NEW DOCUMENT AUGUST 2013 NOW SAME PRICE for ALL Holstein, Jersey & Ayrshires irrespective of Milk

Recording participation

LogixGenomix

Instructions for participation in the Logix Genomix service for Genomic Selection of Holstein, Jersey and Ayrshire cattle.
The Logix
Genomix

service for GENOMIC SELECTION in dairy cattle is aimed at:

Enabling dairy farmers and the breeding industry to identify the genetic merit of young potential breeding animals by means of the genomic (molecular genetic) information of these animals in combination with the BLUP breeding values. Early, accurate assessment of the suitability of replacement heifers, potential bull mothers and bulls destined for breeding purposes (especially artificial insemination, but also for natural mating). Expanding the reference by including genomic information in local breeding value predictions for dairy animals in South Africa.

Who will benefit?

The Logix
Genomix

service for GENOMIC SELECTION in dairy cattle will immediately benefits:

Each farmer/breeder making use of the service. Genomically Enhanced Estimated Breeding Values (GEBVs) or even Direct Genomic Values (DGVs) predict the genetic merit of the tested young animals with higher reliabilities than the current conventional methods.

The AI industry. Progeny testing of potential AI sires is expensive and lead to longer generation intervals that impacts on annual genetic gains. The correct identification of young potential bull mothers by making use of genomic information speeds up the process even more, and assists in minimising wrong choices when animals are considered in AI and Embryo programs.

The whole breed. By joining the progressive countries in adopting this technology for breeding purposes, the South African breeders and commercial milk producers will make strides in changing the genetic merit of their animals. The South African Holstein, Jersey and Ayrshire populations will keep pace (and can even exceed in some traits) with their counterparts elsewhere in the world.

Local research. This service is conducted in collaboration with international partners and research units. Participation will enhance the knowledge base locally and will lead to the development of more sophisticated ways to predict genetic merit, setting up breeding objectives and intimate knowledge of the genetic properties of local animals (also in terms of carriers of desirable and undesirable known genes or markers of genes).

What animals to test

The Logix
Genomix

service for GENOMIC SELECTION in DAIRY CATTLE is suitable for ALL

Holstein, Jersey and Ayrshire cattle, irrespective of participation in Logix

Milk

or recording status.

The biggest benefit is derived where all pedigree records are known, the maximum number of recordings (milk recordings and functional type traits) are available and the Stud Book team is responsible for the BLUP breeding value predictions. These animals will receive Genomically Enhanced Estimated Breeding Values (GEBVs). Genome tests will specifically be of value for picking young bulls as potential breeding sires (especially for AI) and heifers as replacements or as potential bull mothers. Tests can be carried out as young as is physically possible and will still be of benefit as late as the second parity. In order of benefit: 1. Young potential breeding animals from Stud herds taking part in Logix
Milk. Milk.

2. Young potential breeding animals from Commercial herds taking part in Logix 3. Young potential breeding animals from Stud herds not taking part in Logix

Milk. Milk.

4. Young potential breeding animals from Commercial herds not taking part in Logix

The following parties are involved and processes that are be followed.
The following figure gives a quick glimpse into the role-players and processes followed to supply participants with reliable genetic merit predictions based on the combination of genomic information and BLUP breeding values.

How to participate.
1. Identify suitable young animals to be tested. The recommendation is to start with young promising females and males with possible potential as breeding stock or the parents of potential breeding stock (eg. potential dams of sires). This potential can be estimated by means of the lines and proven performance of the parents, but most

importantly by using the BLUP breeding values. For young animals, the BLUP breeding values will still be the parent average values as no measurements (recordings) of performance (milk, milk components, reproduction, functional properties, etc.) have yet been carried out. 2. Collect suitable biological samples, place in an envelope, complete and fill in all particulars and send to SA Stud Book. The sample of preference currently is tail hair with intact hair roots. o Pull at least 20 hair from the tail. MAKE SURE THAT THE HAIR ROOTS ARE INTACT! o Place the hair in an envelope (preferable size of 220mm x 110mm). DO NOT PUT HAIR IN A PLASTIC BAG use ordinary paper envelopes! o The following information should be printed on the envelope (or attached to it as a separate page) and the particulars of the animal should be clearly filled in: Particulars on the envelope (or attached printed page): Animal Number
Sex HDM Year Sequence Y Y Computer number Sire Sex M HDM Year Sequence Y Y Computer number Stud Book Herd Number Breed Y Y Sex F HDM
Dam

