Detection of Genomic Regions with Pleiotropic Effects for Growth and Carcass Quality Traits in the Rubia Gallega Cattle Breed

• Main Authors: Maria Martinez-Castillero, Carlos Then, Juan Altarriba, Houssemeddine Srihi, David López-Carbonell, Clara Díaz, Paulino Martinez, Miguel Hermida, Luis Varona
• Format: Article
• Language: English
• Published: MDPI AG 2021-06-01
• Series: Animals
• Subjects: beef cattle; single-step GBLUP; SNP; candidate genes; GWAS; pleiotropy
• Online Access: https://www.mdpi.com/2076-2615/11/6/1682

The breeding scheme in the Rubia Gallega cattle population is based upon traits measured in farms and slaughterhouses. In recent years, genomic evaluation has been implemented by using a ssGBLUP (single-step Genomic Best Linear Unbiased Prediction). This procedure can reparameterized to perform ssGWAS (single-step Genome Wide Association Studies) by backsolving the SNP (single nucleotide polymorphisms) effects. Therefore, the objective of this study was to identify genomic regions associated with the genetic variability in growth and carcass quality traits. We implemented a ssGBLUP by using a database that included records for Birth Weight (BW-327,350 records-), Weaning Weight (WW-83,818-), Cold Carcass Weight (CCW-91,621-), Fatness (FAT-91,475-) and Conformation (CON-91,609-). The pedigree included 464,373 individuals, 2449 of which were genotyped. After a process of filtering, we ended up using 43,211 SNP markers. We used the GBLUP and SNPBLUP model equivalences to obtain the effects of the SNPs and then calculated the percentage of variance explained by the regions of the genome between 1 Mb. We identified 7 regions of the genome for CCW; 8 regions for BW, WW, FAT and 9 regions for CON, which explained the percentage of variance above 0.5%. Furthermore, a number of the genome regions had pleiotropic effects, located at: BTA1 (131–132 Mb), BTA2 (1–11 Mb), BTA3 (32–33 Mb), BTA6 (36–38 Mb), BTA16 (24–26 Mb), and BTA 21 (56–57 Mb). These regions contain, amongst others, the following candidate genes: <i>NCK1</i>, <i>MSTN</i>, <i>KCNA3</i>, <i>LCORL</i>, <i>NCAPG</i>, and <i>RIN3</i>.