Heritability estimates and predictive ability for pig meat quality traits using identity‐by‐state and identity‐by‐descent relationships in an F2 population

• Published in: Journal of animal breeding and genetics (1986) 2023-01, Vol.140 (1), p.13-27
• Main Authors: Angarita Barajas, Belcy Karine, Cantet, Rodolfo J. C., Steibel, Juan P., Schrauf, Matias F., Forneris, Natalia S.
• Format: Article
• Language: English
• Subjects: Animal models; cross‐validation; Estimates; genomic prediction; Genomics; Genotypes; Heritability; identity by descent; Meat; Meat quality; Pedigree; pigs; predictive ability
• ISSN: 0931-2668; 1439-0388
• DOI: 10.1111/jbg.12742

Genomic relationships can be computed with dense genome‐wide genotypes through different methods, either based on identity‐by‐state (IBS) or identity‐by‐descent (IBD). The latter has been shown to increase the accuracy of both estimated relationships and predicted breeding values. However, it is not clear whether an IBD approach would achieve greater heritability (h2) and predictive ability (r̂y,ŷ) than its IBS counterpart for data with low‐depth pedigrees. Here, we compare both approaches in terms of the estimated of h2 and r̂y,ŷ, using data on meat quality and carcass traits recorded in experimental crossbred pigs, with a pedigree constrained to only three generations. Three animal models were fitted which differed on the relationship matrix: an IBS model (GIBS), an IBD (defined within the known pedigree) model (GIBD), and a pedigree model (A22). In 9 of 20 traits, the range of increase for the estimates of σu2 and h2 was 1.2–2.9 times greater with GIBS and GIBD models than with A22. Whereas for all traits, both parameters were similar between genomic models. The r̂y,ŷ of the genomic models was higher compared to A22. A scarce increment in r̂y,ŷ was found with GIBS when compared to GIBD, most likely due to the former recovering sizeable relationships among founder F0 animals.