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Evaluating the potential of(epi)genotype‑by‑low pass nanopore sequencing in dairy cattle:a study on direct genomic value and methylation analysis

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Journal of animal Science and Biotechnology 2023年第6期14卷 2276-2289页

作者： Oscar Gonzalez‑Recio Adrian Lopez‑Catalina Ramon Peiro‑Pastor Alicia Nieto‑Valle Monica Castro Almudena Fernandez dpt.mejora genetica animal INIA-CSICCtra La Coruna Km 7.528040 MadridSpain. ETSIAAB Universidad Politecnica de Madrid.Ciudad Universitaria S/N28040 MadridSpain.

Background Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome.It requires a low sequencing depth to be cost effective,which may increase the error at the genotype assigment.Third generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation,which provides added value to genotype-by-sequencing.The aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle,and the possibility to obtain methylation marks simultaneously.Results Latest nanopore chemistry(LSK14 and Q20)achieved a modal base calling accuracy of 99.55%,whereas previous kit(LSK109)achieved slightly lower accuracy(99.1%).The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99,depending on the trait(milk,fat or protein yield),with a sequencing depth as low as 2×and using the latest chemistry(LSK114).Lower sequencing depth led to biased estimates,yet with high rank correlations.The LSK109 and Q20 achieved lower accuracies(0.57-0.93).More than one million high reliable methylated sites were obtained,even at low sequencing depth,located mainly in distal intergenic(87%)and promoter(5%)regions.Conclusions This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high reliability.It may provide advantages in populations with no available SNP chip,or when a large density of markers with a wide range of allele frequencies is needed.In addition,low pass sequencing provided nucleotide methylation status of>1 million nucleotides at≥10×,which is an added value for epigenetic studies.

关键词： Genomic selection Genomic values Low pass sequencing Low sequencing imputation Polygenic risk score

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A note on the consistency of a behavioral play marker in piglets

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Journal of animal Science and Biotechnology 2014年第2期5卷 245-250页

作者： Wendy Mercedes Rauw Departamento de mejora genetica animal Instituto Nacional de Investigaciony Tecnologia Agrariay AlimentariaCrtadela Corunakm 7.5Madrid 28040Spain

Background： Play behavior has been proposed as a new potential indicator of animal welfare. animals play only if they are in a relaxed state. Play may improve adaptability to challenging environments which may be of interest in the breeding objective. Little information is available on play behavior in livestock species. The aim of the present study is to investigate whether play behavior in post-weaned piglets can be induced instantly in the presence of additional space and whether play markers are body weight, sex, and litter dependent, it is investigated whether playfulness is elicited by the moment or if this measure is consistent over different days. Methods： Thirty two piglets from four litters were released into a corridor and video recorded for eight min at 37, 41, 44 and 48 d of age. The first test was considered as an adjustment period and was not included in the analysis. In the second to the fourth test, joyful brusque movements （jumping, turning and running） were recorded with a camera and total number of movements （JOY#） and total time （JOYtime） were estimated individually. animals were weighed at 41 d of age. Results： Females had higher scores of JOY# and JOYtime than males but this was significant only for JOY# at 41 d of age （P 〈 0.05）. The effect of age was highly significant both for JOY# and JOYtime （P 〈 0.01）. animals with a higher JOY# and JOYtime also expressed a higher JOY# and JOYtime in the other tests, but this was significant only between 44 and 48 d of age （P〈 0.01）. Body weight at 41 d of age was not significantly related to JOY# and JQYtime in any of the tests. Conclusions： Locomotor play was induced instantly by the provision of increased space allowance. Litter origin had a significant effect on play behavior. In addition, locomotor play scores were consistent between two of the three tests.

