Detection of quantitative trait loci and putative causal variants affecting somatic cell score in dairy sheep by using a 50K SNP chip and whole-genome sequencing

Gutiérrez-Gil, Beatriz; Esteban-Blanco, Cristina; Suárez-Vega, Aroa; Arranz, Juan José

doi:10.3168/jds.2018-14736

Cited by 16 publications

(13 citation statements)

References 53 publications

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“…Moreover, whole-genome re-sequencing of target animals has been used to restrict the number of candidate polymorphisms. Thus, putative causative mutations that affect traits of economic interest have been proposed [21–24].…”

Section: Introductionmentioning

confidence: 99%

Mapping genomic regions affecting milk traits in Sarda sheep by using the OvineSNP50 Beadchip and principal components to perform combined linkage and linkage disequilibrium analysis

et al. 2019

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BackgroundThe detection of regions that affect quantitative traits (QTL), to implement selection assisted by molecular information, remains of particular interest in dairy sheep for which genetic gain is constrained by the high costs of large-scale phenotype and pedigree recording. QTL detection based on the combination of linkage disequilibrium and linkage analysis (LDLA) is the most suitable approach in family-structured populations. The main issue in performing LDLA mapping is the handling of the identity-by-descent (IBD) probability matrix. Here, we propose the use of principal component analysis (PCA) to perform LDLA mapping for milk traits in Sarda dairy sheep.MethodsA resource population of 3731 ewes belonging to 161 sire families and genotyped with the OvineSNP50 Beadchip was used to map genomic regions that affect five milk traits. The paternally and maternally inherited gametes of genotyped individuals were reconstructed and IBD probabilities between them were defined both at each SNP position and at the genome level. A QTL detection model fitting fixed effects of principal components that summarize IBD probabilities was tested at each SNP position. Genome-wide (GW) significance thresholds were determined by within-trait permutations.ResultsPCA resulted in substantial dimensionality reduction, in fact 137 and 32 (on average) principal components were able to capture 99% of the IBD variation at the locus and genome levels, respectively. Overall, 2563 positions exceeded the 0.05 GW significance threshold for at least one trait, which clustered into 75 QTL regions most of which affected more than one trait. The strongest signal was obtained for protein content on Ovis aries (OAR) chromosome 6 and overlapped with the region that harbours the casein gene cluster. Additional interesting positions were identified on OAR4 for fat content and on OAR11 for the three yield traits.ConclusionsPCA is a good strategy to summarize IBD probabilities. A large number of regions associated to milk traits were identified. The outputs provided by the proposed method are useful for the selection of candidate genes, which need to be further investigated to identify causative mutations or markers in strong LD with them for application in selection programs assisted by molecular information.

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Section: Introductionmentioning

confidence: 99%

Mapping genomic regions affecting milk traits in Sarda sheep by using the OvineSNP50 Beadchip and principal components to perform combined linkage and linkage disequilibrium analysis

et al. 2019

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“…The analysis of the genetic variability of the studied animals was carried out by considering the six resistant and six susceptible sheep as a single group, as it has been shown that a higher number of samples considered during variant calling analysis results in a higher coverage and confidence in variant calls (Piskol et al ). To ensure the quality of the variants identified, we performed the variant calling analysis with two different software packages, gatk and Samtools , such as in Gutiérrez‐Gil et al ().…”

Section: Discussionmentioning

confidence: 99%

Identification of potential functional variants underlying ovine resistance to gastrointestinal nematode infection by using RNA‐Seq

