Managing Broken Genes in the Age of

GenomicsJared E. DeckerState Beef Genetics Specialist

DeckerJE@missouri.eduhttp://web.missouri.edu/~deckerje/extension

http://steakgenomics.blogspot.com/https://www.facebook.com/SteakGenomics

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Broken Genes… ~100 genes

where one copy is functional and the other is broken

~20 genes where the broken copy is a lethal mutation

Called Loss of Function mutations

2Science Vol. 335 no. 6070 pp. 823-828 DOI: 10.1126/science.1215040

Broken Genes…

Inconvenient Genetic TruthEverybody has genetic defects!!!

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Even the most

beautiful people in the world

Broken Genes…

Inconvenient Genetic TruthEverybody has genetic defects!!!

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Even the most caring

people in the world

Broken Genes…

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Broken Genes…

What happens when a broken gene is inherited from the father and the mother?Genetic abnormalitySpontaneous abortion

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Broken Genes…

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Broken Genes in Dogs

Dog Breed Canine Disease Gene Basenji Renal Fanconi Syndrome FAN1Chinese Crested Multiple Systems Degeneration SERAC1Kerry Blue Terrier Multiple Systems Degeneration

SERAC1 Jack Russell Terrier Spinocerebellar Ataxia KCNJ10Basenji Progressive Retinal Atrophy

SAGStandard Schnauzer Dilated Cardiomyopathy RBM20Australian Shepherd

Neuronal ceroid lipofuscinosis CLN8

Soft Coated Wheaten Paroxysmal dyskinesia PIGN

Tibetan Terrier Progressive retinal atrophy

FAM161A

Chinese Crested Neuronal ceroid lipofuscinosis MSFD8

Causal mutations identified at Mizzou by whole genome sequencing

Dog Breed Gene Human DiseaseBasenji FAN1 Karyomegalic interstitial

nephritisChinese Crested SERAC1 MEGDEL syndrome†

Kerry Blue Terrier SERAC1 MEGDEL syndrome†

Jack Russell Terrier KCNJ10 SeSAME syndrome‡

Basenji SAG Oguchi disease 1Standard Schnauzer RBM20 Dilated cardiomyopathy 1DDAustralian Shepherd CLN8 NCL8/Northern epilepsyTibetan Terrier FAM161

ARetinitis pigmentosa 28

Soft Coated Wheaten

PIGN MCAHS syndrome 1≠

Chinese Crested MSFD8 Neuronal ceroid lipofuscinosis 7

A documented human disease corresponds to each of the canine diseases caused by mutations identified by whole genome sequencing

Broken Genes in Dogs

Broken Genes in Cats

TRAIT BREED GENEVitamin-D dependent ricketts

DSH CYP27B1

Chediak-Higashi syndrome Persian LYSTAtrichia Sphynx KRT71Hypotrichia Devon Rex KRT71Melanocyte migration Birman KITHypotrichia Cornish Rex P2RY5Hypotrichia Selkirk Rex KRT71Craniofacial defect Burmese CART1Hypokalemia Burmese WNK4Gangliosidosis 1 and 2 Korat / Burmese GBL1 / HEXBPRA Abyssinian CRX /

CEP290PKD Persian PKD1Pyruvate kinase deficiency Several PKLRHypertrophic cardiomyopathy

Maine Coon / Ragdoll MYBPC

Lipoprotein lipase deficiency Several LPLSpinal muscular atrophy Maine Coon LIX1-LNPEP

Mutations found by Lyons Cat Genetics lab

99 Lives Cat Genome Initiative

Full genome sequence 99 cats Centralized and publically

available Any breed or population of cat

worldwide▪ Interesting trait or health issue▪ 12 cats races ▪ 24 major breeds▪ Rare breeds▪ Other felids

Broken Genes…

What happens when a broken gene is inherited from the sire and the dam?Genetic abnormalitySpontaneous abortion

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Broken Genes…Some we know aboutSome we don’t

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KNOWN

Even the most

beautiful cattle in the world

Silver Lining

Silver Lining

DNA tests can now be developed in a few months

With DNA tests available, frequency of the known genetic defect rapidly decreases

Now we can manage genetic defects

Genetic Defects

There are more than 35 genetic defects in cattle with a DNA test

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Tibial hemimelia (TH)

Documented in 1950’s Became prevalent in 2000’s due

to heterozygotes having straight hind limbs and long shaggy hair

Present in Galloway, Shorthorn, %Maine-Anjou, %Chianina, and other breeds with open herd books

Single autosomal recessive17Beever, Jonathan Edward, and Brandy Michele Marron. "Screening for the genetic defect causing tibial hemimelia

in bovines." U.S. Patent 8,158,356, issued April 17, 2012.

