Linkage disequilibrium in Brazilian Santa Inês breed, Ovis aries

Gastrointestinal nematodes are a major cause of disease in grazing livestock; however, individual animals differ in their response to infection. To identify genes whose expression correlates with resistance status, transcriptional profiling of resistant and susceptible sheep was undertaken. Transcription profiles were taken at three time points during the growth of lambs. The number of genes differentially expressed increased as animals were exposed to longer nematode challenge. Almost 300 genes, with a variety of functions, were differentially expressed overall, although genes more highly expressed in resistant animals typically had major histocompatibility complex (MHC) II, free radical scavenging or smooth muscle-specific functions. The Ovar-DQA1 gene was 8.4-fold more highly expressed in resistant animals. This was due in part to a higher frequency of DQA1 null alleles in susceptible animals. The null allele of DQA1 was also associated with susceptibility in a separate selection flock, presenting the hypothesis that failure to present parasite antigens to immune cells led to nematode susceptibility. To test this hypothesis, commercial rams from three breeds were genotyped for the null allele of DQA1. The homozygous null allele was associated with susceptibility in only one of the three breeds tested indicating that the null allele does not cause susceptibility to intestinal parasites per se but is probably in linkage disequilibrium with additional polymorphisms in the MHC region. A combination of these polymorphisms may contribute to susceptibility in some populations. The extent of linkage disequilibrium between polymorphisms may vary from breed to breed or population to population.

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Hemograma de ovinos (Ovis aries) sadios da raça Santa Inês criados na região de Piedade, estado de São Paulo: influências etárias e sexuais

Brazilian Journal of Veterinary Research and Animal Science ◽

10.11606/issn.1678-4456.bjvras.2016.79665 ◽

2017 ◽

Vol 53 (4) ◽

pp. 1

Author(s):

Rafael Cedric Moller Meneghini ◽

Fernano José Benesi ◽

Laura Cristina Sant'Anna Henriques ◽

Huber Rizzo ◽

Enoch Brandão de Souza Meira Junior ◽

...

Keyword(s):

Sao Paulo ◽

Ovis Aries ◽

São Paulo ◽

Santa Inês

Foi investigada a influência dos fatores etários e sexuais sobre o hemograma de ovinos sadios da raça Santa Inês, criados na região de Piedade, no Estado de São Paulo. O hematócrito e o número de hemácias apresentaram maiores valores nas fêmeas mais jovens e houve um decréscimo gradual durante o desenvolvimento etário dos animais. Em contraposição, o número total de leucócitos foi menor nos animais mais jovens e apresentou elevação gradual com a evolução da idade dos animais.

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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

Genetics Selection Evolution ◽

10.1186/s12711-019-0508-0 ◽

2019 ◽

Vol 51 (1) ◽

Cited By ~ 1

Author(s):

Mario Graziano Usai ◽

Sara Casu ◽

Tiziana Sechi ◽

Sotero L. Salaris ◽

Sabrina Miari ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Principal Components ◽

Fixed Effects ◽

Structured Populations ◽

Ovis Aries ◽

Qtl Detection ◽

Dairy Sheep ◽

Milk Traits ◽

Molecular Information ◽

Genomic Regions

Abstract Background The 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. Methods A 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. Results PCA 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. Conclusions PCA 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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Reproductive and productive characteristics of hair sheep raised in the tropical region grassland of Brazil

Research Society and Development ◽

10.33448/rsd-v9i9.7287 ◽

2020 ◽

Vol 9 (9) ◽

pp. e331997287

Author(s):

Jardeson de Souza Pinheiro ◽

Paloma Eleutério ◽

Samuel Pinho Silva ◽

Caio Júlio Lima Herbster ◽

Judite Antunes Cipriano ◽

...

