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McHugh N, O'Brien AC, Pabiou T, McDermott K, Berry DP. Association between the prion protein genotype and animal performance traits in a large multibreed sheep population. Animal 2022; 16:100587. [PMID: 35872388 DOI: 10.1016/j.animal.2022.100587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/26/2022] Open
Abstract
Genetic susceptibility to scrapie, a fatal disease of sheep and goats, is modulated by polymorphisms in the prion protein (PrP). Neither the frequency of the PrP genotypes nor their association with animal performance has been investigated in a large multibreed Irish sheep population. Scrapie genotypes were available on 16 416 animals; the breeds represented included purebred Belclare (733), Charollais (333), Suffolk (739), Texel (1 857), Vendeen (191), and crossbreds (12 563). Performance data on lambing, lamb and ewe performance as well as health traits were available. The association between alternative approaches of describing the PrP genotype (i.e. 15 individually called PrP genotypes, five genotype classes representing susceptibility to scrapie, or number of ARR haplotypes) and animal performance were quantified using animal linear mixed models. All 15 of the possible scrapie genotypes were detected, although the frequency differed by breed. The frequency of the five PrP haplotypes in the entire population were 0.70 (ARR), 0.15 (ARQ), 0.11 (ARH), 0.02 (AHQ) and 0.01 (VRQ); the most susceptible haplotype (VRQ) was only detected in purebred Texels and crossbreds. No association was detected between the PrP genotype of either the animal or dam and any of the lambing traits (i.e. lambing difficulty score, perinatal mortality and birth weight). With the exception of ultrasound muscle depth, no association between the PrP genotype and any of the lamb performance traits (i.e. lamb BW and carcass) was observed. Lambs carrying the category four PrP genotype (i.e. ARR/VRQ) had 1.20 (SE = 0.45) mm, 1.38 (SE = 0.12) mm, 1.47 (S = 0.25) mm shallower ultrasound muscle depth relative to lambs of the less susceptible scrapie categories of 1, 2, 3, respectively (P < 0.05). Nonetheless, no association between PrP genotype and lamb carcass conformation, the ultimate end goal of producers, was detected. Ewe litter size, body condition score or lameness did not differ by PrP genotype of the ewe (P > 0.05). For ewe mature BW, ARH/VRQ ewes differed from most other ewe PrP genotypes and were, on average, 3.79 (SE = 1.66) kg heavier than ARR/ARR genotype ewes. Lamb dag score differed by dam PrP genotype (P < 0.05), although the differences were small. Results from this study show that scrapie is segregating within the Irish sheep population, but the PrP genotype was not associated with most traits investigated and, where associations were detected, the biological significance was minimal. This suggests minimal impact of selection on PrP genotype on performance, at least for the traits investigated in the present study.
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Affiliation(s)
- N McHugh
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy P61 P302, Co. Cork, Ireland.
| | - A C O'Brien
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy P61 P302, Co. Cork, Ireland
| | - T Pabiou
- Sheep Ireland, Highfield House, Shinagh, Bandon P72 X050, Co. Cork, Ireland
| | - K McDermott
- Sheep Ireland, Highfield House, Shinagh, Bandon P72 X050, Co. Cork, Ireland
| | - D P Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy P61 P302, Co. Cork, Ireland
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Steele A, Benning LG, Wirth R, Schreiber A, Araki T, McCubbin FM, Fries MD, Nittler LR, Wang J, Hallis LJ, Conrad PG, Conley C, Vitale S, O'Brien AC, Riggi V, Rogers K. Organic synthesis associated with serpentinization and carbonation on early Mars. Science 2022; 375:172-177. [PMID: 35025630 DOI: 10.1126/science.abg7905] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Water-rock interactions are relevant to planetary habitability, influencing mineralogical diversity and the production of organic molecules. We examine carbonates and silicates in the martian meteorite Allan Hills 84001 (ALH 84001), using colocated nanoscale analyses, to characterize the nature of water-rock reactions on early Mars. We find complex refractory organic material associated with mineral assemblages that formed by mineral carbonation and serpentinization reactions. The organic molecules are colocated with nanophase magnetite; both formed in situ during water-rock interactions on Mars. Two potentially distinct mechanisms of abiotic organic synthesis operated on early Mars during the late Noachian period (3.9 to 4.1 billion years ago).
