An update on the molecular marker development and marker-assisted selection in AAFC bean breeding pr...
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An update on the molecular marker development and marker-assisted selection in AAFC bean breeding programs. Kangfu Yu November 17, 2011. Part One: GTM Development. CBB (Common Bacterial Blight) Disease. - Pathogen : Xanthomonas campestris pv. phaseoli and X. fuscans subsp fuscans strains

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Kangfu Yu November 17, 2011

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Kangfu yu november 17 2011

An update on the molecular marker development and marker-assisted selection in AAFC bean breeding programs

Kangfu Yu

November 17, 2011


Kangfu yu november 17 2011

Part One: GTM Development

CBB (Common Bacterial Blight) Disease

- Pathogen : Xanthomonas campestris pv. phaseoli and X. fuscans subsp fuscans strains

- Region: both temperate and tropical production zones

- Disease control: resistant varieties, disease-free seed, and crop rotation


Kangfu yu november 17 2011

Mapping of CBB- QTL

B6

B8

- Explain 64% phenotypic variation

- Resistant origin from tepary bean

- Marker UBC420

- Explain 17% phenotypic variation

- Resistant origin from tepary bean

- Marker SU91

(Miklas et al., 2006)


Dominant vs codiminant markers

Dominant vs. Codiminant Markers

  • BC420 are SU91 are dominant SCARS

  • Random markers liked to the QTL

  • Less efficient for MAS


Objectives

Objectives

  • Develop co dominant markers

  • Candidate gene markers

  • Test their effectiveness in MAS


Kangfu yu november 17 2011

Characterizing CBB NILs(near isogenic lines)

B6

B8

CBB-2

UBC420

CBB-1

SU91

Complete resistant requires co-dominant genotypes for both CBB-1 and CBB-2 QTLs

Donor (resistant): XAN159

Recurrent parent (susceptible):Teebus

Recessive epistasis

and / or

(Vandemark et al., 2008)

Marker analysis


Kangfu yu november 17 2011

BBSS (Resistant)

7DAI

10DAI

14DAI

18DAI

bbss (Susceptible)

BC420- and SU91-QTL associated to CBB resistance

NILs derived from XAP159 x Teebus;

Gift from Dr. Philips N. Miklas


Kangfu yu november 17 2011

Physical map of BC420-QTL locus

(Liu et al., 2010)


Kangfu yu november 17 2011

De novo assembly of BAC sequences

Trimmed 454 reads

CLC Genomics Workbench

(de Bruijun Algorithm)

Newbler

(OLC Algorithm)

Geneious

(Greedy Algorithm)

Assembled BAC sequence


Kangfu yu november 17 2011

BAC sequence annotation


Kangfu yu november 17 2011

BC420

BC420

gene 3

gene 4

gene 9

bbss

bbss

bbss

bbss

BBSS

BBSS

BBSS

BBSS

Gene-targeted marker development (BC420-QTL locus)

gene 10A

gene 10B

gene 11

Gene 14

gene 15

gene 17

bbss

bbss

bbss

bbss

bbss

bbss

BBSS

BBSS

BBSS

BBSS

BBSS

BBSS

1kb

500 bp


Kangfu yu november 17 2011

SU91

bbss

BBSS

gene 12

gene 3

Gene 11

gene 9B

Gene 10

gene 9A

bbss

bbss

bbss

bbss

bbss

bbss

BBSS

BBSS

BBSS

BBSS

BBSS

BBSS

Gene-targeted marker development (SU91-QTL locus)

1kb

500 bp


Kangfu yu november 17 2011

SU91-CG11 accounts for greater phenotypic variations than SU91

Single marker QTL analysis

***, p <0.001


Kangfu yu november 17 2011

Part Two: Genome-wide association mapping

Plant materials (469 genotypes)


Kangfu yu november 17 2011

CBB rating

Note: CBB rating was conducted in 2009 field trial at Harrow, Ontario.


Kangfu yu november 17 2011

SNP genotyping

  • Genome-wide distributed SNPs were found from McClean (NDSU) 2007 genetic map (McConnell et al., 2010);

  • Sequenom iPLEX Gold genotyping platform was used in Genome Quebec;

  • 132 SNPs were tested and 106 SNPs (80.3%) worked;

  • Of 106 working SNPs, 12 SNPs were monomorphic and 94 SNPs were polymorphic.


Kangfu yu november 17 2011

K=1 K=2 K=3 K=4 K=5 K=6 K=7 K=8 K=9 K=10

Andean

Mesoamerican

Ancestry (%)

Population structure estimation

  • STSTRUCTURE 2.3.3 software was used

  • Based on 496 genotypes with 75 SNPs

  • K=2


Kangfu yu november 17 2011

Population kinship estimation

  • The K matrix was generated based on 75 SNPs using kinship matrix function in TASSEL software

Unrelated genotypes

Closely related genotypes


Kangfu yu november 17 2011

Association analysis

  • Unified MLM (Mixed Linear Model) method in TASSEL software was used to test association between marker loci and common bacterial blight severity;

  • Population structure (Q) and relative kinship (K) were taken into account.

a n.s., not statistically significant;

*, P ≤ 0.05;

**, P ≤ 0.01;

***, P ≤ 0.001.

bR2_marker was calculated as the proportion of sum square due to marker after accounting for all other effects in model.


Kangfu yu november 17 2011

Co-localization of DNA markers and CBB-QTLs

  • The mapping information was extracted from McClean (NDSU) 2007 genetic map;

  • 15 significant SNP markers were co-localized with or close to previously identified CBB-QTLs;

  • These markers, if proved to be effective in different backgrounds may help the breeders to facilitate the pyramiding of the QTLs from diverse sources and to attain higher levels of CBB resistance in newly-developed bean cultivars.


Acknowledgements

Acknowledgements

  • Funding:

  • OWBPMB, OCBGA, ORF, AAFC

  • Collaborators:

    Navabi, A., Hou, A.

    Balasubramanian,P

  • Techanical Assistance:

  • Shi, C. Rupert, T. Zhang, B. Xie, W.


Kangfu yu november 17 2011

Thank You


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