Keyword(s):

Body Weight ◽

Coat Color ◽

Tropical Climate ◽

Ovis Aries ◽

Genetic Group ◽

Reproductive Efficiency ◽

Tropical Region ◽

Hair Sheep ◽

Tropical Conditions ◽

Santa Inês

We aimed to characterize the energetic profile of hair sheep (Ovis aries) raised on pasture in a tropical climate country and verify it is influence on productive and reproductive parameters. A total of 68 non-pregnant adult ewes were randomly distributed into four genetic groups (GGs) according to coat color (Red-coated Santa Inês GG – 17, Black-coated Santa Inês GG – 13, White-coated Morada Nova GG – 28 and Red-coated Morada Nova GG – 10). We collected blood samples at the beginning and at the end of the breeding season. The reproductive efficiency of the ewes was evaluated by fertility, prolificacy, lamb survival rate, and lamb body weight at birth and weaning. We performed statistical analyses using the package PROC GLM and the chi-square (χ2) test from SAS software. The genetic group influenced serum glucose and β-hydroxybutyrate concentrations, prolificacy, and lamb body weight. Male lambs were heavier than female lambs at birth and weaning. Twin lambs were lighter at birth and at weaning than were single lambs. The genetic group, lamb birth rank, and sex influenced the lamb body weight at birth and weaning. This study presents important information on the reproductive efficiency of these hair sheep that are relevant to tropical climate countries. The blood parameters found in this research show that there are important metabolic differences between hair sheep in the semi-arid region of Northeast Brazil. Morada Nova sheep with independent white coat color, higher reproductive performance in tropical conditions.

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Ocorrência de ovinos (Ovis aries) soropositivos ao vírus da Leucemia Bovina no Brasil

Brazilian Journal of Veterinary Research and Animal Science ◽

10.11606/issn.1678-4456.bjvras.2010.26811 ◽

2010 ◽

Vol 47 (6) ◽

pp. 483 ◽

Cited By ~ 1

Author(s):

Claudia Del Fava ◽

Marianna De Lima Freitas Basílio ◽

Talita Maria de Donato ◽

Claudia Pestana Ribeiro ◽

Líria Hiromi Okuda ◽

...

Keyword(s):

Rio Grande ◽

Sao Paulo ◽

Ovis Aries ◽

São Paulo ◽

Rio Grande Do Sul ◽

Mato Grosso ◽

Santa Inês

A ocorrência de ovinos sororreagentes ao vírus da Leucemia Bovina (VLB) pelo teste de imunodifusão em gel de ágar (IDGA) utilizando o antígeno gp51 foi avaliada no período de 2005-2007, em diferentes regiões do Brasil. Amostras foram colhidas de ovinos dos Estados do Rio Grande do Sul, Paraná, São Paulo, Pernambuco, Maranhão, Pará, Bahia, Mato Grosso, Rondônia e Acre. Duas em 35 cabanhas (5,7%) e dois em 2592 ovinos (0,077%) foram soropositivos. Os únicos animais com anticorpos contra o VLB eram fêmeas, uma com 13 meses de idade e da raça Santa Inês e a outra não se conhecia a idade e raça, ambas provenientes do Estado de São Paulo. A distribuição da soropositividade na população estudada demonstrou ser rara a infecção pelo VLB em ovinos no Brasil.

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How to better conserve with genetic data: origin and population structure of Brazilian locally adapted hair sheep (Ovis aries) breeds

10.1101/815217 ◽

2019 ◽

Author(s):

Tiago do Prado Paim ◽

Samuel Rezende Paiva ◽

Natália Martins de Toledo ◽

Michel Beleza Yamaghishi ◽

Paulo Luiz Souza Carneiro ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Resources ◽

