3934 / SD3948 // Oxen HRSW 238 Fhb1AZ10-2029 SD3934 / SD4011 // Granger HRSW 238 Fhb1AZ10-2158 SD3934 / SD3948 // SD3934 / SD4102 HRSW 238 Fhb1NZ10-3716 SD3746 / SD3776 // SD4032 HRSW 238 Fhb1NZ10-3750 MN01197 / SD3851 // SD4070 HRSW 238 Fhb1NZ10-3785 MN01057-3-1 / SD3851 // SD4032 HRSW null .NZ10-3772 FN1504-124 / SD3851 // Glenn HRSW 238 Fhb1NZ10-3773 FN1504-124 / SD3851 // Glenn HRSW 238 Fhb1NZ10-3789 WEAVERCOMPLEX / SD3851 // Glenn HRSW 238 Fhb1NZ10-3790 WEAVERCOMPLEX / SD3851 // Glenn HRSW 238 Fhb1NZ10-3794 WEAVERCOMPLEX / SD3851 // Glenn HRSW 238 Fhb1MN99112-10-2-4 MN93377 / MN94350 HRSW 235 .MN99126-1-3-7-5 MN94053 / MN2514 HRSW 235 .RIL35 Wheaton / PI 81791 HRSW 235 2B, 3B, 3DRIL59 Wheaton / PI 81791 HRSW 235 2B, 3B, 3DMULT 757 PI 271127 HRSW 235 7B

Founders of Winter Wheat Breeding Populations

Founder Pedigree Class Loci

Wesley-Fhb1-BC06 Wesley / 2*ND2928 HWW FHB1

Wesley-Fhb1-BC56 Wesley / 2*ND2928 HWW FHB1

AL-107-6106 Alsen / NE00403 // NE02583-107 HWW FHB1

Ernie Pike / MO9965 SWW 5A, 3B, 4B, 2B

Freedom GR876 / OH217 SWW 2AS

Lyman KS93U134 / Arapahoe HWW .

Overland Millennium sib // Seward / Archer HWW .

NE06545 KS92-946-B-I5-1 / Alliance HWW .

NI08708 CO980829 / Wesley HWW .

McGill NE92458 / Ike HWW .