关键词： Behavior Locomotor play Pigs Play marker Welfare

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Proteomic analysis of F_(1)hybrids and intermediate variants in a Littorina saxatilis hybrid zone

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Current Zoology 2022年第3期68卷 351-359页

作者： Angel P.DIZ Mónica R.ROMERO Juan GALINDO María SAURA David O.F.SKIBINSKI Emilio ROLÁN-ALVAREZ Centro de Investigación Mariña(CIM-UVIGO) Universidade de VigoVigo 36310Spain Departamento de mejora Genética animal INIAMadrid 28040Spain Institute of Life Science Swansea University Medical SchoolSwansea SA28PPUK

Proteomic analysis was carried out on the Crab(upper-shore)and Wave(lower-shore)ecotypes of Littorina saxatilis from a hybrid zone at Silleiro Cape,Spain.Proteome profiles of individual snails were obtained.Protein expression in F_(1)hybrid snails bred in the laboratory and snails with intermediate shell phenotypes collected from the mid-shore were compared with Crab and Wave ecotypes using analytical approaches used to study dominance.Multivariate analysis over many protein spots showed that the F_(1)snails are distinct from both ecotypes but closer to the Wave ecotype.The intermediate snails are highly variable,some closer to the Crab and others to the Wave ecotype.Considered on a protein by protein basis,some proteins are significantly closer in expression to the Crab and others to the Wave ecotype for both F_(1)and intermediate snails.Furthermore,a significant majority of proteins were closer in expression to the Wave ecotype for the F_(1),consistent with the multivariate analysis.No such significant majority toward either the Crab or Wave ecotype was observed for the intermediate snails.The closer similarity of F_(1)and Wave ecotype expression patterns could be the result of similar selective pressures in the similar mid-shore and low-shore environments.For a significantly larger number of proteins,intermediate snails were closer in expression to the ecotype having the lower expression,for both Crab and Wave ecotypes.This is somewhat unexpected as lower expression might be expected to be an indication of impairment of function and lower fitness.Proteomic analysis could be important for the identification of candidate proteins useful for gaining improved understanding of adaptation and barriers to gene flow in hybrid zones.

关键词： F_(1)hybrids gene expression marine invertebrates molecular phenotype reproductive isolation speciation

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Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations

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Journal of animal Science and Biotechnology 2014年第1期5卷 38-52页

作者： Luis Gomez-Raya Amanda M Hulse David Thain Wendy M Rauw Departamento de mejora Genética animal Instituto Nacional deInvestigación y Tecnología Agraria y Alimentaria (INIA) Interdisciplinary Program in Genetics Texas A&M University College Station Department of animal Biotechnology University of Nevada

A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 （SD 0.00） and 0.19 （SD 0.03） for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by： a） estimation of the recombination fraction and LD in consecutive SNPs using family information, b） linkage analyses between fragments, c） phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual （sire level）. SNPs for which the sire and calf were heterozygotes became informative （over 90%） after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes （with at least 20 SNP） in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.

关键词： Breeding Haplotype phasing Linkage disequilibrium SNP

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Genomic patterns of homozygosity and inbreeding depression in MurcianoGranadina goats

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Journal of animal Science and Biotechnology 2022年第3期13卷 721-734页

作者： María Gracia Luigi-Sierra Almudena Fernández Amparo Martínez Dailu Guan Juan Vicente Delgado Javier FernándezÁlvarez Vincenzo Landi Francesc Xavier Such Jordi Jordana María Saura Marcel Amills Centre for Research in Agricultural Genomics(CRAG) CSIC-IRTA-UAB-UBUniversitat Autònoma de Barcelona08193 BellaterraSpain Departamento de mejora Genética animal INIACarretera de la Coruña km 7528040 MadridSpain Departamento de Genética Universidad de Córdoba14071 CórdobaSpain Department of Veterinary Medicine University of Bari“Aldo Moro”62 per Casamassima km.370010 ValenzanoSPItaly Group of Research in Ruminants(G2R) Department of Animal and Food ScienceUniversitat Autònoma de Barcelona(UAB)BellaterraBarcelonaSpain Departament de Ciència animal i dels Aliments Facultat de VeterinàriaUniversitat Autònoma de Barcelona08193 BellaterraSpain

Background:Inbreeding depression can adversely affect traits related to fitness,reproduction and productive performance.Although current research suggests that inbreeding levels are generally low in most goat breeds,the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data.Results:We genotyped 1040 goats with the Goat SNP50 BeadChip.This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns.We detected38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1,2,4,6,14,16 and 17.Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes.Four regions on chromosomes 8 and 25were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count.Notably,these regions contain several genes related with immunity,such as SYK,IL27,CCL19 and CCL21.Moreover,one region on chromosome 2 was significantly associated with inbreeding depression for milk yield.Conclusions:Although genomic inbreeding levels are low in Murciano-Granadina goats,significant evidence of inbreeding depression for the logarithm of the somatic cell count,a phenotype closely associated with udder health and milk yield,have been detected in this population.Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis,which is one of the main causes of dairy goat culling.

