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. 2022 Mar 10;13(1):35.
doi: 10.1186/s40104-022-00684-5.

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

María Gracia Luigi-Sierra  1 , Almudena Fernández  2 , Amparo Martínez  3 , Dailu Guan  1 , Juan Vicente Delgado  3 , Javier Fernández Álvarez  3 , Vincenzo Landi  4 , Francesc Xavier Such  5 , Jordi Jordana  6 , María Saura  7 , Marcel Amills  8   9
Affiliations

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

María Gracia Luigi-Sierra et al. J Anim Sci Biotechnol. .

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.

Keywords: Goat; Inbreeding; Milk yield; Murciano-Granadina; Somatic cell score.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
A Number of ROH classified according to their length. Purple and yellow bars represent the counts of ROH shorter and longer than 5 Mb, respectively. B Number of ROH classified according to their length category by the farm of origin
Fig. 2
Fig. 2
Relationship between ROH number and length in 1040 Murciano-Granadina goats genotyped with the Goat SNP50 BeadChip
Fig. 3
Fig. 3
A Proportion of individuals with homozygous genotypes for each SNP marker. The y-axis displays the proportion of individuals for which a specific SNP displays a homozygous genotype, while the x-axis corresponds to the positional coordinates of SNPs distributed in the 29 caprine autosomes. B ROH hotspots identified in the population of Murciano-Granadina goats under study. The y-axis displays the frequency at which a given SNP is found within a ROH in the population; while the x-axis corresponds to the positional coordinates of SNPs distributed in the 29 caprine autosomes. Markers above the red line are in the top 1% of each category (homozygosity or frequency of being within a ROH). Markers highlighted in green are located in genomic regions consistently identified as regions of high homozygosity and ROH hotspots
Fig. 4
Fig. 4
Boxplots depicting the magnitude and dispersion of molecular inbreeding FROH, FROHLong, FROHShort, FHOM, FIS and FYANG coefficients estimated in 1040 female Murciano-Granadina goats. Differences in magnitude between FHOM and the other molecular coefficients are due to the fact that they indicate identity-by-state and identity-by-descent allele-sharing proportions, respectively
See this image and copyright information in PMC

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