Mahdi&Saatchi,&IowaState&University& 6/2/17Mahdi&Saatchi,&IowaState&University& 6/2/17...

Mahdi Saatchi, Iowa State University 6/2/17

2017 BIF Symposium, Athens, Ga. 1

Mahdi Saatchi

“Development of genomics pipeline for IGS BOLT geneKc evaluaKons”

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BIF meeKng, Athens, GA June 2, 2017

Outlines:

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!   InternaKonal GeneKc SoluKons (IGS).

!   IGS BOLT GeneKc EvaluaKons.

!   Development of IGS Genomics Database (iGDB).

!  QCs on Genotypes at iGDB

InternaKonal GeneKc SoluKons (IGS)

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American Chianina Association (ACA)

American Gelbvieh Association (AGA)

American Maine Anjou Association (AMAA)

American Shorthorn Association (ASA)

American Simmental Association (ASA)

Canadian Simmental Association (CSA)

Canadian Angus Association (CAA)

Canadian Limousin Association (CLA)

Canadian Shorthorn Association (CSA)

Canadian Gelbvieh Association (CGA)

North American Limousin Foundation (NALF)

Red Angus Association of America (RAAA)

Current IGS geneKc evaluaKon model:

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!   A mulK-‐step blending approach:

•   Molecular breeding values (MBV) are calculated separately

from the tradiKonal mulK-‐breed internaKonal caYle evaluaKon

(MB-‐ICE) and then combined.

GE-‐EPD = w1*MBV + w2*MB-‐ICE

Why Single-‐step GE-‐EPDs?

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!   GE-‐EPD are available only for genotyped animals while in the

single-‐step the DNA has impact on all the relaKves of the

genotyped animals.

!   Improved accuracy and removed bias in esKmaKon of blending

parameters.

!   Avoids the double counKng problem (high EPD animals turns to

get high MBV and vice versa)!

!  We have powerful tools, such as BOLT, today!

SS-‐BR vs SS-‐BLUP:

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!   SS-‐BLUP is a breeding value model:

!   SS-‐HM is a marker effect model:



BOLT Single-‐step Super Hybrid model:

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The MME for Super Hybrid model:

CG Non-‐

Genotyped

Gen.

CG

EBV

ME

CG

Obs.n

Obs.g

Ang

Development of IGS Genomics DB (iGDB):

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!   A genomic data-‐flow pipeline is a need for the BOLT SS-‐SHM as

all the performance, pedigree and DNA informaKon needs to

be inserted to the BOLT geneKc evaluaKon simultaneously.

Challenges for developing iGDB:

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!   Genomic data were everywhere but not at IGS!

!   Genomic data are in different marker densiKes (50K, LD, HD, …)

!   Genomic data comes from different labs (GeneSeek, ZoeKs and

Delta Genomics) with different formats.

!   InternaKonal and sample ID issues!!

Number of genotyped/pedigreed animals at iGDB:

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BRD/CNT 161209 170123 170130 170206 170315 170419

AANUSA 2270 2270 2271 2269 2269 2269

BSHCAN 23 23 52 52 52 52

BSHUSA 908 908 995 994 1017 1037

CHAUSA 320 320 322 322 322 322

GVHCAN 1449 1156 1449 1447 1447 1447

GVHUSA 9659 9642 9680 9670 10241 10487

HERUSA 522 514 522 522 523 523

LIMCAN 0 532 823 821 821 821

LIMUSA 18 5113 5182 5167 5169 5169

RANUSA 13528 13528 13561 13547 17038 19014

RDPUSA 752 752 752 751 752 752

SIMCAN 18127 18329 18717 18650 18820 18888

SIMUSA 17390 17702 18303 18748 20220 20752

TOTAL 65129 70950 72793 73124 78855 81722

QCs applied at iGDB:

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!  QC on genotypes is more important for BOLT SS-‐SHM

(genotype quality extends to the whole pedigree).

!  QCs on raw genotype call rates. !   Extreme homozygote genotypes.

!   Parent-‐progeny miss-‐match.

!  QCs on imputaKon.

iGDB: QCs on raw genotype call rates

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!   Remove animals with low call rate before pooling genotypes

(call rate < 0.85).

!   Remove animals with low call rate aner pooling genotypes (call

rate < 0.05).



iGDB: QCs on extreme homozygote genotypes

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!  We observed some animals with extreme unusual homozygote

genotypes (AA or BB > 20%). An example: AA 1,199 AB 9,927 BB 41,382

!  We found not many animals with such genotypes (only 11 so

far) that we removed them from iGDB.

iGDB: QCs on Parent-‐progeny miss-‐match

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!  We used all 50K markers to check parent-‐progeny genotype

agreement (similar to the parentage test).

Table 1 – From Megan Rolf, KSU, hYp://arKcles.extension.org/


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!   Genotype dis-‐agreement > 2% -‐" miss-‐match.


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!   Genotype dis-‐agreement > 2% -‐" miss-‐match.

ImputaKon:

•   Is a method of determining some genotypes on a computer using actual genotypes on relaKves.

•   It is a necessary process to combine genotypes with different densiKes before any geneKc evaluaKon.

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Progeny

Sire

Dam

paternal maternal

paternal maternal

paternal maternal

ImputaKon:

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Progeny

Sire

Dam

paternal maternal

paternal maternal

paternal maternal

ImputaKon:

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Progeny

Sire

Dam

paternal maternal

paternal maternal

paternal maternal

ImputaKon:

We use FImpute sonware (Sargolzaei, M. et al.) for our imputaKon pipeline at iGDB.

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iGDB: QCs on imputaKon (switch rate)

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!  We expect to see the same genotype status aner each

imputaKon (consistent genotypes).

!   For some markers in some animals this is not true:

!   AA switches to AB, or AB switched to BB …

Switch rates by breed associaKon data

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Number of genotyped animals at IGS (as of 9/30/16):

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50K 802 1593 3763 1941 1125 7939 17163

9K 186 6007 6193

BOS1 414 461 1602 2477

GGP-‐HD 172 1151 8 2187 4374 7892

GGP-‐UHD 6 567 48 569 4 3679 4873

HD 136 430 1278 226 544 2614

SupperLD 111 5206 1984 10699 17164 35164

ZeoKs 3500 3500

Total 1227 9547 7542 19122 1129 41309 79876

Switch rates by marker posiKon

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Switch rates by breed

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Summary:

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!  We have developed a genomics pipeline for the IGS BOLT

geneKc evaluaKons (iGDB).

!   The are always challenges working with genotype data, mostly

the animal/sample IDs that which have to be resolved.

!   The low quality genotypes have been detected and removed

form the geneKc evaluaKons. These animals need to be re-‐

genotyped if interested.

Summary:

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!   Parent-‐progeny genotypes dis-‐agreement is exist. We have

found some of these issues but needs further improvement

(idenKfy potenKal sire/grans sire …).

!  We need to improve our imputaKon process (including

pedigree informaKon, pooled breed, …)

!  We recommend breeders to use a higher density genotypes on

animals that don’t have any close relaKves with genotypes in

iGDB.

iGDB pipeline:

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50K GGP-‐LD GGP-‐HD ZL5 …

Pooled Genotypes

Imputed Genotypes

BOLT

Raw genotypes

Pre-‐imputaKon QC

ImputaKon

QC’d Pooled Genotypes

Post-‐imputaKon QC

It takes less than a day to complete the process.

Acknowledment:

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QuesKons?

•   Iowa State University Hailin Su, potdoc. •   Theta SoluKons, LLC Bruce Golden •   IGS Lauren Hyde Steve McGuire Wade Shafer

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