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Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in Cotton with additional molecular approach FOV4 Genetics and QTL Mapping FOV4 Transcriptomics / Gene Expression USDA-ARS, University Cooperators, CA Cotton Growers, and Cotton Incorporated Cooperative Project - Prepared by Dr. Mauricio Ulloa

Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

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Page 1: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

Cotton Breeding for Fusarium wilt

race 4 (FOV4) Resistance in Cotton

with additional molecular approach

FOV4 Genetics and QTL Mapping

FOV4 Transcriptomics / Gene Expression

USDA-ARS, University Cooperators, CA Cotton Growers, and

Cotton Incorporated

– Cooperative Project - Prepared by Dr. Mauricio Ulloa

Page 2: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

California FOV4 Nursery 2017

2006

2017

Breeding Efforts Supported by California Cotton

Grower’s Organizations, including CCGGA and CI

University of California,

Dr. Robert Hutmacher, Mark Keeley, Steve

Wright with many other staff and students,

and more recently Tarilee Frigulti have

performed the breeding activities since

2012 of this collaborative effort.

Continue Breeding Support

Effort 2012-Present

of Dr. Ulloa, USDA-ARS,

Lubbock, TXPrepared by Dr. Mauricio Ulloa, USDA, ARS

Page 3: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

Cotton Germplasm Collections Evaluated by

USDA-ARS and Univ. of CA. for FOV4 Resistance

New Mexico State University – Dr. Roy Cantrell

• NM 59-851, ACALA 1517-75, ACALA 1517-88, ACALA 1517-91, ACALA

1517-95, ACALA 1517-99, etc., Dr. Ulloa/Research Associate -1996 - 1998,

Pima lines provided MS. Cindy Waddell – 2003

USDA-ARS – Maricopa AZ – Dr. Percy 2003

• Pima S-series, PS1-PS32, Pima lines from NMSU, Pima population

developed for Genetics/QTLs mapping 1999 -2000 F1 and F2. (around 186

F6 lines - collaborative project with Dr. Ulloa).

USDA-ARS Shafter, CA - & College Station, TX Collection

• Acala FBCX-2, Shorty, Acala Shafter Station, Del Cerro SS227, UCD368

Hopi M5-11, Acala 8, Acala 4-42 1958-A , Acala 4-42 1966-A, Acala SJ-2,

SJ-3SJ-5, etc., 2003 – 2006.

Regional Breeding Testing Network (RBTN) germplasm

• from more than 12 breeding cotton programs across the belt. Since 2004

- Present.

Prepared by Dr. Mauricio Ulloa, USDA, ARS

Page 4: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

International Cotton Germplasm Programs/Collections

Evaluated for FOV4 Resistance

Australia CSIRO – Fiber Max germplasm collection2004 visited and exchanged germplasm.

• Tested germplasm for this program which also included tolerant Upland

Sicot 189 and resistance source MCU-5 germplasm lines to FOV

Australian races.

• Australian germplasm lines were susceptible to the California FOV4.

Republic of Uzbekistan germplasm collection FOV racesSince 2006 and visited several times since 2009, 2011, 2103.

Tested several germplasm lines.

• Discovered new potential source of FOV4 resistance.

Country of Peru Visited in 2009, 2016 and had the opportunity to visit cotton fields and

evaluate germplasm known as Tanguis.

2016 started new Agreement with IPA Peru to exchange and develop

germplasm. In 2017, Seven breeding lines ongoing evaluation.

Prepared by Dr. Mauricio Ulloa, USDA, ARS

Page 5: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

FIRST TIMELY RESPONSE FROM FOV4

RESISTANCE EVALUATIONS

Identified Pima Germplasm resistant to FOV4

Some USDA-ARS Pima (e.g., Pima-S6) – Original

Pima-S6 (PS6) release was a variable/heterozygous-pool, but it is a good

source for FOV4 resistance from USDA-ARS compared to other PS1,2…

releases. PS6 resistance source has been confirmed by independent

labs (UC, Davis, UC Riverside, USDA-ARS College Station, and

Phytogen Seed Co.)

