Genomic selection through single-step genomic best linear unbiased prediction improves the accuracy of evaluation in Hanwoo cattle

Abstract

Objective: Genomic selection (GS) is becoming popular in animals' genetic development. We, therefore, investigated the single-step genomic best linear unbiased prediction (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 and carcass weight (kg), backfat thickness, eye muscle area, and marbling score 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 genomic estimated breeding value (GEBV) with EBV of all animals (r M1) and ii) correlation using inverse of coefficient matrix from the mixed-model equations (r M2). 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 r M1 estimates in the study were between 0.90 and 0.96 among five traits. The r M1 estimates varied slightly by population and info-type, but noticeably by bull-type for traits. Generally average r M2 estimates were much smaller than r M1 (pedBLUP, 0.40 to0.44; ssGBLUP, 0.41 to 0.45) at population level. However, r M2 from both BLUP models varied noticeably across info-types and bull-types. The ssGBLUP estimates of r M2 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 r M2 estimates ranged between 0.54 and 0.57, 0.55 and 0.62, and 0.70 and 0.74, respectively. The pedBLUP based r M2 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% to 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% to 35.7%; CBULL, 3.3% to 9.3%; PBULL, 2.8% to 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 provenbull evaluation program.

Genetic Analysis of Major Carcass Traits of Korean Hanwoo Males Raised for Thirty Months

“…Similarly, MS is found to be highly heritable (h 2 : 0.48-0.63) in various reports [5,9,14,18,19]. Previous reports generally suggest low and positive genetic correlations between CWT, BFT, and MS [5,9,14]. The BFT and EMA association is also found as being low and oppositely correlated [5,9,14].…”

“…The backfat thickness (BFT) is also reported as being highly heritable in Hanwoo males, i.e., h 2 : 0.46-0.51 [5,9,14,18]. Similarly, MS is found to be highly heritable (h 2 : 0.48-0.63) in various reports [5,9,14,18,19]. Previous reports generally suggest low and positive genetic correlations between CWT, BFT, and MS [5,9,14].…”

“…In this regard, the inclusion of PROD30 males in the national evaluation through a proper genetic evaluation method could help increase the number of progeny records per bull and contribute to the accuracy of evaluation in the long run. The recently adopted single-step genomic BLUP (ssGBLUP)-based genomic selection (GS) in PGT [7][8][9] could provide an opportunity in this regard as it would allow all animals to participate in the evaluation process of animals. Thus, the currently implemented ssGBLUP-based animal evaluation coupled with PROD30 males could be a solution to the current PGT limitations.…”

“…Previously, the genetic parameters for the PROD24 population have been reported in numerous studies [1,5,9,[14][15][16][17]. In these reports, carcass weight (CWT) and eye muscle area (EMA) are generally found as being moderately heritable, such as between 0.298 and 0.36 and between 0.27 and 0.44, respectively [5,9,14]. The backfat thickness (BFT) is also reported as being highly heritable in Hanwoo males, i.e., h 2 : 0.46-0.51 [5,9,14,18].…”

“…In these reports, carcass weight (CWT) and eye muscle area (EMA) are generally found as being moderately heritable, such as between 0.298 and 0.36 and between 0.27 and 0.44, respectively [5,9,14]. The backfat thickness (BFT) is also reported as being highly heritable in Hanwoo males, i.e., h 2 : 0.46-0.51 [5,9,14,18]. Similarly, MS is found to be highly heritable (h 2 : 0.48-0.63) in various reports [5,9,14,18,19].…”