Strong Relationship ◽

Ovis Aries ◽

East African ◽

Hair Sheep ◽

Sheep Breeds ◽

Fat Tail ◽

Santa Inês

AbstractBrazilian hair sheep constitute a genetic diversity hotspot of sheep breeds. These locally adapted genetic resources developed in harsh environments of the Brazilian Northwest (semi-arid) and maintained important traits for this region, such as parasite resistance, heat tolerance and high pelt quality. Genotypes (50K SNP chip) from seven Brazilian sheep breeds (5 hair and 2 coarse wool types) and 87 worldwide breeds were used to verify population structure, admixture and genetic diversity, using PCA and ADMIXTURE analyses. We constructed a phylogenetic tree and evaluated migration events between genetic groups using TREEMIX software. Brazilian Somali, a fat-tailed breed, was the unique breed with high relationship with East African breeds and formed a distinct cluster from other Brazilian breeds. This breed seems to contribute to formation of Santa Inês, Morada Nova and Brazilian Fat-tail breeds. Brazilian Blackbelly had a clear relationship with Barbados Blackbelly, which appeared as another group. Other Brazilian breeds seem to form a further genetic group with some recent admixtures. Morada Nova remained as a separate group, not showing a strong relationship with European or African breeds, only revealing a migration event from Sidaoun, an Algerian hair breed. Brazilian Fat-tail and Morada Nova share a common ancestor, but the first received introgressions from Brazilian Somali and Afrikaner breeds, explaining the fat-tail phenotype. Santa Inês received strong contribution from Bergamasca and had an admixed origin with recent introgressions from other breeds, mainly from Suffolk animals. In conclusion, Brazilian Somali and Brazilian Fat-tail are the most endangered sheep genetic resources in Brazil.

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Polymorphisms in MyoD1, MyoG, MyF5, MyF6, and MSTN genes in Santa Inês sheep

Pesquisa Agropecuária Brasileira ◽

10.1590/s1678-3921.pab2019.v54.01132 ◽

2019 ◽

Vol 54 ◽

Cited By ~ 1

Author(s):

Luis Paulo Batista Sousa Junior ◽

Ariana Nascimento Meira ◽

Hymerson Costa Azevedo ◽

Evandro Nevez Muniz ◽

Luiz Lehmann Coutinho ◽

...

Keyword(s):

Association Studies ◽

Ovis Aries ◽

Allele Frequencies ◽

Reference Sequence ◽

Coding Region ◽

Weinberg Equilibrium ◽

Hardy Weinberg Equilibrium ◽

Santa Inês ◽

Genotype And Allele Frequencies

Abstract: The objective of this work was to sequence the MyoD1, MyoG, MyF5, MyF6, and MSTN genes and to identify polymorphisms in Santa Inês sheep (Ovis aries). A total of 192 lambs with 240 days of age were evaluated, and these genes were sequenced to be compared with the reference sequence in the Ovis aries genome. Genotype and allele frequencies were estimated, and the Hardy-Weinberg equilibrium was tested. Fragments containing 2,493 bp (MyoD1), 1,836 bp (MyoG), 2,813 bp (MyF5), 1,126 bp (MyF6), and 2,380 bp (MSTN) were obtained, and, in these sequences, 160 variants were identified. These polymorphisms were distributed as follows: 59 (MyoD1), 24 (MyoG), 63 (MyF5), 4 (MyF6), and 10 (MSTN). One hundred and four were novel polymorphisms, 45 in MyoD1, 2 in MyoG, 56 in MyF5, and 1 in MSTN. Regarding site, 61 were in intron (27 in MyoD1, 16 in MyoG, 5 in MyF5, 3 in MyF6, and 10 in MSTN), 87 in coding region (22 in MyoD1, 8 in MyoG, 56 in MyF5, and 1 in MyF6), and 12 on 3’UTR (10 in MyoD1 and 2 in MyF5). Therefore, the MyoD family and MSTN genes have several polymorphisms in Santa Inês sheep, which can be useful for association studies.

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Association analysis and functional annotation of imputed sequence data within genomic regions influencing resistance to gastro-intestinal parasites detected by an LDLA approach in a nucleus flock of Sarda dairy sheep

Genetics Selection Evolution ◽

10.1186/s12711-021-00690-7 ◽

2022 ◽

Vol 54 (1) ◽

Author(s):

Sara Casu ◽

Mario Graziano Usai ◽

Tiziana Sechi ◽

Sotero L. Salaris ◽

Sabrina Miari ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Candidate Genes ◽