Year Sequence Y Y Computer number

SA Stud Book Logix

Holstein Jersey Date Collected Y Y M M

Milk

Genomic Test for (mark one)

Ayrshire

To be used for DGV/GEBV

D D

Example:

o Place the individual envelopes (with the tail hair of the animals te be evaluated in each envelope) in a larger envelope. The following information should then also be completed and placed in this larger envelope:
OWN Address: Animals recorded on LogixMilk? Yes No Member number

Collected by: Name & eMail

Phone:

Please send to:

STUD BOOK MILK GENOMIC TEST PO Box 270 BLOEMFONTEIN 9300

Surname

Signature

Tests and Evaluations included and extra tests required:

Genomic predictions

Price
R 1 540 R 964 FREE
SAME Price

GGP 80K (High Density) RECOMMENDED FOR AI BULLS GGP LD (Low Density) DEFAULT COWS & YOUNG ANIMALS

DGV Canadian LPI (On Canadian scale) Non Logix Milk participant (just indicate same price)
Parentage profile & 22 Genetic Tests (Public Domain)

X
X

FREE

Additional Tests and Evaluations required:

DGV USA TPI (On USA Scale)
Female Initial (test) Male Male accepted as AI sire (irrespective of country) Tibial Hemimelia Pulmonary Hypoplasia with Anasarca Neuropathic Hydrocephalus Hypotrichosis_KRT71 Arthrogryposis (Curly Calf, AM) Fawn Calf Syndrome or Contractural Arachnodactylyl Beta Casein A2 Brachyspina CVM Coat Colour (346, 358, 373) & Dilutor

Price
R 144 R 5 040 R 26 400 R 222 R 144 R 96 R 96 R 180 R 192 R 120 R 240 R 348 R 84

ROYALTIES to be paid

Pick One

DGV/GEBV SA Traits

o Mail the tightly sealed larger envelope (containing al the individual envelopes with hair in them and the instruction page) to: S A STUD BOOK MILK GENOMICS TEST PO BOX 270 BLOEMFONTEIN 9300

What happens next?

As soon as the envelope containing the hair and particulars has been received, the sender will be notified. All animal Identification and computer numbers will be verified on the Logix Animal Recording database. This will be possible for all Stud Animals and Grade animals participating in Logix Milk. Individual animal identification numbers of non-Stud animals not participating in Logix Milk can not be verified and the completed information will be accepted as is. Any discrepancies or unclear information will be cleared out with the sender before further actions. Batches of envelopes containing the individual animals hair will be sent by courier to UniStel (Stellenbosch) for DNA extraction. The sender will receive an invoice from SA Stud Book based on the indicated services required. UniStel will do the DNA extractions and will then send the extracted DNA to the GeneSeek laboratory in the USA that will conduct the genomic evaluation. Once completed, GeneSeek will notify UniStel and SA Stud Book and will make the SNP (Genomic) information available from their database to Stud Book and will also place a copy on the North American Genomic Consortiums database. SA Stud Book will extract the SNP data to the Logix Database and also place a copy on the IGenoP database in Ireland for safekeeping an as possible copy for future exchange of information to the IGenoP participants. The Canadian Dairy Network will incorporate the SNP information in their genetic evaluations and supply SA Stud Book with the results, including the Canadian LPI values. The SA Stud Book team will make use of the Interbull conversions to present the breeder/client with either GEBVs (animals part of the Logix Genetic evaluations) or DGVs (other animals) as well as all the other extra services and information indicated.

What makes this service unique? The Logix Genomix service for Genomic Selection of Holstein, Jersey and Ayrshire cattle relies on sound scientific animal breeding principles.
The Genomic tests are conducted on the universal exchangeable Illumina SNP chips enabling local breeders and the industry to be in line with the rest of the leading countries. Information will also immediately form part of the local genetic evaluations building an even more trustworthy system predicting the genetic merit of dairy cattle.

All genetic merit values (GEBVs and DGVs) are expressed on the South African Scale enabling the users to directly compare these values with the current Logix BLUP values for the rest of the breed. No guesses and no conversions. The following additional tests will also be made available, free of charge, as part of the deal:
Parentage profile Osteopetrosis (Marble Bone Disease) Alpha MannosidosisCitrullinemia DUMPS BLAD Factor XI Hypotrichosis_PMel17 DNA Tests included in price Idiopathic Epilepsy Beta Lactoglobulin Holstein Haplotypes1 USDA Holstein Haplotypes2 USDA Holstein Haplotypes3 USDA Jersey Haplotypes1 Dun Colour Chondrodysplasia Beta Casein A/B Kappa Casein I Kappa Casein II Y chromosome infertility - Free Martin (blood sample) Calpain 316 Calpain 4751 Calpain 530

The service also allows for participation in the USA genomic evaluations whereby the TPI values will be issued (at the extra costs indicated) on request. This is also done as part of the agreements between SA Stud Book and its international partners. Obviously these values will then be expressed on the USA scale (and can then be directly compared to the USA population for the particular breed).

