Genomic prediction by single-step genomic BLUP using cow reference population in Holstein crossbred cattle in India

Publikation: Bidrag til bog/antologi/rapport/proceedingKonferencebidrag i proceedingsForskningpeer review

  • Nilesh Kumar Nayee, National Dairy Development Board, Anand 388 001, Gujarat, India. nileshn@nddb.coop, Indien
  • Guosheng Su
  • Swapnil Gajjar, National Dairy Development Board, Anand 388 001, Gujarat, India, Indien
  • Goutam Sahana
  • Sujit Saha, National Dairy Development Board, Anand 388 001, Gujarat, India, Indien
  • Kamlesh R. Trivedi, National Dairy Development Board, Anand 388 001, Gujarat, India, Indien
  • Bernt Guldbrandtsen
  • Mogens Sandø Lund
Advantages of genomic selection in breeds with limited numbers of progeny tested bulls have been demonstrated by adding genotypes of females to the reference population (Thomasen et al., 2014). The current study was conducted to explore the feasibility of implementing genomic selection in a Holstein Friesian crossbred population with cows kept under small holder conditions using test day records and single step genomic BLUP (ssGBLUP). Milk yield records from 10,797 daughters sired by 258 bulls were used Of these 2194 daughters and 109 sires were genotyped with customized genotyping chip on the Illumina platform. A conventional test day random regression model with Legendre Polynomials of 3rd order for both fixed and random regression was compared with an ssGBLUP model with same structure and effects as the conventional model. The conventional test day model and the ssGBLUP model were assessed using a 5-fold cross validation in two scenarios. In scenario 1, half-sibs in the whole data were randomly divided into 5 subsets. In scenario 2, individuals in the whole data were randomly divided into 5 subsets. The predictive ability of the two models was assessed for accuracy of EBV. Accuracy was calculated as the correlation between 305 day EBV and corrected 305 day phenotypic values (Yc). Validation results showed that genomic prediction using ssGBLUP led to higher accuracy than the conventional test-day model. In validation Scenario 2 where validation animals had a relatively close relationship with training animals, there was a marginal increase of correlations in genotyped animals from 0.397 to 0.405. The difference between genomic and conventional prediction was more marked in validation scenario 1 where validation animals had more distant relationship with training animals. Correlations increased from 0.150 to 0.194 for all animals and from 0.247 to 0.276 for genotyped animals. In addition, correlation between average daughter Yc and predicted breeding values of sires increased from 0.126 when using conventional BLUP to 0.202 when using ssGBLUP. These results indicate that genomic selection is feasible in Indian HF Crossbred cattle even though only recent female animals have been genotyped. It is expected that the prediction accuracy will increase further as more animals are genotyped. Keywords: test day random regression model, ssGBLUP, genomic selection, Holstein Crossbred cows, small holder.
OriginalsprogEngelsk
TitelProceedings of the World Congress on Genetics Applied to Livestock Production, 2018 : Volume Electronic Poster Session - Theory to Application - 1
Antal sider5
Vol/bind11
Udgivelsesår2018
Artikelnummer11.411
StatusUdgivet - 2018
BegivenhedThe 11th World Congress on Genetics Applied to Livestock Production - Aotea Centre, Auckland 1010, Auckland, New Zealand
Varighed: 11 feb. 201816 feb. 2018
Konferencens nummer: 11

Konference

KonferenceThe 11th World Congress on Genetics Applied to Livestock Production
Nummer11
LokationAotea Centre, Auckland 1010
LandNew Zealand
ByAuckland
Periode11/02/201816/02/2018

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