Spring Wheat Breeding PopulationsCross Four-way F1

sibsAZ10-1859 / MN99126 // NZ10-3785 / MULT757 24

AZ10-1859 / MN99126 // NZ10-3794 / RIL35 12

AZ10-1859 / RIL59 // NZ10-3716 / MN99112 20

AZ10-1859 / RIL59 // MN99126 / NZ10-3772 23

AZ10-1876 / RIL59 // AZ10-1859 / MN99112 23

AZ10-1876 / RIL59 // MULT757 / NZ10-3750 21

AZ10-1913 / MULT757 // NZ10-3772 / RIL35 24

AZ10-1913 / MULT757 // MULT757 / MN99112 9

AZ10-1941 / MULT757 // MN99126 / NZ10-3772 19

NZ10-3750 / MN99112 // NZ10-3785 / MULT757 20

NZ10-3785 / MULT757 // NZ10-3716 / MN99112 22

NZ10-3785 / MULT757 // RIL35 / AZ10-2158 18

NZ10-3772 / RIL35 // MN99126 / MULT757 20

NZ10-3790 / MN99112 // RIL35 / NZ10-3772 25

NZ10-3790 / RIL35 // MN99126 / MULT757 18

NZ10-3794 / RIL35 // MULT757 / MN99112 18

MN99112 / MN99126 // NZ10-3716 / MN99112 18

MN99112 / MN99126 // RIL35 / NZ10-3716 21

MN99112 / MN99126 // MULT757 / NZ10-3773 15

MN99112 / RIL59 // MN99126 / NZ10-3785 20

MN99112 / RIL59 // RIL59 / NZ10-3750 20

MN99126 / AZ10-1941 // AZ10-2029 / MN99112 22

Cross Four-way F1sibs

MN99126 / AZ10-1941 // MULT757 / NZ10-3772 23

MN99126 / NZ10-3785 // MN99112 / MN99126 15

MN99126 / NZ10-3785 // RIL35 / MN99112 20

MN99126 / MULT757 // NZ10-3750 / MN99112 21

MN99126 / MULT757 // RIL59 / NZ10-3750 14

RIL35 / AZ10-2158 // NZ10-3789 / MN99126 21

RIL35 / AZ10-2158 // RIL35 / MULT757 19

RIL35 / AZ10-2158 // MULT757 / NZ10-3772 18

RIL35 / NZ10-3772 // MN99112 / NZ10-3789 26

RIL35 / NZ10-3789 // AZ10-2029 / MN99112 19

RIL35 / MN99112 // NZ10-3785 / MULT757 22

RIL35 / MN99112 // MULT757 / AZ10-1859 17

RIL35 / MULT757 // MN99126 / NZ10-3772 22

RIL59 / NZ10-3750 // MN99126 / NZ10-3750 17

MULT757 / NZ10-3750 // AZ10-1859 / MN99112 15

MULT757 / NZ10-3750 // RIL35 / NZ10-3772 20

MULT757 / NZ10-3750 // RIL59 / NZ10-3794 26

MULT757 / MN99112 // AZ10-1859 / RIL59 17

MULT757 / MN99112 // MN99126 / NZ10-3750 25

MULT757 / RIL59 // AZ10-1859 / MN99126 15

MULT757 / RIL59 // MN99126 / AZ10-1941 2

Total population: 826

Winter Wheat Breeding PopulationsCross Four-way

F1 sibsWesley-Fhb1-BC56 / NE06545 // Ernie / Overland 20

Ernie / Wesley-Fhb1-BC06 // Ernie / NE06545 26

Ernie / Wesley-Fhb1-BC06 // Lyman / AL-107-6106 22

Ernie / Wesley-Fhb1-BC56 // Ernie / Lyman 40

Ernie / Wesley-Fhb1-BC56 // NI08708 / Lyman 40

Ernie / Lyman // Ernie / Wesley-Fhb1-BC06 12

Ernie / Overland // Freedom / Wesley-Fhb1-BC56 5

Ernie / Overland // Overland / Wesley-Fhb1-BC56 24

Ernie / Overland // NI08708 / Wesley-Fhb1-BC06 33

Ernie / NE06545 // McGill / Wesley-Fhb1-BC56 28

Ernie / McGill // Lyman / Wesley-Fhb1-BC06 12

Freedom / Wesley-Fhb1-BC06 // Ernie / Overland 12

Freedom / Wesley-Fhb1-BC06 // Lyman / AL-107-6106 7

Freedom / Wesley-Fhb1-BC06 // Overland / Wesley-Fhb1-BC56 11

Freedom / Wesley-Fhb1-BC56 // Ernie / NE06545 4

Freedom / Ernie // Overland / Wesley-Fhb1-BC56 34

Freedom / Ernie // NI08708 / Wesley-Fhb1-BC06 29

Freedom / Overland // Lyman / AL-107-6106 8

Freedom / NI08708 // Wesley-Fhb1-BC56 / NE06545 7

AL-107-6106 / Overland // Lyman / Wesley-Fhb1-BC06 11

AL-107-6106 / Overland // NI08708 / Lyman 14

Lyman / Wesley-Fhb1-BC56 // Ernie / Lyman 37

Cross Four-wayF1 sibs

Lyman / Wesley-Fhb1-BC56 // NI08708 / Lyman 31

Overland / Wesley-Fhb1-BC56 // Ernie / Lyman 44

Overland / Wesley-Fhb1-BC56 // Ernie / NE06545 5

Overland / McGill // Lyman / Wesley-Fhb1-BC06 12

NI08708 / Wesley-Fhb1-BC06 // Ernie / NE06545 8

NI08708 / Lyman // Overland / Wesley-Fhb1-BC56 29

Total population: 565

Greenhouse Evaluations of FHB Severity in Spring Wheat Populations

14 days after inoculation 21 days after inoculation

RIL 35MULT 757

Wheaton

MN99112AZ10-1859 (Fhb1)NZ10-3772 (Fhb1)

MN99126

RIL 59

MULT 757Wheaton

MN99126RIL 59

NZ10-3772 (Fhb1)

RIL 35

MN99112AZ10-1859 (Fhb1)

BLUPs

Spring Wheat Self-progeny Testing Four-way F1 Plants

Evaluation Inoculation method

F1 plants evaluated

Biological replicates

Spikes evaluated

Ave. FHB severity

Brookings, SD Spawn / spray 388 1 20 0.15

Volga, SD Spawn / spray 485 1 20 0.10

St. Paul, MN Spawn / spray 346 1 20 0.24

Prosper, ND Spawn 341 3 60 0.18

Combined Mixed 744 1-6 20-120 0.17

RIL 35,MULT 757

MN99126, MN99112,AZ10-1859 (Fhb1)

RIL 59

Wheaton

NZ10-3772 (Fhb1)

Winter Wheat Selfed-progeny Testing Four-way F1 Plants

Evaluation Inoculation method

F1 plants evaluated

Biological replicates

Spikes evaluated

Volga, SD Spawn / spray 501 1 20Manhattan, KS Spawn / spray 380 1 20Carrington, ND Spawn 201 1 20Combined Mixed 531 1-3 20-60