An experimental, later known as commercial cultivar

Phytogen 800

This research identified potentially new improved resistant

germplasm for release

Greenhouse EvaluationsField Evaluations

Prepared by Dr. Mauricio Ulloa, USDA, ARS

Page 6: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

2007/2008

PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA-

ARS, UNIV. OF CALIFORNIA, & UNV. OF NEW MEXICO

SJ-07P-FR01, SJ-07P-FR02, SJ-07P-FR03, and SJ-07P-FR04

Pedigrees: 8810 (P72xP73 Pima Series AZ) and NMSI-1601 originated from a Sea Island cotton

2015/2016

PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA-

ARS & UNIV. OF CALIFORNIA

SJ-FR05, SJ-FR06, SJ--FR07, SJ-FR08, and SJ-FR09

Pedigrees: Pima S6 (Series AZ) and 89590 Line (P62 x Sea Island St. Vicent)

Projected New Pima Releases

2018 Pedigree: Pima-S6 x Pima-S7

Prepared by Dr. Mauricio Ulloa, USDA, ARS

Page 7: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

Field Site with Fusarium wilt - FOV4

Susceptible Resistant

USDA-ARS and University of California Davis – Cooperative -

Prepared by Dr. Mauricio Ulloa

Page 8: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

Fusarium wilt RACE 4 (FOV4)

USDA-ARS and University of California Davis – Cooperative

Project - Prepared by Dr. Mauricio Ulloa

ROOT DIP GREENHOUSE FOV4 TEST FOV race 4 Seedling

Inoculation

Vascular stem and root staining (VRS)

VRS = 0 VRS = 2 - 3 VRS =5

Susceptible CheckPima-S7 (PS7)

Resistant CheckPima-S6 (PS6)

DSI = 0 DSI = 2 - 3 DSI = 5

Disease severity index (DSI) of leaves, (scale 0 – 5)

Page 9: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

Present Summary for FOV4 Resistance

Upland Germplasm Evaluated from the USDA-ARS

Collection, College Station, TX

More than 400 obsolete cultivars and/or SA lines Upland Lines

Identified Upland SA lines tolerant to FOV4

Developed Upland Progeny with identified

Resistant/Tolerant Sources

More than 500 crosses combinations

More than 1,500 progeny developed and so far about 400 FOV4

evaluated

Identified an Upland RBTN source Now clean of AP and tested-

Negative for AP from NMSU

Identified and Developed new progeny resistant to FOV4 from

PS6xUzbekistan germplasm

Prepared by Dr. Mauricio Ulloa, USDA, ARS

Page 10: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

Seed Increase for Germplasm Release under Clean

or Uninfested FOV4 Field

Continue Breeding Efforts 2012-Present

of Dr. Ulloa, USDA-ARS, Lubbock, TX with the CA group -

Dr. Hutmacher. Univ. of CA.

Page 11: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

UPLAND FOV4 TOLERANCE/RESISTANCE

UPDATE

Upland TM-1 x Pima-S6 and Upland Shorty X Pima-S6 AND

Reciprocal-Progeny

Upland SA-Lines (obsolete cultivars) X US63 (Uzbek x Pima-S6)

AND Reciprocal-Progeny

Upland SA-Lines (obsolete cultivars)

Upland SA-Lines (obsolete cultivar) X Upland SA-Lines (obsolete

cultivars) AND Reciprocal-Progeny

Upland RBTN-NMSU Line X Upland SA-Lines (obsolete cultivars)

AND Reciprocal-Progeny

DEVELOPING FOV4 TOLERANT BREEDING LINES OR PROGENY

Sources of Breeding/Selection made for FOV4 Tolerance/Resistance

Cleaning lines of AP (transgenic contamination – USDA-ARS and UC Davis)Prepared by Dr. Mauricio Ulloa, USDA, ARS

Page 12: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

bp

527

404 F1 S R S S S S S S S S R R R R R R R R R R

1 2

SSR marker evaluated on susceptible (S) Upland Shorty [ No. 1, (Gossypium

hirsutum L.)]; resistant (R) Pima-S6 [No. 2, (G. barbadense L.)], and R F2

(Shorty x Pima-S6) single plants.

Molecular marker such as Microsatellite or SSR

Previous research identified/developed approximately 150 SSRs

published (www.cottongen.com) with Major and Minor association to

Disease Resistance which include all FOV races and root-knot nematode

(RKN)

SSR markers have been and could be used for marker assisted selection

or MAS.

Additional Research of Inheritance, Genetic and

QTL Mapping for FOV race 4 Resistance Ongoing

Prepared by Dr. Mauricio Ulloa, USDA, ARS

Page 13: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

Different gene-specificity for FOV resistance:

Fov1 (race 1) – chromosomes 6,8,11, 12, 16 and 19

(Ulloa et al., 2011; Wang et al. 2017 submitted).