Association Analysis ◽

Functional Annotation ◽

Sequence Data ◽

Ovis Aries ◽

Differentially Expressed ◽

Phenotypic Variance ◽

Major Health Problem ◽

Functional Variants

Abstract Background Gastroinestinal nematodes (GIN) are one of the major health problem in grazing sheep. Although genetic variability of the resistance to GIN has been documented, traditional selection is hampered by the difficulty of recording phenotypes, usually fecal egg count (FEC). To identify causative mutations or markers in linkage disequilibrium (LD) to be used for selection, the detection of quantitative trait loci (QTL) for FEC based on linkage disequilibrium-linkage analysis (LDLA) was performed on 4097 ewes (from 181 sires) all genotyped with the OvineSNP50 Beadchip. Identified QTL regions (QTLR) were imputed from whole-genome sequences of 56 target animals of the population. An association analysis and a functional annotation of imputed polymorphisms in the identified QTLR were performed to pinpoint functional variants with potential impact on candidate genes identified from ontological classification or differentially expressed in previous studies. Results After clustering close significant locations, ten QTLR were defined on nine Ovis aries chromosomes (OAR) by LDLA. The ratio between the ANOVA estimators of the QTL variance and the total phenotypic variance ranged from 0.0087 to 0.0176. QTL on OAR4, 12, 19, and 20 were the most significant. The combination of association analysis and functional annotation of sequence data did not highlight any putative causative mutations. None of the most significant SNPs showed a functional effect on genes’ transcript. However, in the most significant QTLR, we identified genes that contained polymorphisms with a high or moderate impact, were differentially expressed in previous studies, contributed to enrich the most represented GO process (regulation of immune system process, defense response). Among these, the most likely candidate genes were: TNFRSF1B and SELE on OAR12, IL5RA on OAR19, IL17A, IL17F, TRIM26, TRIM38, TNFRSF21, LOC101118999, VEGFA, and TNF on OAR20. Conclusions This study performed on a large experimental population provides a list of candidate genes and polymorphisms which could be used in further validation studies. The expected advancements in the quality of the annotation of the ovine genome and the use of experimental designs based on sequence data and phenotypes from multiple breeds that show different LD extents and gametic phases may help to identify causative mutations.

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Estrutura e ultra-estrutura de membranas biológicas de ovinos da raça Santa Inês (Ovis aries, L., 1758) a fresco e conservadas em glicerina.

Biotemas ◽

10.5007/2175-7925.2012v25n2p97 ◽

2012 ◽

Vol 25 (2) ◽

Cited By ~ 1

Author(s):

Roméria Rodrigues Barbosa ◽

Leonardo Martins Leal ◽

Leandro Luis Martins ◽

Sergio Pinter Garcia Filho ◽

Andréa Cristina Scarpa Bosso ◽

...

Keyword(s):

Ovis Aries ◽

Santa Inês

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Predação e canibalismo entre protozoários ciliados (Ciliophora: Entodiniomorphida: Ophryoscolecidae) no rúmen de ovinos (Ovis aries)

Revista Brasileira de Zoologia ◽

10.1590/s0101-81752008000300010 ◽

2008 ◽

Vol 25 (3) ◽

pp. 451-455 ◽

Cited By ~ 4

Author(s):

Isabel Martinele ◽

Marta D'Agosto

Keyword(s):

Ovis Aries ◽

Santa Inês

O objetivo deste trabalho foi registrar ocorrências de predação e canibalismo em protozoários ciliados no rúmen de ovinos. Foram analisadas amostras de conteúdo ruminal de cinco ovinos mestiços Santa Inês, fistulados no rúmen, mantidos em pastagem natural de caatinga, no município de Sertânia, Pernambuco. Foram obtidas seis amostras de conteúdo ruminal de cada ovino, totalizando 30 amostras, as quais foram fixadas em formalina 18,5% (v/v). De cada amostra foi retirada uma alíquota de 1 ml de conteúdo ruminal ao qual se adicionaram três gotas de solução de lugol para a coloração e identificação dos protozoários ciliados. Estas alíquotas foram analisadas utilizando-se lâminas e lamínulas, em campos determinados randomicamente. Constatou-se a ocorrência de interações do tipo predador-presa entre ciliados de Ophryoscolecidae Stein, 1859, onde Elytroplastron bubali (Dogiel, 1928) apresentou comportamento predatório sobre Enoploplastron triloricatum (Dogiel, 1925) e sobre outras espécies de Epidinium Crawley, 1923 e de Entodinium Stein, 1859. Foram ainda observados casos de canibalismo entre espécimes de E. bubali, o que consiste no primeiro registro deste tipo de interação nesta espécie. Registra-se, ainda, pela primeira vez a ocorrência de E. bubali no rúmen de ovinos no Brasil.

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