Genomic Analysis of Inbreeding Depression on Productive Traits in Rubia Galega Beef Cattle Breed

Abstract

In autochthonous livestock breeds with small populations, such as the Rubia Galega from Galicia (Spain), mating between relatives is common and can lead to inbreeding depression. Genomic inbreeding coefficients were estimated for 4984 animals using~63,000 SNPs to assess inbreeding depression in four key traits: age at first calving (AFC) with 3503 records, calving interval (CI) with 3315 records, birth weight (BW) with 4878 records and weight at 210 days (W210) with 3285 records. Runs of homozygosity were sorted by length ([1,2], (2,4], (4,8], (8,16], > 16 Mb), and the corresponding inbreeding coefficients (FROH>1, FROH>2, FROH>4, FROH>8, FROH>16) were calculated using the consecutiveRUNs R package. A Genomic BLUP (GBLUP) was conducted for each FROH estimate using the BLUPF90+ programs. The results revealed significant inbreeding depression for AFC and CI, whereas W210 and BW exhibited similar inbreeding trends, but the effects of inbreeding on these traits were not statistically significant. To further explore the genetic basis of inbreeding depression, SNPs located within ROHs were tested, though a t-test, for their association with phenotypic traits. Genes located in significant regions (−log(p-value) > 3 from t-test) were annotated using EnsemblBioMart within a ± 0.5 Mb window. Recent inbreeding (ROH > 8 Mb) showed significant negative effects on reproductive traits, and key genomic regions—particularly on chromosome 2 involving MSTN, NAB1, and COL5A2—were linked to increased AFC and reduced BW and W210; ROH-based inbreeding estimates proved effective in detecting inbreeding depression in this native breed. Overall, ROH-based analyses revealed genomic regions and candidate genes, notably MSTN, contributing to inbreeding depression and key production traits in Rubia Galega cattle.