Fov3 (race 3) – Chromosomes – Ongoing (Uzbek - USDA

Collaboration)

Fov4 (race 4) – chromosomes 3,6,8,14 and 17

(Ulloa et al. 2013; Wang et al. 2014; Ulloa et al. 2016; Wang et al.

2017 submitted).

FWR (race 7) - chromosome 17

(Wang et al., 2009).

Australian race of Fov – chromosomes 6,

22, and 25 (Becerra et al., 2012).

Reported Loci/genes associated to FOV Resistance

Explaining 10% - 80% FOV4

resistance variation. Approximately – 10 SSRs with major and 55

with minor Association with FOV resistance.Prepared by Dr. Mauricio Ulloa, USDA, ARS

Page 14: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

Information about FOV4 Research - California Selected Publications

2005 Kim, Y.f, R.B. Hutmacherd, R.M. Davisd. 2005. Characterization of California

Isolates of Fusarium oxysporum f. sp. Vasinfectum. Plant Disease 89:366-372.

2005 Hutmacher, R.B.d, R.M. Davisd, S.D. Wrightg, M. Ulloac, D.S. Munkg, B.H.

Marshg, B.A. Robertsg, R.N. Vargasg, M.P.Keeleyb. 2005. New Fusarium Issues

for California Cotton. Cotton Industry – National Cotton Council and J. Cotton

Sci.

2006 Ulloa, M.d, R.B. Hutmacherd, R. M. Davisg, S.D. Wrightg, R. Percyc, B. Marshg.

2006. Breeding for Fusarium Wilt Race 4 Resistance in Cotton Under Field and

Greenhouse Conditions. J. Cotton Sci. 10:114-127.

2006 Hutmacher, R.B.a, R.N. Vargasg, S.D. Wrightg. 2006. Methods to Enable the

Coexistence of Diverse Cotton Production Systems. Agricultural Biology In

California Series, Publication # 8191. Univ. of CA Div. Agric. Nat. Resources,

http://anrcatalog.ucdavis.edu

2006 Ulloa, M.a, R. Percyc, R.B. Hutmacherg, R.G. Cantrellh. 2006. Registration of

SJ-U86 Cotton Germplasm Line with High Yield and Excellent Fiber Quality.

Crop Sci. 46:2336-2338.

2007 Ulloa, M.a, R.G. Percyc, R.B. Hutmacherg, R.G. Cantrellh. 2007. Notice of

release of one Upland cotton germplasm line (SJ-U86) for California possessing

superior lint yield, fiber traits and heat tolerance. Germplasm Release. Crop Sci.:

47:106-107.

2007 Ulloa, M.a, Percy, R.c, R.B. Hutmacherg, J.F. Zhange 2007. The Future of cotton

breeding in the Western United States. Paper #1355. Proc. World Cotton

Research Conference IV, September 11-14, 2007, Lubbock, TX, Cotton Council

International, 15 pp. electronic:

http://www.icac.org/meetings/wcrc/wcrc4/presentations/data/html

2007 Bennett, R.S.a, R.M. Davisg, R.B. Hutmacherg. 2007. Fusarium oxsysporun f,

Sp, vasinfectum Race 4 in California: A Reemerging Threat to Cotton

Production. Paper #1383. Proc. World Cotton Research Conference IV,

September 11-14, 2007, Lubbock, TX, Cotton Council International, 9 pp.

electronic: http://www.icac.org/meetings/wcrc/wcrc4/presentations/data/html

Contributions to

2008 Bennett, Rebecca S., R.B. Hutmacher, R. Michael Davis. 2008. Seed

Transmission of Fusarium oxysporum f. sp. vasinfectum Race 4 in California. J.

Cotton Science. 12: 160-164.

2008 Ulloa, M., Percy, R.G., Hutmacher, R.B., Wright, S. and Davis, M. 2008.

Release of SJ-07P-FR01, SJ-07P-FR02, SJ-07P-FR03, and SJ-07P-FR04

‘Cotton’. USDA Germplasm Release. Pp. 79-81.

2008 Gilbert, C.A., N. Zhang, R.B. Hutmacher, R. M. Davis, C.D. Smart. 2008.

Development of a DNA-based Macroarray for the Detection and Identification of

Fusarium oxysporum f. sp. vasinfectum in cotton tissue. J. Cotton Science

12:165-170.

