Genomic selection risks benefits alternatives Jack J. Windig - PDF document

Low Input Breeds ECO AB Symposium, 15�16 24/03/2011 March, 2011 Genomic selection risks benefits alternatives Jack J. Windig Animal Breeding & Genomics Centre Animal Breeding & Genomics Centre Animal breeding � Can be very effective � Scrapie incidence in the Netherlands � Even effective when heritability is low � Animal breeding works cumulative � Effects are permanent � Right breeding goal is crucial � Too narrow breeding goal gives problems • Fertility problems and mastitis in Holstein • In general: production at the cost of welfare and health Animal Breeding & Genomics Centre 1

Low Input Breeds ECO AB Symposium, 15�16 24/03/2011 March, 2011 What is Genomic selection? � based on SNP data � 3K -> 50K ->300K Animal Breeding & Genomics Centre Genomic selection Breeding Value 1205 = A1 + A2 + B1 + B1 + C1 + C2 + D2 + D2 + E1 Animal Breeding & Genomics Centre 2

Low Input Breeds ECO AB Symposium, 15�16 24/03/2011 March, 2011 Genomic selection Breeding value 1205 = A1 + A2 + B1 + B1 + C1 + C2 + D2 + D2 + E…. Breeding value 1211 = A1 + A1 + B1 + B2 + C1 + C2 + D1 + D2 + E…. � Find animals with reliable beeding values � Based on performance (of relatives) and pedigree � Determine value of A1, A2, B1, B2 etc. � Compute SNP-breeding value for animals without Animal Breeding & performance data (of enough relatives) Genomics Centre Reference population Young animals SNPs Statistic model Reference Data base: SNP1: T = +1 g milk A = -1 g milk SNP2: G = +2 g milk C = -2 g milk Measured performance Etc, etc, etc, ……….. Breeding value animals for genomic selection Animal Breeding & Genomics Centre 3

Low Input Breeds ECO AB Symposium, 15�16 24/03/2011 March, 2011 Generation interval in a typical dairy cattle program ������������ ������� ���������� �������������������������������� �������������������������������� ������������������������ ������������������������ ������� ������� ↓ ↓ ������������������������� �����"#$���� ���������#%� �� ���������� ���� �������������������� ↓ ↓ ������������� ����������� ����������������������������� ���������������������������� ������������������� ��������������� �!�������� ↓ ����������������������������� ������������������ Animal Breeding & Genomics Centre Accuracy in genomic selection � Size reference population � More is better � Should capture the SNPs in the current population and their combination with trait determining genes � Relationship with reference population � Linkage between SNPs and genes changes over time � Additive (and non-additive) effects change with gene frequencies � Number of SNPs � More is better Animal Breeding & Genomics Centre 4

Low Input Breeds ECO AB Symposium, 15�16 24/03/2011 March, 2011 One step further � Velo- and Whizzo -genetics � Breeding in the lab • Cell cultures derived from oocytes • Select best cultures with genomic selection • Induce meiosis • Fertilization • Repeat X generations � 10 (or more) generations squeezed into 1 � Huge size of breeding program possible � Not yet feasible � Ever feasible? � Acceptance by society is doubtful � Doubtful if animal after x generations is as expected • Natural selection is turned off • Reference population in genomic selection functions for a limited time Animal Breeding & Genomics Centre Current situation � Large breeding companies are implementing genomic selection, especially in dairy cattle � Global high input/high output breeds will increase their genetic progress Animal Breeding & Genomics Centre 5

Low Input Breeds ECO AB Symposium, 15�16 24/03/2011 March, 2011 Low input breeds and Genomic Selection � Breeding value estimation for other than usual traits � Disease resistance � Energy balance � Methane emissions � Performance on special diets � Performance in special environments � Enables breeding value estimation in populations without a reliable pedigree � Reliable reference population is crucial but can (will) be problematic � Expertise and high investment needed Animal Breeding & Genomics Centre Breeding polled cattle as an alternative to dehorning? � Dehorning is painful but necessary to prevent injuries later in life � Breeding polled cattle is an alternative Polledness based on a single gene but rare or absent in most breeds Dehorned Polled Animal Breeding & Genomics Centre 6

Low Input Breeds ECO AB Symposium, 15�16 24/03/2011 March, 2011 Situation 2009 in Holstein � Only 38 polled bulls (36 Pp and 2 PP) � Farmers opinion � Will not use them • Too few to choose from • Too low production etc. • Dehorning is not a problem � If bulls with good breeding values available • Will certainly use them � Breeding program needed Animal Breeding & Genomics Centre Breeding program? Was succesfull in Fleckvieh and Charolais � Now >90% of bulls in Fleckvieh for suckler cows are � polled Classic introgression program � � Takes > 20 years Cannot close the gap completely � Genomic selection � Can produce bulls with high breeding values <10 � years Animal Breeding & Genomics Centre 7

Low Input Breeds ECO AB Symposium, 15�16 24/03/2011 March, 2011 Social research under Dutch citizens � Livestock and breeding in general: � Citizens • Animal welfare is very important • The more natural the better • Strong negative opinion on genetic modification • No distinction between genetic modification and animal breeding � Farmers • Animal welfare is very important • Best farmer is a farmer that cares for its animals • Strong negative opinion on genetic modification • Distinction between genetic modification and animal breeding � Information changes the opinion of a part of the citizens Animal Breeding & Genomics Centre Social research under Dutch citizens � Breeding polled cattle � Cows with horns are seen as more natural and better for animal welfare than cows without horns � No distinction is being made between naturally polled cattle and dehorned cattle � Opinions are not very strong � Breeding polled cattle only acceptable if � Distinction breeding - genetic modification is clear � Polled cattle is seen as natural Animal Breeding & Genomics Centre 8

Low Input Breeds ECO AB Symposium, 15�16 24/03/2011 March, 2011 Pros and cons � Polledness is a genetic defect � Polledness is completely natural � Polledness occurs since prehistoric times � Horns are an integral part of the animal � Animals function perfectly without horns � Compare with sheep � It is not ethical to adapt animals to the production environment (should be the other way round) � Larger stables with space to avoid other cows also prevent injuries � It is not ethical to leave animals as they are when the environment changes � In the past selection was against polled animals to adapt them to tie stalls Animal Breeding & Genomics Centre Conclusions � Breeding goal comes first! � Genomic selection � Accelerates animal breeding � Can be beneficial for low input breeding � Small population size is a handicap � General public � Distrusts genetics � Whizzo-genetics will be totally unacceptable Animal Breeding & Genomics Centre 9