Performance of genomic selection under a single‐step approach in autochthonous Spanish beef cattle populations

Mouresan, E. F.; Altarriba, J.; Moreno, C.; Munilla, S.; González‐Rodríguez, A.; Varona, L.

doi:10.1111/jbg.12253

Cited by 4 publications

(3 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The simulation was carried out based on the work done by Mouresan et al (2017Mouresan et al ( , 2018 with a fortran 90 code, available upon request. A summary of the simulation structure is presented in Figure 1.…”

Section: Simulationmentioning

confidence: 99%

Genotyping strategies for maximizing genomic information in evaluations of the Latxa dairy sheep breed

Granado-Tajada

Varona

Ugarte

2021

Journal of Dairy Science

Self Cite

View full text Add to dashboard Cite

Genomic selection has been implemented over the years in several livestock species, due to the achievable higher genetic progress. The use of genomic information in evaluations provides better prediction accuracy than do pedigree-based evaluations, and the makeup of the genotyped population is a decisive point. The aim of this work is to compare the effect of different genotyping strategies (number and type of animals) on the prediction accuracy for dairy sheep Latxa breeds. A simulation study was designed based on the real data structure of each population, and the phenotypic and genotypic data obtained were used in genetic (BLUP) and genomic (single-step genomic BLUP) evaluations of different genotyping strategies. The genotyping of males was beneficial when they were genetically connected individuals and if they had daughters with phenotypic records. Genotyping females with their own lactation records increased prediction accuracy, and the connection level has less relevance. The differences in genotyping females were independent of their estimated breeding value. The combined genotyping of males and females provided intermediate accuracy results regardless of the female selection strategy. Therefore, assuming that genotyping rams is interesting, the incorporation of genotyped females would be beneficial and worthwhile. The benefits of genotyping individuals from various generations were highlighted, although it was also possible to gain prediction accuracy when historic individuals were not considered. Greater genotyped population sizes resulted in more accuracy, even if the increase seems to reach a plateau.

show abstract

Section: Simulationmentioning

confidence: 99%

Genotyping strategies for maximizing genomic information in evaluations of the Latxa dairy sheep breed

Granado-Tajada

Varona

Ugarte

2021

Journal of Dairy Science

Self Cite

View full text Add to dashboard Cite

show abstract

“…This could be because of excessive human intervention in the management of livestock farms. The indel genotype distributions of four Chinese yellow cattle breeds were significantly different from each other (P < 0.01), which illustrated the transformation of Chinese cattle from draft cows to beef cattle (François et al, 2017;Mouresan et al, 2017).…”

Section: Discussionmentioning

confidence: 84%

Identification of a novel 24 bp insertion–deletion (indel) of the androgen receptor gene and its association with growth traits in four indigenous cattle breeds

Zhao

Wang

et al. 2018

Arch. Anim. Breed.

View full text Add to dashboard Cite

Abstract. During the past decades, insertions and deletions (indels) have become increasingly popular in animal breeding for understanding the relationship between genotypes and phenotypes. The androgen receptor (AR) plays the vital role of a bridge on the function of the androgen and has sexual size dimorphism. For this reason, the objective of this study was to explore the novel indel variants within the cattle AR gene and to detect their effects on growth traits in four breeds of Chinese yellow cattle. Herein, we first confirmed a novel 24 bp indel (AC_000187.1g.4187270-4187293delAATTTATTGGGAGATTATTGAATT) within the intron of the cattle AR gene. This is consistent with the results predicted from the NCBI SNP database. The distribution of the indel genotypes of four Chinese yellow cattle were significantly different from each other (P < 0.01). After significant correlation analysis, many remarkable phenotypic differences among the three genotypes were found (P < 0.05).In conclusion, a novel 24 bp indel within the AR gene significantly affected growth traits, suggesting that this indel may be a useful DNA marker for the elimination or selection of excellent individuals for cattle breeding.

show abstract

“…This approach is beneficial for traits that are difficult to measure and traits with low heritability. This method has been successfully applied to other livestock species, such as dairy cattle, beef, pigs, chickens, and sheep ( 5 – 9 ). Due to the limited marginal economic value of a goat breeding system, to the substantial number of markers required for genomic selection and to the high cost of sequencing, genomic selection in goats is still limited.…”

Section: Introductionmentioning

confidence: 99%

Accuracy of Genomic Selection for Important Economic Traits of Cashmere and Meat Goats Assessed by Simulation Study

et al. 2022

View full text Add to dashboard Cite

Genomic selection in plants and animals has become a standard tool for breeding because of the advantages of high accuracy and short generation intervals. Implementation of this technology is hindered by the high cost of genotyping and other factors. The aim of this study was to determine an optional marker density panel and reference population size for using genomic selection of goats, with speculation on the number of QTLs that affect the important economic traits of goats. In addition, the effect of buck population size in the reference population on the accuracy of genomic estimated breeding value (GEBV) was discussed. Based on the previous genetic evaluation results of Inner Mongolia White Cashmere Goats, live body weight (LBW, h2 = 0.11) and fiber diameter (FD, h2 = 0.34) were chosen to perform genomic selection in this study. Reasonable genome parameters and generation transmission processes were set, and phenotypic and genotype data of the two traits were simulated. Then, different sizes of the reference population and validation population were selected from progeny. The GEBVs were obtained by six methods, including GBLUP (Genomic Best Linear Unbiased Prediction), ssGBLUP (Single Step Genomic Best Linear Unbiased Prediction), BayesA, BayesB, Bayesian ridge regression, and Bayesian LASSO. The correlation coefficient between the predicted and realized phenotypes from simulation was calculated and used as a measure of the accuracy of GEBV in each trait. The results showed that the medium marker density Panel (45 K) could be used for genomic selection in goats, which can ensure the accuracy of the GEBV. The reference population size of 1,500 can achieve greater genetic progress in genomic selection for fiber diameter and live body weight in goats by comparing with the population size below this level. The accuracy of the GEBV for live body weight and fiber diameter was better when the number of QTLs was 100 and 50, respectively. Additionally, the accuracy of GEBV was discovered to be good when the buck population size was up to 200. Meanwhile, the accuracy of the GEBV for medium heritability traits (FDs) was found to be higher than the accuracy of the GEBV for low heritability traits (LBWs). These findings will provide theoretical guidance for genomic selection in goats by using real data.

show abstract

Performance of genomic selection under a single‐step approach in autochthonous Spanish beef cattle populations

Cited by 4 publications

References 21 publications

Genotyping strategies for maximizing genomic information in evaluations of the Latxa dairy sheep breed

Genotyping strategies for maximizing genomic information in evaluations of the Latxa dairy sheep breed

Identification of a novel 24 bp insertion–deletion (indel) of the androgen receptor gene and its association with growth traits in four indigenous cattle breeds

Accuracy of Genomic Selection for Important Economic Traits of Cashmere and Meat Goats Assessed by Simulation Study

Contact Info

Product

Resources

About