2009 Ulloa, M., R. Percy, R.B. Hutmacher, J. Zhang, R.M. Davis, S.D. Wright. 2009.

Registration of Four Pima Cotton Germplasm lines (SJ-07P-FR01 – FR04)

Possessing Good Levels of Resistance to Fusarium wilt race 4 With Moderate

Yields, and Good Fibers. J. Plant Registration. 3(2):198-202.

2011 Bennett, D.W. Spurgeon, W.R. DeTar, J.S. Gerik, R.B. Hutmacher, B.D. Hanson.

2011. Efficacy of four soil treatments against Fusarium oxysporum f sp.

Vasinfectum Race 4 on cotton. J. Plant Disease. 95:967-976..

2011. Ulloa, M., C. Wang, R.B. Hutmacher, S.D. Wright, R. Michael Davis, S.A. Saski,

P.A. Roberts. 20__. Mapping Fusarium Wilt Race 1 Resistance Genes in

Cotton by Inheritance, QTL, and Sequencing Composition. Molec. Genetic

Genomics. 286(1): 21-36.

2011 Bennett, R.S., W. O’Neill, L. Smith, R.B. Hutmacher. 2011. Commercial

detergents effective against conidian and chlamydospores of Fusarium

oxysporum f. sp. Vasinfectum. J. Cotton Science. 15:162-169

2013 Ulloa, M., Hutmacher, R.B., Roberts, P.A.. Wright, S.D., Nichols, R.L. and Davis,

R.M. 2013. Inheritance and QTL mapping of Fusarium wilt race 4 resistance in

cotton. Journal of Theoretical and Applied Genetics. 126:1405-1418.

2013 Hutmacher, R.B., Ulloa, M., Wright, S.D., Campbell, B.T., Percy, R.G., Wallace,

T., Myers, G., Bourland, F., Weaver, D., Chee, P., Thaxton, P., Zhang, J., Smith,

W., Dever, J., Kuraparthy, V., D. Bowman, D. Jones, J.Burke. Elite Upland

Cotton Germplasm-Pool Assessment of Fusarium wilt resistance in California.

Agronomy Journal 105:1635-1644. 2013.

2015 Cianchetta, A., T.W. Allen, R.B. Hutmacher, R.C. Kemerait, TL. Kirkpatrick, G.W.

Lawrence, K.S. Lawrence, J.D. Mueller, R.L. Nichols, M. Olsen, C. Overstreet,

J.E. Woodward, R.M. Davis. 2015. Survey of Fusarium oxysporum f. spp. Vas

infectum in the United States. J. Cotton Science. 19: 328-336.

2015 Ulloa, M., Hutmacher, R., Percy, R.G., Wright, S., Burke, J.J. Release of Pima

SJ-FR05, Pima SJ-FR06, Pima SJ-FR07, Pima SJ-FR08, and Pima SJ-FR09

Pima cotton with improved FOV4 resistance, and good lint yield and fiber quality.

Germplasm Release. p.1-2. 2015.

2016 Ulloa, M., Hutmacher, R.B., Percy, R.G., Wright, S.D., Burke, J.J. Registration of

five pima cotton germplasm lines (SJ-FR05 - FR09) with improved resistance to

fusarium wilt race 4 and good lint yield and fiber quality. Journal of Plant

Registrations. 10:154-158. 2016.

2016 Ulloa, M., Wang, C., Saha, S., Hutmacher, R.B., Stelly, D.M., Jenkins,

J.N., Roberts, P. Analysis of root-knot nematode and fusarium wilt

disease resistance in cotton (Gossypium spp.) using chromosome

substitution lines from two alien species. Genetica. 144(2):167-179.