et al. 2020

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Summary In dairy sheep flocks from Mediterranean countries, replacement and adult ewes are the animals most affected by gastrointestinal nematode (GIN) infections. In this study, we have exploited the information derived from an RNA‐Seq experiment with the aim of identifying potential causal mutations related to GIN resistance in sheep. Considering the RNA‐Seq samples from 12 ewes previously classified as six resistant and six susceptible animals to experimental infection by Teladorsagia circumcincta, we performed a variant calling analysis pipeline using two different types of software, gatk version 3.7 and Samtools version 1.4. The variants commonly identified by the two packages (high‐quality variants) within two types of target regions – (i) QTL regions previously reported in sheep for parasite resistance based on SNP‐chip or sequencing technology studies and (ii) functional candidate genes selected from gene expression studies related to GIN resistance in sheep – were further characterised to identify mutations with a potential functional impact. Among the genes harbouring these potential functional variants (930 and 553 respectively for the two types of regions), we identified 111 immune‐related genes in the QTL regions and 132 immune‐related genes from the initially selected candidate genes. For these immune‐related genes harbouring potential functional variants, the enrichment analyses performed highlighted significant GO terms related to apoptosis, adhesion and inflammatory response, in relation to the QTL related variants, and significant disease‐related terms such as inflammation, adhesion and necrosis, in relation to the initial candidate gene list. Overall, the study provides a valuable list of potential causal mutations that could be considered as candidate causal mutations in relation to GIN resistance in sheep. Future studies should assess the role of these suggested mutations with the aim of identifying genetic markers that could be directly implemented in sheep breeding programmes considering not only production traits, but also functional traits such as resistance to GIN infections.

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“…Both Lacaune and Manech Tête Rousse populations were genotyped with a 960 custom-designed ovine SNP chip [10]. The chip was designed and developed within the 3SR EU project [3] based on several QTL for SCC that were previously identified in Spanish Churra [11], French Lacaune [4] and Italian Sardinian–Lacaune backcross populations ([12] and personal communication). Using these previous association studies, seven regions of interest (Table 3) on Ovis aries (OAR) chromosomes 2, 3, 5, 16 and 18 were selected based on commonalities among populations found at the time (in 2012) or on their high significance.…”

Section: Methodsmentioning

confidence: 99%

A validation study of loci associated with mastitis resistance in two French dairy sheep breeds

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et al. 2019

Genet Sel Evol

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Background The identification of loci associated with resistance to mastitis or of the causative mutations may be helpful in breeding programs for dairy sheep as it is for cattle worldwide. Seven genomic regions that control milk somatic cell counts, an indirect indicator of udder infection, have already been identified in sheep (Spanish Churra, French Lacaune and Italian Sardinian–Lacaune backcross populations). In this study, we used a 960 custom-designed ovine single nucleotide polymorphism (SNP) chip in Lacaune and Manech Tête Rousse dairy sheep to validate these seven genomic regions associated with mastitis. Results The most significant SNP ( rs868996547) on Ovis aries chromosome (OAR) 3 was a previously described mutation in the suppressor of cytokine signalling 2 ( SOCS2 ) gene. An antagonist effect of this causal candidate between health and growth in Lacaune sheep was confirmed. Effects of the mutation on the infectious status of the udder, i.e. increases in milk somatic cell counts and bacteria shedding, were also identified. This SNP was not present in the data available on Manech Tête Rousse. Three other regions associated with mastitis were also confirmed on OAR16 (Manech Tête Rousse), 19 (Lacaune) and 2 (both breeds). For the OAR2 region, we validated previously detected SNPs in several other breeds (Sarda, Churra, and Chios). For significant SNPs in the four mastitis regions, the effect varied from 0.24 to 0.67 phenotypic standard deviation of the traits. Two of the mastitis quantitative trait loci (QTL) regions (OAR2 and 16) that we validated here were also associated in opposite ways with milk production traits in both populations. Conclusions These results indicate, at least in part, a genomic basis for the trade-off between milk production and mastitis resistance. Four of the seven mastitis QTL regions that were previously identified in independent populations, were confirmed in this study, which demonstrates partial sharing of mastitis-related genetic mechanisms between different distant dairy sheep populations.

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Detection of quantitative trait loci and putative causal variants affecting somatic cell score in dairy sheep by using a 50K SNP chip and whole-genome sequencing

Cited by 16 publications

References 53 publications

Mapping genomic regions affecting milk traits in Sarda sheep by using the OvineSNP50 Beadchip and principal components to perform combined linkage and linkage disequilibrium analysis

Mapping genomic regions affecting milk traits in Sarda sheep by using the OvineSNP50 Beadchip and principal components to perform combined linkage and linkage disequilibrium analysis

Identification of potential functional variants underlying ovine resistance to gastrointestinal nematode infection by using RNA‐Seq

A validation study of loci associated with mastitis resistance in two French dairy sheep breeds

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