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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.18.0936    [Accepted] Published online November 12, 2019.
Genomic selection through single-step genomic BLUP improves the accuracy of evaluation in Hanwoo cattle
Mi Na Park1,*  , Mahboob Alam2  , Sidong Kim3  , Byoungho Park4  , Seung Hwan Lee5  , Sung Soo Lee6 
1Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea
2Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea
3Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Korea
4Poultry Research Institute, National Institute of Animal Science, Rural Development Administration, Pyeongchang 25342, Korea
5Division of Animal and Dairy Science, Chungnam National University, Daejeon, 34134, Korea
6Hanwoo Genetic Improvement Center, NongHyup Agribusiness Group Inc, Seosan, 31948, Korea
Correspondence:  Mi Na Park,Email: mahboob.abg@gmail.com
Received: 10 December 2018   • Revised: 24 January 2019   • Accepted: 30 October 2019
Abstract
Objective
Genomic selection (GS) is becoming popular in animals’ genetic development. We, therefore, investigated the single-step genomic BLUP (ssGBLUP) as tool for GS, and compared its efficacy with the traditional pedigree BLUP (pedBLUP) method.
Methods
A total of 9,952 males born between 1997 and 2018 under Hanwoo Proven-Bull Selection program was studied. We analyzed body weight at 12 months (BW12) and carcass traits (CWT, kg), backfat thickness (BFT), eye muscle area (EMA), and marbling score (MS) traits. About 7,387 bulls were genotyped using Illumina 50K BeadChip Arrays. Multiple-trait animal model analyses were performed using BLUPF90 software programs. Breeding value accuracy was calculated using two methods: (i) Pearson’s correlation of GEBV with EBV of all animals (rM1) and (ii) correlation using inverse of coefficient matrix from the mixed-model equations (rM2). Then, we compared these accuracies by overall population, info-type (PHEN: phenotyped-only, GEN: genotyped-only, and PH+GEN: phenotyped and genotyped), and bull-types (YBULL: young male calves, CBULL: young candidate bulls, and PBULL: proven bulls)
Results
The rM1 estimates in the study were between 0.90 and 0.96 among five traits. The rM1 estimates varied slightly by population and info-type, but noticeably by bull-type for traits. Generally average rM2 were much smaller than rM1 (pedBLUP: 0.40-0.44; ssGBLUP: 0.41-0.45) at population level. However, rM2 from both BLUP models varied noticeably across info-types and bull-types. The ssGBLUP estimates of rM2 in PHEN, GEN and PH+GEN ranged between 0.51 and 0.63, 0.66 and 0.70, and 0.68 and 0.73, respectively. In YBULL, CBULL and PBULL, the rM2 estimates ranged between 0.54 and 0.57, 0.55 and 0.62, and 0.70 and 0.74, respectively. The pedBLUP based rM2 estimates were also relatively lower than ssGBLUP estimates. At the population level, we found an increase in accuracy by 2.0 to 4.5% among traits. Traits in PHEN were least influenced by ssGBLUP (0 to 2.0%), whereas the highest positive changes were in GEN (8.1-10.7%). PH+GEN also showed 6.5 to 8.5% increase in accuracy by ssGBLUP. However, the highest improvements were found in bull-types (YBULL: 21-35.7%; CBULL: 3.3-9.3%; PBULL: 2.8-6.1%).
Conclusion
A noticeable improvement by ssGBLUP was observed in this study. Findings of differential responses to ssGBLUP by various bulls could assist in better selection decision making as well. We, therefore, suggest that ssGBLUP could be used for GS in Hanwoo proven-bull evaluation program.
Keywords: Genomic Selection; Single-step Genomic BLUP; Evaluation Accuracy; Proven-bull; Hanwoo Cattle
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