Genetic diversity and population structure of Boer and Nubian goats in Mexico

Hidalgo-Moreno, J.A.; Núñez-Domínguez, Rafael; García-Muñiz, José Guadalupe; Ramírez‐Valverde, Rodolfo; Larios-Sarabia, Neon; Zaabza, Hafedh Ben

doi:10.1016/j.smallrumres.2020.106093

Cited by 4 publications

(2 citation statements)

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“…This inbreeding level is slightly lower than values reported for Sarda (0.04) and Sardinian Ancestral black (0.06) sheep from Italy by Cesarani et al (2019). Similar estimates for average inbreeding were reported in Boer (0.01) and Nubian (0.01) goats (Hidalgo-Moreno et al, 2020). It is possible that the inbreeding coefficient reported in this manuscript could be a result of the breeding program utilized at the studied commercial farm.…”

Section: Discussionsupporting

confidence: 74%

Estimation of genetic parameters for parasite resistance and genome-wide identification of runs of homozygosity islands in Florida Cracker sheep

Hidalgo,

Estrada-Reyes,

Ogunade

et al. 2023

Front. Anim. Sci.

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In this study, we estimated genetic parameters for parasite resistance traits and the distribution of runs of homozygosity islands in Florida Cracker sheep. The dataset contained 365 animals with phenotypic records at 38 days post-infection for fecal egg count (FEC), packed cell volume (PCV), FAMACHA score (FAM), and body condition score (BCS). The pedigree file contained 695 animals born between 2016 and 2020 and included 279 individuals with genotypes. Genetic parameters were estimated using a multi-trait model with a Bayesian implementation via Gibbs sampling in the GIBBS3F90 program. Heritability was 0.33 ± 0.09 for FEC, 0.31 ± 0.10 for FAM, 0.22 ± 0.09 for PCV, and 0.19 ± 0.07 for BCS. The genetic correlation between FEC and FAM was 0.51 ± 0.21; the remaining genetic correlations had large posterior standard deviations and yielded 95% posterior intervals including zero or with values out of the parameter space because of our small dataset. Analysis of the distribution of runs of homozygosity islands revealed 113 hot spots with annotated genes related to immune response and parasite resistance traits. Our results suggest that the genetic selection for FAMACHA score can be effective in improving parasite resistance because of its ease of recording, high heritability, and favorable genetic correlation with FEC. Additionally, runs of homozygosity islands related to parasite resistance could harbor important candidate genes for controlling this trait in Florida Cracker sheep.

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Section: Discussionsupporting

confidence: 74%

Estimation of genetic parameters for parasite resistance and genome-wide identification of runs of homozygosity islands in Florida Cracker sheep

Hidalgo,

Estrada-Reyes,

Ogunade

et al. 2023

Front. Anim. Sci.

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“…The analysis of the effects of inbreeding has been historically performed using pedigree information, but those estimations are only reliable in deep pedigrees (Kardos et al, 2015). This is particularly relevant in goats because pedigree databases are characterized in some cases by a moderate deepness (Hidalgo‐Moreno et al, 2020; Paiva et al, 2020). During the last decade, inbreeding studies shifted to the use of genomic‐based methodologies, mostly because they are more efficient to detect runs of homozygosity (ROH) (Ceballos et al, 2018), which are long continuous homozygous stretches located across the genome.…”

Section: Introductionmentioning

confidence: 99%

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

Ziegler

Molina

Ramón

et al. 2023

J Animal Breeding Genetics

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The analysis of the genomic landscape of inbreeding using runs of homozygosity (ROH) patterns is becoming an interesting tool to partially understand phenotypic differences among individuals. In this study, we analysed genome-wide ROH patterns in two groups of Florida goats. We first determined the inbreeding levels of each individual by calculating ROH-based inbreeding coefficients (F ROH ). Then, the individuals were divided into two groups based on F ROH : high inbreeding (HI, F ROH >0.1) and low inbreeding (LI, F ROH <0.03). Finally, we performed an extensive in-depth analysis of ROH distribution in each group separately. We found a higher abundance of short ROH in LI, whereas long ROH was more frequent in HI. Furthermore, ROH abundance was not evenly distributed among chromosomes within groups, with some chromosomes showing larger numbers of ROH, like CHI6, CHI7 and CHI27. A different landscape was observed in recent inbreeding (ROH >8 Mb), with significant increases in CHI6, CHI11 and CHI28.Determination of genomic regions with significantly increased ROH (ROH islands-ROHi) showed 13 ROHi related to whole inbreeding and five ROHi associated with recent inbreeding analysis. Within these genomic regions, 123 and 101 genes were identified in HI and LI, respectively, including 10 and seven candidate genes previously related to production, fertility and heat resistance in goats and livestock species.

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