2016

Page 15: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

SNPi10463Gh0.0SNPi00939Gh0.5SNPi10435Gh3.3SNPi16247Gh4.4SNPi36282Gh6.1SNPi50131Gb7.2SNPi28797Gh16.3SNPi27871Gh16.9SNPi10336GhSNPi64224GmSNPi68839GlSNPi61786Gt

17.4

SNPi16965Gh21.3SNPi10321Gh23.0SNPi36890Gh29.8SNPi33150Gh30.4SNPi16938GhSNPi16939GhSNPi31262Gh

30.9

SNPi10283Gh31.5SNPi24610Gh37.7SNPi16848Gh38.0SNPi26445Gh38.3SNPi25750Gh43.9SNPi42467GhSNPi45830Gh

46.2

SNPi43120Gh48.1SNPi37157GhSNPi47122Gh

51.8

SNPi09946GhSNPi09948Gh

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SNPi09938Gh53.9SNPi09934GhSNPi09936Gh

54.5

SNPi09923GhSNPi34271Gh

55.0

SNPi09931Gh55.3SNPi09927GhSNPi09926Gh

55.6

SNPi09907GhSNPi21238Gh

59.5

SNPi27444Gh60.0SNPi09899Gh60.6SNPi38357Gh61.1SNPi09874Gh62.2SNPi09882Gh62.7SNPi09860Gh63.8SNPi19596Gh64.1SNPi09859Gh64.3SNPi16790Gh64.9SNPi09856Gh66.0SNPi43441GhSNPi47610Gh

66.5

SNPi16787GhSNPi36035Gh

67.1

SNPi25234GhSNPi26095GhSNPi39248Gh

67.6

SNPi00674Gh70.4SNPi26374Gh70.9SNPi00935Gh72.0SNPi09781Gh76.8SNPi23394Gh77.4SNPi09680Gh101.0SNPi00997GhSNPi09691GhSNPi09697GhSNPi40913GhSNPi41356Gh

101.6

SNPi41938Gh102.1SNPi09677Gh102.7SNPi00462GhSNPi23971Gh

110.2

SNPi48064Gh111.8SNPi09594GhSNPi46042GhSNPi09595Gh

112.4

SNPi41393Gh114.0SNPi09569Gh114.2SNPi21925Gh114.6SNPi22725Gh115.1SNPi09551Gh115.6SNPi09546GhSNPi26620Gh

116.2

SNPi09526GhSNPi09536Gh

118.4

SNPi14159Gh118.9SNPi09486Gh124.1SNPi69754Gl124.6SNPi30503Gh132.2SNPi09353Gh132.7SNPi59127Gb134.9SNPi21916GhSNPi09340Gh

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154.3

SNPi00362Gh156.0SNPi09172GhSNPi09182GhSNPi16618Gh

156.5

SNPi09181Gh156.9SNPi09180Gh157.1SNPi09169Gh157.6SNPi09163Gh158.1SNPi25035Gh159.2SNPi00269GhSNPi09121Gh

162.0

SNPi09106Gh163.6SNPi34361Gh165.3SNPi09098Gh165.8SNPi09058GhSNPi34897Gh

167.5

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SNPi08797Gh201.0SNPi08796Gh201.6SNPi08789Gh202.7SNPi08786Gh203.2

Chr_19_ML

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SNPi16824Gh40.0

SNPi10014Gh43.0SNPi43120Gh44.0

SNPi37157Gh47.0SNPi09946Gh49.0SNPi09934Gh50.0SNPi09907Gh54.0SNPi09899Gh55.0SNPi09874Gh56.0SNPi09865Gh57.0SNPi09853Gh58.0SNPi09836Gh59.0SNPi25234Gh60.0SNPi00558Gh62.0SNPi00935Gh63.0

SNPi09781Gh67.0

SNPi00997Gh83.0SNPi09680Gh84.0

SNPi00461Gh92.0SNPi48064Gh93.0SNPi09591Gh94.0SNPi09567Gh95.0SNPi09562Gh96.0SNPi22725Gh97.0SNPi09526Gh99.0

SNPi09486Gh104.0SNPi69754GI105.0

SNPi09352Gh112.0SNPi09353Gh113.0SNPi59127Gb114.0SNPi09340Gh115.0SNPi09334Gh117.0

SNPi00193Gh121.0

SNPi09290Gh124.0SNPi09287Gh125.0SNPi09227Gh127.0SNPi09210Gh130.0SNPi00362Gh131.0SNPi09169Gh132.0SNPi25035Gh133.0SNPi00269Gh136.0SNPi09106Gh138.0SNPi34361Gh139.0SNPi09098Gh140.0SNPi09058Gh141.0SNPi09051Gh142.0SNPi09053Gh143.0SNPi00328Gh144.0SNPi26444Gh145.0SNPi09032Gh146.0SNPi09004Gh148.0SNPi08958Gh149.0SNPi08914Gh153.0SNPi08908Gh154.0SNPi08906Gh155.0SNPi08887Gh158.0SNPi08878Gh159.0SNPi08860Gh162.0SNPi08855Gh163.0SNPi08852Gh165.0SNPi08828Gh167.0SNPi08825Gh168.0SNPi08802Gh170.0SNPi08789Gh172.0SNPi08797Gh174.0