Tibial hemimelia (TH)

Due to ~46,000 bp deletion in ALX homeobox 4 (ALX4) gene, a transcription factor expressed in developing bones, limbs, hair, teeth, and mammary tissue.

“Note the twisted hind limbs and the large abdominal hernia. The calf also had a meningocele and cryptorchidism.” (Whitlock, Kaiser, and Maxwell, 2008)

18Beever, Jonathan Edward, and Brandy Michele Marron. "Screening for the genetic defect causing tibial hemimelia in bovines." U.S. Patent 8,158,356, issued April 17, 2012.

Pulmonary Hypoplasia with Anasarca (PHA)

Present in Maine-Anjou, %Chianina, and Shorthorn

Lethal autosomal recessive

“Note the severe anasarca.” (Whitlock, Kaiser, and Maxwell, 2008)

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Bovine Arthrogryposis Multiplex Congenita (AM)

Also known as “curly calf” Recognized by American

Angus Association as a genetic defect on September 16, 2008.

Recessive mutation Twisted spin, contracted

legs, light muscled20

Neuropathic Hydrocephalus (NH)

Recognized by American Angus Association as a genetic defect on June 12, 2009.

Recessive mutation Calves carried to near term Weigh 25 to 35 lbs Head is severely enlarged Bones of skull are malformed No brain tissue is present and skull

is filled with fluid21

Idiopathic Epilepsy (IE)

In Hereford cattle Autosomal recessive Calves experience

seizures, especially during stress such as temperature or handling

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Osteopetrosis (OP) Also known as “Marble Bone

Disease” In Red Angus Cattle are typically born dead or

die in first 24 hours Bones are extremely brittle and

lower jaw is short ~2721 bp deletion in the SLC4A2

gene affecting exons 2 and 3

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Congenital Hypotrichosis (HY)

In Hereford cattle Autosomal recessive 8 base pair deletion

mutation in first exon of the keratin 71 (KRT71) gene

Complete or partial loss of hair

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Contractual Arachnodactyly (CA)

Also known as “Fawn Calf”

Nonlethal recessive genetic abnormality

Upper limb joints have a reduced range of motion

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Developmental Duplications(DD)

PolymeliaMost die as embryos

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The Truth

The Truth: Every Living Thing Is A Genetic Defect Carrier

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What to do before breeding

Seedstock:Test at-risk breeding stock for

genetic defects Do we know the pedigree of the

animals? Are there carriers in the pedigree?

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What to do before breeding

Commercial:CrossbredOutcross

Avoid using the same bloodlinesTest at-risk breeding stock for

genetic defects Do we know the pedigree of the

animals? Are there carriers in the pedigree?

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What to Do with an Abnormal Calf

Create a documented record of what happened

Take a picture or video of affected calves

Freeze the entire animal if possible, otherwise preserve the abnormal body part

Obtain 40 hair bulbs from the calf, dam, and sire 30

What to Do with an Abnormal Calf

Breeders should contact their breed association and local veterinarian

Need intensive description of phenotype

The majority of abnormalities are caused by the environment, not genetics

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Broken Genes…

What happens when a broken gene is inherited from the sire and the dam?Genetic abnormalitySpontaneous abortion

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Sequence the genomes of 165 registered bulls

We will discover hundreds of broken genes Most embryonic lethals Breeds co-sponsoring sequencing:

Variants Reducing Fertility

Variants Reducing Fertility

Sequencing completed for all 165 of the animals

Currently running data thru analysis pipeline

Variants reducing Fertility

We have already analyzed the genomes of 11 bulls

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Variants reducing Fertility

We have already analyzed the genomes of 11 bulls

Identified 176 possibly lethal alleles

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Validation

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Validation

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Genomic Prediction

Predictions are sums of marker effects

For lethal mutations Homozygous normal: effect is 0 Heterozygous lethal: effect is -qif

Allows publication of a fertility EPD

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Mate Selection Software

Avoid mating carriers of the same lethal mutation

Will also manage Genetic merit Genetic diversity

Built upon economic selection indexes

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The Old Paradigm

See abnormal calfBury calf

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The Current Paradigm

Report abnormal calvesCollect dataCreate a testManage the defect

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The Genomics Paradigm?

Sequence influential AI siresCreate tests for LOF mutationsManage the mutations while

accounting for overall genetic merit

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Optimal practices

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Thank You!

Questions?http://web.missouri.edu/~deckerje/extension

http://steakgenomics.blogspot.com/https://www.facebook.com/SteakGenomics