Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats

Abstract

Background Inbreeding depression can adversely affect traits related to fitness, reproduction and productive performance. Although current research suggests that inbreeding levels are generally low in most goat breeds, the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data. Results We genotyped 1040 goats with the Goat SNP50 BeadChip. This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns. We detected 38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1, 2, 4, 6, 14, 16 and 17. Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes. Four regions on chromosomes 8 and 25 were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count. Notably, these regions contain several genes related with immunity, such as SYK, IL27, CCL19 and CCL21. Moreover, one region on chromosome 2 was significantly associated with inbreeding depression for milk yield. Conclusions Although genomic inbreeding levels are low in Murciano-Granadina goats, significant evidence of inbreeding depression for the logarithm of the somatic cell count, a phenotype closely associated with udder health and milk yield, have been detected in this population. Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis, which is one of the main causes of dairy goat culling.

Analysis of the genomic landscape of inbreeding in two divergent groups of Spanish Florida goats

“…The whole population averaged 28 ROH with a length of 3.14 Mb. Similar results were observed in goat breeds characterized by average values of inbreeding (Cortellari et al, 2021;Luigi-Sierra et al, 2022). However, the separate analysis of HI and LI animals showed large differences in the number and average length of ROH segments in HI compared with LI.…”

“…Its negative consequences are evidenced mainly in traits related to fertility and adaptation to environmental stress (Doekes et al, 2021). Despite the importance of such traits in extensive production systems, specific studies assessing inbreeding in goats are still scarce (Dadousis et al, 2021; Luigi‐Sierra et al, 2022; Oget et al, 2019; Onzima et al, 2018).…”

“…Finally, the length of the ROH fragments is associated with the occurrence of an ancestral (short ROH) or recent (long ROH) inbreeding event (Howrigan et al, 2011), revealing genetic insights associated with the selection history of a given population or breed. Despite ROH analysis is largely performed in livestock (Meyermans et al, 2020), specific studies in goat populations are still scarce and very novel (Cardoso et al, 2018; Dadousis et al, 2021; Islam et al, 2019; Luigi‐Sierra et al, 2022).…”

Relationship between inbreeding and milk production traits in two Italian dairy sheep breeds

“…Moreover, several studies showed that inbreeding based on ROH provides a better measure of individual inbreeding than using pedigree information (Ferenčaković et al, 2013b ; Forutan et al, 2018 ). Thus, F ROH has been largely adopted as inbreeding coefficient to study depression phenomena in cattle (e.g., Doekes et al, 2019 ; Hidalgo et al, 2021 ; Pilon et al, 2021 ), sheep (Antonios et al, 2021 ; Tao et al, 2021a ) and goat (Luigi‐Sierra et al, 2022 ).…”

An empirical evaluation of the estimation of inbreeding depression from molecular markers under suboptimal conditions

“…Numerous studies have demonstrated the growing applicability of genomic inbreeding in both wild and domestic populations (e.g., Antonios et al, 2021;Foster et al, 2021;Gagnon et al, 2019;Luigi-Sierra et al, 2022;Saura et al, 2015;Townsend & Jamieson, 2013).…”