Lyman

Wesley-Fhb1-BC06Wesley-Fhb1-BC56

EverestAL-107-6106

Freedom, NE6545, McGill

Overland

Ernie, NI8708Overly

Targeted Genotyping For 72 SSR Markers in Spring Wheat Breeding Populations

2A 2B 3A 3B 3D 4B 4D 7B

Genome Wide Genotyping for 3,875 SNPs and 22 SSR Loci in Winter Wheat Populations

Chrom Mapped loci Geneticbins

Total cM distance

Mean interval

1A 350 88 174 2.01B 193 59 160 2.81D 110 30 92 3.22A 214 92 225 2.52B 364 72 142 2.02D 50 25 103 4.33A 231 76 171 2.33B 288 116 156 1.43D 30 11 78 7.84A 104 56 151 2.84B 104 47 140 3.14D 9 7 39 6.65A 296 104 255 2.55B 335 113 212 1.95D 39 22 190 9.16A 242 72 176 2.56B 338 85 133 1.66D 44 16 45 3.07A 316 105 206 1.97B 189 58 186 3.37D 29 15 36 2.7Overall 3,875 1,269 3,080 2.5

Methods For Linkage Analysis

• Statistical Analysis for Genetic Epidemiology (S.A.G.E)

1. Pedigree error checking – ‘PEDINFO’

2. Mendelian error checking – ‘MARKERINFO’

3. Allele frequency estimation – ‘FREQ’

4. Multipoint IBD estimation – ‘GENIBD’

5. IBD-based linkage analysis – ‘RELPAL’

http://darwin.cwru.edu/sage/

Results From IBD-based Linkage Analysis

Xbarc2120Xgwm614.25

Xgwm35944

Xwmc52275

Xwmc29684

Xgwm296116

Xgwm658162

0 1 2 3 4

Xwmc7640Xgwm614.12

Xgwm42969

Xbarc16789Xgwm38896Xgwm501101Xbarc101.1104Xgwm120108Xwmc332117

Xgwm526127

Xwmc317154

0 1 2 3 4

-log10(p-value) for Vg -log10(p-value) for Vg

Greenhouse-14DAIGreenhouse-21DAISelfed-progeny

Chr.2A Chr.2B

Xgwm5330Xbarc1335Xbarc1477Xgwm49314

Xbarc101.238Xwmc62345

Xgwm56667Xgwm28573

Xbarc16484

Xwmc78796Xwmc291104Xgwm108107

Xbarc77139

Xgwm299159

Xgwm340182

0 1 2 3 4

Xgwm5690

Xgwm40034Xwmc7637

Xwmc75853Xgwm33358

Xbarc17666

Xwmc51785

Xwmc31197

Xgwm146135

0 1 2 3 4

-log10(p-value) for Vg -log10(p-value) for Vg

Greenhouse-14DAIGreenhouse-21DAISelfed-progenySelfed-progeny-Volga,SD

Results From IBD-based Linkage Analysis

Chr.3B Chr.7B

Cumulative Effects of QTL Alleles in Spring Wheat Populations

Greenhouse 14 DAI Selfed progeny

Greenhouse AUDPC

Selfed progeny

Qfhb-sdsu-1AS (5-10%) Lyman,

Overland

Qfhb-sdsu-1BS (5-12%) Lyman,

Overland

Fhb1(5-10%)

Qfhb-sdsu-4AC (5-10%) Lyman,Qfhb-sdsu-4AL

(7%) Wfhb1Qfhb-sdsu-4B (7%)Wfhb1

Qfhb-sdsu-6AC (5-15%)Wfhb1,

OverlandQfhb-sdsu-6AS

(10%) Overland,

Qfhb-sdsu-7D (3-5%) Wfhb1,AL

Qfhb-sdsu-6D (12%) Wfhb1,

Overland

Pyramiding Resistance Alleles Reduces FHB in

Winter Wheat Populations

F1 progeny in GH screenings

Self progeny in field screenings

SUMMARY1. We can develop reliable dense genetic maps using early generation

breeding populations.

2. We can detect multiple resistance QTL using generation breeding populations.

3. At the same time we generated breeding material; ~3,000 early generation lines and ~500-600 DHs

4. We need to address assumptions underlying existing implementations of linkage analysis for general pedigrees:1. Related pedigrees, Hermaphroditic mating systems, Inbred founders

and Simplifying MCMC algorithm

2016 USWBSI Annual MeetingDecember 4-6; St Louis, MO