关键词： Goat Inbreeding Milk yield Murciano-Granadina Somatic cell score

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Fine‑tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book:the case of the Pura Raza Española horse

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Journal of animal Science and Biotechnology 2023年第2期14卷 515-528页

作者： Davinia Isabel Perdomo‑Gonzalez Nora Laseca Sebastian Demyda‑Peyras Mercedes Valera Isabel Cervantes Antonio Molina Departamento Agronomia Escuela Tecnica Superior de Ingenieria AgromomicaUniversidad de SevillaCtra Utrera Km 141013 SevillaSpain Departamento de genetica Universidad de CordobaCordobaSpain Facultad de Ciencias Veterinarias Universidad Nacional de La PlataLa PlataArgentina Consejo Nacional de Investigaciones Cientificas y Tecnicas(CONICET) La PlataArgentina Departamento de Produccion animal Facultad de VeterinariaUniversidad Complutense de MadridMadridSpain.

Background:Estimating inbreeding,which is omnipresent and inevitable in livestock populations,is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding.Inbreeding coefficients have been historically estimated by using pedigree information;however,over the last decade,genome-base inbreeding coefficients have come to the forefront in this field.The Pura Raza Espanola(PRE)horse is an autochthonous Spanish horse breed which has been recognised since 1912.The total PRE population(344,718 horses)was used to estimate Classical(F),Ballou’s ancestral,Kalinowski’s ancestral,Kalinowski’s new and the ancestral history coefficient values.In addition,genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques(methods of moments-FHOM-,the diagonal elements of the genomic-FG-,and hybrid matrixes-FH-)and ROH measures(FRZ).The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse,with proven parenteral information for the last 40 years and a high degree of completeness(over 90%for the last 70 years)will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.Results:The mean values of the pedigree-based inbreeding coefficients ranged from 0.01(F for the last 3 generations-F3-)to 0.44(ancestral history coefficient)and the mean values of genomic-based inbreeding coefficients varied from 0.05(FRZ for three generations,FH and FHOM)to 0.11(FRZ for nine generations).Significant correlations were also found between pedigree and genomic inbreeding values,which ranged between 0.58(F3 with FHOM)and 0.79(F with FRZ).In addition,the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total

关键词： Genomic inbreeding Horses Pedigree inbreeding

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Impact of hormonal modulation at proestrus on ovarian responses and uterine gene expression of suckled anestrous beef cows

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Journal of animal Science and Biotechnology 2018年第1期9卷 77-90页

作者： Manoel Francisco de Sá Filho Angela Maria Gonella-Diaza Mariana Sponchiado Marcio Ferreira Mendanha Guilherme Pugliesi Roney dos Santos Ramos Sónia Cristina da Silva Andrade Gustavo Gasparin Luiz Lehmann Coutinho Marcelo Demarchi Goissis Fernando Silveira Mesquita Pietro Sampaio Baruselli Mario Binelli Departamento de Reproducao animal FMVZ USP Sao Paulo SP Brazil Departamento de genetica e Biologia Evolutiva IB-USP- Sao Paulo SP Brazil Laboratorio de Biotecnologia animal ESALQ USP Av Padua Dias Piracicaba SP 11 Brazil Universidade Federal do Pampa Uruguaiana RS Brazil Universidade de Sao Paulo Faculdade de Medicina Veterinriae Zootecnia Departamento de Reprodcao Animal Avenida Duque de Caxias Norte 225 Pirassununga SP Zip Code 13635900 Brazil

