PSVIII-41 Study of functional variants in homozygous islands in Nelore cattle

Abstract The aim of this study was to identify functional variants within runs of homozygosity (ROH) islands present in the genome of Nellore cattle. Genotypic information of 3,492 animals and 755,319 single nucleotide polymorphism (SNPs), were used. ROH segments were detected using PLINK software. Only ROH segments shared by more than 50% of the population individuals were used for identifying homozygosity islands. The islands functional variants were classified using the VEP tool (predictor of variant effect) from ENSEMBL software. If the variant SIFT score was less than 0.05 it was considered to be “deleterious,” otherwise it was “tolerant.” We found five islands of homozygosity, located in chromosome 5, 7, 12, 21 and 26. Within the islands, a total of 1,181 variants were processed by VEP and all of them were recognized as existing variants. In total, 51 overlapped genes and 69 overlapped transcripts were found. Most of the variants were SNPs located in the intronic regions (55%), followed by intergenic spaces (14%), upstream (13%) and downstream gene variants (12%). The intronic variants can be related to specific QTLs, either because they are associated with regions affecting gene expression or in linkage disequilibrium with the causative mutation or even because they have an unknown function. Only a small portion of the variants is in synonymous regions (4%), splice regions (1%), untranslated regions (UTRs) (1%) or are missense variants (1%). We have found 11 missense variants, being three considered deleterious and eight tolerant. The deleterious variants were annotated: INHBC, SMIM33 e FBXW4 genes. The knowledge of functional variants distribution is important for improving annotation of the bovine genome. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001 and by São Paulo Research Foundation FAPESP (grants 2018/04313-7 and 2017/10630–2).

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Warmblood fragile foal syndrome causative single nucleotide polymorphism frequency in horses in Ireland

Irish Veterinary Journal ◽

10.1186/s13620-021-00206-1 ◽

2021 ◽

Vol 74 (1) ◽

Author(s):

Áine Rowe ◽

Sharon Flanagan ◽

Gerald Barry ◽

Lisa M. Katz ◽

Elizabeth A. Lane ◽

...

Keyword(s):

Autosomal Recessive ◽

Scientific Literature ◽

Genetic Test ◽

Low Frequency ◽

Autosomal Recessive Disorder ◽

Causative Mutation ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Hair Samples ◽

Heterozygous Carriers

Abstract Background Warmblood Fragile Foal Syndrome (WFFS) is an autosomal recessive disorder caused by a mutation in the procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 (PLOD1) gene. Homozygosity for the mutation results in defective collagen synthesis which clinically manifests as the birth of non viable or still born foals with abnormally fragile skin. While the mutation has been identified in non Warmblood breeds including the Thoroughbred, to date all homozygous clinically affected cases reported in the scientific literature are Warmblood foals. The objective of this study was to investigate the carrier frequency of the mutation in the Thoroughbred and sport horse populations in Ireland. Methods A test was developed at the UCD School of Veterinary Medicine using real-time PCR to amplify the PLOD1 gene c.2032G > A variant. A subset of the samples was also submitted to an external laboratory with a licensed commercial WFFS genetic test. Results Warmblood Fragile Foal Syndrome genotyping was performed on hair samples from 469 horses representing 6 different breeds. Six of 303 (1.98%) sport horses tested and three of 109 (2.75%) Thoroughbreds tested were heterozygous for the WFFS polymorphism (N/WFFS). The WFFS polymorphism was not identified in the Standardbred, Cob, Connemara, or other pony breeds. Conclusions The study identified a low frequency of the WFFS causative mutation in sport horses and Thoroughbreds in Ireland, highlighting the importance of WFFS genetic testing in order to identify phenotypically normal heterozygous carriers and to prevent the birth of nonviable foals.

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Mitochondrial DNA single nucleotide polymorphism associated with weight estimated breeding values in Nelore cattle (Bos indicus)

Genetics and Molecular Biology ◽

10.1590/s1415-47572007000600005 ◽

2007 ◽

Vol 30 (4) ◽

pp. 1058-1063 ◽

Cited By ~ 4

Author(s):

Fernando Henrique Biase ◽

Flávio Vieira Meirelles ◽

Ricardo Gunski ◽

Pedro Alejandro Vozzi ◽

Luiz A.F. Bezerra ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Mitochondrial Dna ◽

Bos Indicus ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Breeding Values ◽

Estimated Breeding Values ◽

Nelore Cattle

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HandyCNV: Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH

10.1101/2021.04.05.438403 ◽

2021 ◽

Author(s):

Jinghang Zhou ◽

Liyuan Liu ◽

Thomas J Lopdell ◽

Dorian Garrick ◽

Yuangang Shi

Keyword(s):

Copy Number Variants ◽

R Package ◽

Single Nucleotide Polymorphism Genotyping ◽

Runs Of Homozygosity ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Livestock Species ◽

One Stop ◽

Analysis System ◽

User Friendly

Here we present an R package for summarizing, annotating, converting, comparing and visualizing CNV (copy number variants) and ROH (runs of homozygosity) detected from SNP (single nucleotide polymorphism) genotyping data. This one-stop post-analysis system is standardized, comprehensive, reproducible, timesaving and user friendly for research in humans and most diploid livestock species.