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Affiliation(s)
- A Steele
- Carnegie Institution for Science, Earth and Planets Laboratory, Washington, DC 20015, USA
| | - L G Benning
- Deutsches GeoForschungsZentrum, Telegrafenberg, 14473 Potsdam, Germany.,Department of Earth Sciences, Free University of Berlin, 12249 Berlin, Germany
| | - R Wirth
- Deutsches GeoForschungsZentrum, Telegrafenberg, 14473 Potsdam, Germany
| | - A Schreiber
- Deutsches GeoForschungsZentrum, Telegrafenberg, 14473 Potsdam, Germany
| | - T Araki
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - F M McCubbin
- NASA Johnson Space Center, Houston, TX 77058, USA
| | - M D Fries
- NASA Johnson Space Center, Houston, TX 77058, USA
| | - L R Nittler
- Carnegie Institution for Science, Earth and Planets Laboratory, Washington, DC 20015, USA
| | - J Wang
- Carnegie Institution for Science, Earth and Planets Laboratory, Washington, DC 20015, USA
| | - L J Hallis
- School of Geographical and Earth Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - P G Conrad
- Carnegie Institution for Science, Earth and Planets Laboratory, Washington, DC 20015, USA
| | - C Conley
- NASA Ames Research Center, Mountain View, CA 94035, USA
| | - S Vitale
- Carnegie Institution for Science, Earth and Planets Laboratory, Washington, DC 20015, USA
| | - A C O'Brien
- School of Geographical and Earth Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - V Riggi
- Carnegie Institution for Science, Earth and Planets Laboratory, Washington, DC 20015, USA
| | - K Rogers
- Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Berry DP, Dunne FL, Evans RD, McDermott K, O'Brien AC. Concordance rate in cattle and sheep between genotypes differing in Illumina GenCall quality score. Anim Genet 2021; 52:208-213. [PMID: 33527466 DOI: 10.1111/age.13043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 11/30/2022]
Abstract
Proper quality control of data prior to downstream analyses is fundamental to ensure integrity of results; quality control of genomic data is no exception. While many metrics of quality control of genomic data exist, the objective of the present study was to quantify the genotype and allele concordance rate between called single nucleotide polymorphism (SNP) genotypes differing in GenCall (GC) score; the GC score is a confidence measure assigned to each Illumina genotype call. This objective was achieved using Illumina beadchip genotype data from 771 cattle (12 428 767 genotypes in total post-editing) and 80 sheep (1 557 360 SNPs genotypes in total post-editing) each genotyped in duplicate. The called genotype with the lowest associated GC score was compared to the genotype called for the same SNP in the same duplicated animal sample but with a GC score of >0.90 (assumed to represent the true genotype). The mean genotype concordance rate for a GC score of <0.300, 0.300-0.549, and ≥0.550 in the cattle (sheep in parenthesis) was 0.9467 (0.9864), 0.9707 (0.9953), and 0.9994 (0.99997) respectively; the respective allele concordance rate was 0.9730 (0.9930), 0.9849 (0.9976), and 0.9997 (0.99998). Hence, concordance eroded as the GC score of the called genotype reduced, albeit the impact was not dramatic and was not very noticeable until a GC score of <0.55. Moreover, the impact was greater and more consistent in the cattle population than in the sheep population. Furthermore, an impact of GC score on genotype concordance rate existed even for the same SNP GenTrain value; the GenTrain value is a statistical score that depicts the shape of the genotype clusters and the relative distance between the called genotype clusters.
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Affiliation(s)
- D P Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, P61 P302, Ireland
| | - F L Dunne
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, P61 P302, Ireland
| | - R D Evans
- Irish Cattle Breeding Federation, Highfield House, Shinagh, Bandon, Co. Cork, P72 X050, Ireland
| | - K McDermott
- Sheep Ireland, Highfield House, Shinagh, Bandon, Co. Cork, P72 X050, Ireland
| | - A C O'Brien
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, P61 P302, Ireland
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Berry DP, Bohan A, O'Brien AC, Campion FC, McHugh N, Wall E. Heteropaternal superfecundation frequently occurs in multiple-bearing mob-mated sheep. Anim Genet 2020; 51:579-583. [PMID: 32343851 DOI: 10.1111/age.12939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 11/30/2022]
Abstract
Heteropaternal superfecundation may be defined as the fertilisation of two or more ova during the same oestrus cycle as a result of more than one coital act from different males; this results in foetuses being born in the same litter of the same age but different paternity. Heteropaternal superfecundation is more likely to occur in poly-ovulatory species like sheep; moreover, female sheep are often mob-mated with several rams concurrently, thus providing an opportunity for a given female to be served by multiple males during the same oestrus cycle. The objective of the present study was to determine the frequency of heteropaternal superfecundation in six sheep flocks where most of the ewes, lambs and rams were genotyped. A total of 685 multiple-birth litters were available where the sire, dam and all lambs were genotyped. Of the 539 pairs of twins included in the analysis, 160 (i.e. 30%) were sired by two different rams. Of the 137 sets of triplets included in the analysis, 73 (i.e. 53%) were sired by more than one ram. Of the nine sets of quadruplets, eight were sired by two rams with the remaining litter being mono-paternal. The overall incidence of heteropaternal superfecundation among litters was therefore 35%. Given that the incidence of multiple births in these flocks was 65%, heteropaternal superfecundation is expected to be relatively common in sheep; this is especially true as all but two of the litter-mates were polyzygotic. Genotyping of progeny is one practical solution to identity such individuals.
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Affiliation(s)
- D P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy Co. Cork, P61 P302, Ireland
| | - A Bohan
- Sheep Ireland, Highfield House, Shinagh, Bandon Co. Cork, P72 X050, Ireland
| | - A C O'Brien
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy Co. Cork, P61 P302, Ireland
| | - F C Campion
- Animal and Grassland Research and Innovation Centre, Teagasc, Mellows Campus, Athenry, Co. Galway, H65 R718, Ireland
| | - N McHugh
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy Co. Cork, P61 P302, Ireland
| | - E Wall
- Sheep Ireland, Highfield House, Shinagh, Bandon Co. Cork, P72 X050, Ireland
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