Background： This study evaluated the impact of hormonal modulation at the onset of proestrus on ovarian response and uterine gene expression of beef cows.Methods： A total of 172 anestrous beef cows were assigned to one of four groups according to the treatment with estradiol cypionate（ECP） and/or equine chorionic gonadotropin（eCG） [CON（n = 43）, ECP（n = 43）, eCG（n = 44）and ECP ＋ eCG（n = 42）].Results： ECP-treated cows（ECP and ECP ＋ eCG groups） presented greater occurrence of estrus（44.6% vs. 65.4%; P = 0.01） and pregnancy per AI [47.1% vs. 33.3%; P = 0.07], but similar progesterone（P4） concentration at subsequent diestrus than cows not treated with ECP（CON and eCG groups）. Nonetheless, eCG-treated cows（eCG and ECP ＋ eCG groups） presented larger follicle at timed AI（12.6 ± 0.3 vs. 13.5 ± 0.3 mm; P = 0.03）, greater ovulation rate（96.5%vs. 82.6%; P = 0.008） and greater P4 concentration at d 6（3.9 ± 0.2 vs. 4.8 ± 0.2 ng/mL; P = 0.001） than cows not treated with eCG（CON and ECP groups）. Next, cows with a new corpus luteum 6 d after TAI were submitted to uterine biopsy procedure. Uterine fragments [CON（n = 6）, ECP（n = 6）] were analyzed by RNA-Seq and a total of 135 transcripts were differentially expressed between groups（73 genes up-regulated by ECP treatment）. Subsequently,uterine samples were analyzed by q PCR（genes associated with cell proliferation）. ECP treatment induced greater abundance of PTCH2（P = 0.07） and COL4 A1（P = 0.02）, whereas suppressed EGFR（P = 0.09） expression. Conversely, eCG treatment increased abundance of HB-EGF（P = 0.06）, ESR2（P = 0.09）, and ITGB3（P = 0.05）, whereas it reduced transcription of ESR1（P = 0.05）. Collectively, supplementation with ECP or eCG at the onset of proestrous of anestrous beef cows influenced ovarian responses, global and specific endometrial gene expression.Conclusion： Proestrus estradiol regulate the endometrial transcriptome, particularly stimulating proliferative activity in the endometrium.

关键词： Cattle eCG Endometrium Estradiol Transcriptome

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Different maternal investment strategies for male and female calves in a polygynous mammal

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Current Zoology 2019年第3期65卷 269-277页

作者： Francisco CEACERO Martina KOMARKOVA Andres J.GARCIA Laureano GALLEGO Department of animal Science and Food Processing Faculty of Tropical AgriSciencesCzech University of Life Sciences Kamycka 12916500 Praha 6-Suchdol Czech Republic Department of Ethology Institute of Animal Science Pratelstvi 815 10401 Praha - Uhnneves Czech Republic Instituto de Investigacion en Recursos Cinegeticos (IREC) Consejo Superior de Investigaciones Cientificas-Universidad de Castilla-La Mancha-Junta de Comunidades de Castilla-La Mancha (CSIC-UCLM-JCCM) Ronda de Toledo s/n 13071 Ciudad RealSpain Seccion de Recursos Cinegeticos y Ganaderos Instituto de Desarrollo Regional (IDR)02071 AlbaceteSpain Departamento de Ciencia y Tecnologia Agroforestal y genetica ETSIAM Universidad de Castilla-La Mancha(UCLM)02071 AlbaceteSpain

Mater nal effects occur whe n the phe no type of the mother in flue nces that of the young to the detriment of her survival, growth or fitn ess. The in vestment of the mother can be affected by mater nal body condition and/or experience. Trivers-Willard Hypothesis (TWH) and Local Resource Competition Hypothesis (LRCH) are the main hypotheses used to explain bias in birth sex-ratios in mammals, as well as for sex-biased maternal investment. Both hypotheses suggest that a different amount of investment must be expected according to the sex of the young. However, recent studies suggest that these differences are not in quantity but in the strategies: mechanisms and objectives may differ for each sex. We studied how maternal characteristics (age, body mass, body condition, and domi nance status) influence re leva nt aspects of the birth and early growth of the calf (birth date, birth body mass, body mass at weaning, and body condition at weaning) separately for each sex;and how that investment is mediated by milk production and composition (lactose, fat, and protein). One hundred eighty-eight newborns from 75 captive red deer hinds aged from 2 to 19 years were analyzed. The main differential investment observed was related to birth date: when producing a female, hinds give birth earlier in the season only if they have a good body condition;however, when gestating a male it is the older hinds those which deliver earlier. Subsequently, milk production and composition are correlated with birth body mass in female calves, but to weaning body mass in males. Thus, only hind body mass affects the weaning body mass of female calves, compared with age and hind body mass in males. These results suggest that while TWH fits the maternal investment strategy found for male calves, it is LRCH which correlates with the maternal investment patterns observed for females.