More information?
Please contact your nearest SA Stud Book Technical Advisor or any of the following people: Japie van der Westhuizen Charl Hunlun Bobbie van der Westhuizen japie@studbook.co.za charl@studbook.co.za bobbie@studbook.co.za 082 331 9923 082 576 6736 082 802 6606

Checklist
Action
Identify the correct animals to be tested Prepare the appropriate envelopes for tail hair (with the information printed or attached to the envelope) Pull tail hair from the identified animals (checked the correctness of the ID numbers) Make sure that the hair roots are intact and at least 20 hair per animal are included Make sure there was no cross contamination of hair (hair from different animals were handled separately) Place hair from each animal in the correct envelope Generate and complete the Instruction page for each group of animals to be tested carefully by also ticking the appropriate boxes on the form for additional services wanted Place the individual envelopes with hair AND the instruction page in a bigger envelope Make sure the address and return address are indicated correctly and clearly on the bigger envelope Mail or Send (Koerier) the envelope to SA Stud Book for further actions Receive conformation that the samples reached Stud Book in good condition or that corrections are needed
Completed

PRINT THE FOLLOWING PAGES: They can be used for printing op envelopes and/or separate pages to be attached to envelopes and the instructions (for the batch of samples).

Animal Number
Sex HDM Year Sequence Y Y Computer number Sire Sex M HDM Year Sequence Y Y Computer number Stud Book Herd Number Breed Y Y Sex F HDM

Dam

Year Sequence Y Y Computer number

SA Stud Book Logix

Holstein Jersey Date Collected Y Y M M

Milk

Genomic Test for (mark one)

Ayrshire

To be used for DGV/GEBV

D D

Animal Number
Sex HDM Year Sequence Y Y Computer number Sire Sex M HDM Year Sequence Y Y Computer number Stud Book Herd Number Breed Y Y Sex F HDM

Dam

Year Sequence Y Y Computer number

SA Stud Book Logix

Holstein Jersey Date Collected Y Y M M

Milk

Genomic Test for (mark one)

Ayrshire

To be used for DGV/GEBV

D D

Animal Number
Sex HDM Year Sequence Y Y Computer number Sire Sex M HDM Year Sequence Y Y Computer number Stud Book Herd Number Breed Y Y Sex F HDM

Dam

Year Sequence Y Y Computer number

SA Stud Book Logix

Holstein Jersey Date Collected Y Y M M

Milk

Genomic Test for (mark one)

Ayrshire

To be used for DGV/GEBV

D D

OWN Address:

Animals recorded on LogixMilk?

Yes No

Member number

Collected by: Name & eMail

Phone:

Please send to:

STUD BOOK MILK GENOMIC TEST PO Box 270 BLOEMFONTEIN 9300

Surname

Signature

Tests and Evaluations included and extra tests required:

Genomic predictions

Price
R 1 540 R 964 FREE
SAME Price

GGP 80K (High Density) RECOMMENDED FOR AI BULLS GGP LD (Low Density) DEFAULT COWS & YOUNG ANIMALS

DGV Canadian LPI (On Canadian scale) Non Logix Milk participant (just indicate same price)
Parentage profile & 22 Genetic Tests (Public Domain)

X
X

FREE

Additional Tests and Evaluations required:

DGV USA TPI (On USA Scale)
Female Initial (test) Male Male accepted as AI sire (irrespective of country) Tibial Hemimelia Pulmonary Hypoplasia with Anasarca Neuropathic Hydrocephalus Hypotrichosis_KRT71 Arthrogryposis (Curly Calf, AM) Fawn Calf Syndrome or Contractural Arachnodactylyl Beta Casein A2 Brachyspina CVM Coat Colour (346, 358, 373) & Dilutor

Price
R 144 R 5 040 R 26 400 R 222 R 144 R 96 R 96 R 180 R 192 R 120 R 240 R 348 R 84

ROYALTIES to be paid

Pick One

DGV/GEBV SA Traits