Transition from Conventional to Genomic Selection (ssGBLUP) led to improve in accuracy gains and selection decisions in Sahiwal Cattle

Abstract

By using genome-wide markers to predict an individual’s genetic potential, the introduction of Genomic Selection (GS) has transformed animal breeding. This greatly accelerated selection for complex traits by lowering reliance on drawn-out field trials, allowing for faster genetic gains in livestock. However, there is little research on the effects of genomic selection on Sahiwal cattle in India, and comparing it to the current culling or selection process is even more uncommon, particularly in nations with fewer genotyped animals. This study is an initial effort to address the aforementioned gaps in knowledge. Genomic selection was implemented in Sahiwal cattle for the 305 days milk yield using univariate animal model and the single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) method. The Effective Population size (Ne) of the Sahiwal herd was calculated using genomic data and was reported for the previous generation to be 71.927. The heritability of 305 days milk yield was estimated as 0.177 ± 0.068. Genomic estimated breeding values (GEBVs) were predicted for each individual using ssGBLUP, yielding a mean prediction accuracy of 43.11%, compared with 40.88% obtained using conventional pedigree-based BLUP. Cross-validation further demonstrated superior predictive performance of ssGBLUP, with accuracies of 76.82% and 70.50% for ssGBLUP and PBLUP, respectively. To further check the effectiveness of the genomic selection methodology, we also compared the GEBVs obtained and compared it with the Expected Progeny Difference (EPD) which is being applied in our farm for culling decisions. It was seen that GEBVs obtained from ssGBLUP methodology were also in line with the conventionally used method of EPD. The use of genomic selection enables genetic studies with limited pedigree information. Additionally, the ssGBLUP methodology allows to check for pedigree errors, where family relationships are incorrectly recorded. The EPD and GEBVs were consistent with one another, indicating that genomic selection may also be utilised to support culling and selection decisions in a farm. Thus, in a conventional animal breeding program with constraint resources and an incomplete pedigree, we recommend employing the ssGBLUP model for regular genomic assessment and identification of suitable candidates to effectively carry out a genomic selection program.