关键词： birth date body condition local resources competition hypothesis milk production sex-ratio Trivers-Willard hypothesis

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An elastin-like recombinamer-based bioactive hydrogel embedded with mesenchymal stromal cells as an injectable scaffold for osteochondral repair

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Regenerative Biomaterials 2019年第6期6卷 335-347页

作者： Filippo Cipriani Blanca Arino Palao Israel Gonzalez de Torre Aurelio Vega Castrillo Hector Jose Aguado Hernandez Matilde Alonso Rodrigo Angel Jose Alvarez Barcia Ana Sanchez Veronica Garcıa Diaz Monica Lopez Pena Jose Carlos Rodriguez-Cabello Technical Proteins Nanobiotechnology S.L. Paseo Belen 9AValladolid 47011Spain Departamento de traumatologıa Hospital Clınico de ValladolidAv.Ramon y Cajal 3Valladolid 47003Spain Bioforge University of Valladolid CIBER-BBNPaseo de Belen 19Valladolid 47011Spain SIBA-UVA:servicio investigacion y bienestar animal University of ValladolidC/Plaza de Santa Cruz 8Valladolid 47002Spain Instituto de Biologıa y genetica Molecular(IBGM) Universidad de Valladolid y CSICCalle Sanz y Fores 3Valladolid 47003Spain Facultad de veterinaria Campus UniversitarioAvda.Carballo Calero s/nLugo 27002Spain

The aim of this study was to evaluate injectable,in situ cross-linkable elastin-like recombinamers(ELRs)for osteochondral repair.Both the ELR-based hydrogel alone and the ELR-based hydrogel embedded with rabbit mesenchymal stromal cells(rMSCs)were tested for the regeneration of critical subchondral defects in 10 New Zealand rabbits.Thus,cylindrical osteochondral defects were filled with an aqueous solution of ELRs and the animals sacrificed at 4months for histological and gross evaluation of features of biomaterial performance,including integration,cellular infiltration,surrounding matrix quality and the new matrix in the defects.Although both approaches helped cartilage regeneration,the results suggest that the specific composition of the rMSC-containing hydrogel permitted adequate bone regeneration,whereas the ELR-based hydrogel alone led to an excellent regeneration of hyaline cartilage.In conclusion,the ELR cross-linker solution can be easily delivered and forms a stable well-integrated hydrogel that supports infiltration and de novo matrix synthesis.

关键词： biopolymer animal test cartilage bone

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Presence of blaOXA-48-carrying IncF plasmid in an Escherichia fergusonii strain isolated from a sugarcane soil

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Pedosphere 2020年第2期30卷 293-294页

作者： Jessica Aparecida Silva MORETTO Joao Pedro Rueda FURLAN Vania Santos BRAZ Tamires Aparecida BITENCOURT Eliana Guedes STEHLING Departamento de Analises Clinicas Toxicologicas e BromatologicasFaculdade de Ciencias Farmaceuticas de Ribeirao PretoUniversidade de Sao PauloRibeirao Preto SP 14040-903(Brazil Departamento de genetica Faculdade de Medicina de Ribeirao PretoUniversidade de Sao PauloRibeirao Preto SP 14040-903(Brazil

Dear Editor,A large number of antimicrobial agents used for the treatment of humans and animals reach water sources and agricultural soils in different ways,including animal excreta.Therefore,antimicrobial-resistant bacteria,carrying important antimicrobial resistance genes(ARGs),circulate between humans,animals,and the environment,giving attention to the concept of One Health(Topp,2017;Tiedje et al.,2019).

关键词： soil soils sugarcane

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