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3′-Untranslated regions are important in mRNA localization and translation: lessons from selenium and metallothionein

Biochemical Society Transactions ◽

10.1042/bst0320990 ◽

2004 ◽

Vol 32 (6) ◽

pp. 990-993 ◽

Cited By ~ 30

Author(s):

J. Hesketh

Keyword(s):

Nuclear Localization ◽

Transcriptional Control ◽

Regulatory Elements ◽

Mrna Localization ◽

Untranslated Regions ◽

Physiological Effects ◽

Nucleotide Polymorphisms ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Control Of Gene Expression

There is increasing evidence that 3′-UTRs (3′-untranslated regions) of mRNAs contain regulatory elements that have important roles in post-transcriptional control of gene expression. For example, 3′-UTRs are important in determining mRNA localization and directing selenocysteine insertion during selenoprotein synthesis. Metallothionein mRNA is localized around the nucleus and associated with the cytoskeleton; this is determined by the 3′-UTR. Deletion and mutagenesis studies are defining the nature of the signal. Incorrect mRNA localization prevents subsequent nuclear localization of metallothionein protein and affects its function. Selenium (Se) is incorporated as selenocysteine into approx. 30 mammalian proteins by a mechanism that requires a specific structure within the 3′-UTR of the corresponding mRNAs. When Se supply is low the effect on selenoprotein expression is not uniform but shows differential effects that are tissue- and protein-specific; there is a ‘prioritization’ of selenoprotein synthesis that is partly influenced by the 3′-UTRs of the different mRNAs. Single-nucleotide polymorphisms in the gene regions corresponding to 3′-UTRs could potentially influence gene regulation. We have discovered a common polymorphism in a part of the glutathione peroxidase 4 gene which corresponds to the 3′-UTR, and our recent results suggest that this single-nucleotide polymorphism has functional and physiological effects, as well as altered frequency in disease.

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Litter Size of Sheep (Ovis aries): Inbreeding Depression and Homozygous Regions

Genes ◽

10.3390/genes12010109 ◽

2021 ◽

Vol 12 (1) ◽

pp. 109

Author(s):

Lin Tao ◽

Xiaoyun He ◽

Xiangyu Wang ◽

Ran Di ◽

Mingxing Chu

Keyword(s):

Litter Size ◽

Inbreeding Depression ◽

Embryo Implantation ◽

Ovis Aries ◽

Runs Of Homozygosity ◽

Nucleotide Polymorphism ◽

Genetic Management ◽

Single Nucleotide ◽

Important Trait ◽

Hu Sheep

Ovine litter size (LS) is an important trait showing variability within breeds. It remains largely unknown whether inbreeding depression on LS exists based on genomic homozygous regions, and whether the homozygous regions resulted from inbreeding are significantly associated with LS in sheep. We here reanalyze a set of single nucleotide polymorphism (SNP) chip of six breeds to characterize the patterns of runs of homozygosity (ROH), to evaluate inbreeding levels and inbreeding depressions on LS, and to identify candidate homozygous regions responsible for LS. Consequently, unique ROH patterns were observed among six sheep populations. Inbreeding depression on LS was only found in Hu sheep, where a significant reduction of 0.016, 0.02, and 0.02 per 1% elevated inbreeding FROH4–8, FROH>8 and the total inbreeding measure was observed, respectively. Nine significantly homozygous regions were found for LS in Hu sheep, where some promising genes for LS possibly via regulation of the development of oocytes (NGF, AKT1, and SYCP1), fertilization (SPAG17, MORC1, TDRD9, ZFYVE21, ADGRB3, and CKB), embryo implantation (PPP1R13B, INF2, and VANGL1) and development (DPPA2, DPPA4, CDCA4, CSDE1, and ADSSL1), and reproductive health (NRG3, BAG5, CKB, and XRCC3) were identified. These results from the present study would provide insights into the genetic management and complementary understandings of LS in sheep.

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