Chr_19_ML63kCotton Chromosome 19

Map molecular markers such as SNPs

using the 63K Array Cotton Chip

Examples of mapping Populations or progeny-

lines from different cross-combinations

Acala Phytogen 72 x Upland Stoneville 474

Acala Phytogen 72 x NM67

TM-1 x Pima-S6

Upland TM-1 x Pima 3-79 (USDA-ARS)

Pima-S7 x Acala NemX (UC Riverside)

Cotton Accessions from the Cotton

Collection or SA-lines

Ongoing Genetic Mapping and QTL Analyses

Approach to map more than 25,000 SNPs on the 26

Cotton Chromosomes using around 1,900 lines,

progeny, and accessions

Biomarker - SNP Discovery

Prepared by Dr. Mauricio Ulloa, USDA, ARS

Page 16: Cotton Breeding for Fusarium wilt race 4 (FOV4) Resistance in … · 2018-12-05 · 2007/2008 PUBLIC PIMA GERMPLASM LINES JONTLY RELEASED BY USDA- ARS, UNIV. OF CALIFORNIA, & UNV

Discovery of genes involved in FOV race 4 (FOV4)

resistance for molecular breeding

Collection of infected roots with FOV races 1 and 4, and non-infected rootsInoculation Control Entry

Entry FOV race 1 FOV race 4 No Inoculation Total

Pima-S6 (PS6) 5 plants 5 plants 5 plants 15

Pima-S7 (PS7) 5 plants 5 plants 5 plants 15

Pima 3-79 5 plants 5 plants 5 plants 15

Upland TM-1 5 plants 5 plants 5 plants 15

Upland Shorty 5 plants 5 plants 5 plants 15

Acala FBCX-2b 5 plants 5 plants 5 plants 15

PS7 and 3-79 are susceptible to FOV4 and are tolerant to FOV race 1 (FOV1), but 3-79 is

more susceptible to race 1 than PS7.

Upland Shorty and TM-1 are very susceptible to FOV1. Shorty also is susceptible to FOV4.

FBCX-2 (tolerant to race 1) and TM-1 are moderately tolerant to FOV4. TM-1 is less

tolerant than FBCX-2 for race 4.

Next-Gen Sequencing Illumina MiSeq and HiSeq

FOV4 Gene Expression

Prepared by Dr. Mauricio Ulloa, USDA, ARS

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SNP-Biomarkers target important genes

of different plant functional processes

Exploring gene diversity and discovering molecular

markes [SNP-Biomarkers] for assisting breeding

Illumina MiSeq & HiSeq Sequencers

Infected Root and Non-infected Root Genes

(Transcriptome) – Many TB of data

from FOV4 Resistant and Susceptible genotypes from

Upland and Pima Cottons

Next Generation Sequencing

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SUMMARY

Investigate the Inheritance of FOV4. Different disease response between Upland vs. Pima

cottons

Improving assay & selection criteria of tolerant/resistant

Upland/Acala cottons during the breeding process

Pathogenicity evaluation of races and new FOV

biotypes

Discover candidate genes involved in FOV resistance. Validate Identified SNPs/Alleles/Genes from the

SNP63k array and Genome Reference(s) on diverse

Genotypes

Use of Next-Gen Sequencing (NGS) for gene

discovery

Develop Upland germplasm resistant to FOV. Continue searching for new sources of FOV resistance

Prepared by Dr. Mauricio Ulloa, USDA, ARS

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University of California Davis

--Robert Hutmacher, Mark Keeley,Tarilee

Frigulti, and Steve Wright.

University of California Riverside

Philip Roberts, Congli Wang, and Tra Duong.

Texas A&M University

David Stelly, Amanda Hulse-Kemp, Luis De

Santiago, and Lin Yu-Ming.

USDA-ARS

Mauricio Ulloa, John Burke, Lori Hinze,

James Frelichowski, Richard Percy, John Yu,

Sukumar Saha, and many other cooperators

from different Areas.

Texas Tech University, Lubbock, TX

Rao & Pratibha Kottapalli from the Center for

Biotechnology and Genomics, and Glen

Ritchie, TTU.