NAGRP Host of
Supplementary Data to Publications

• 2007:
  Benjaporn Somridhivej et al. Characterization, polymorphism assessment, and database construction for microsatellites from BAC end sequences of catfish: a resource for integration of linkage and physical maps. Aquaculture, Volume 275, Issues 1-4, 31 March 2008, Pages 76-80.
• 2010:
  Shaolin Wang et al. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biology 2010, 11:R8.
• 2011:
  Qinghua Nie et al. Analysis of Muscle and Ovary Transcriptome of Sus scrofa: Assembly, Annotation and Marker Discovery. DNA Res. 2011;18(5):343-51. Epub 2011 Jul 5.
• 2011:
  Zhi-Liang Hu et al. Use of Genome Sequence Information for Meat Quality Trait QTL Mining for Casual Genes and Mutations on Pig Chromosome 17. Frontiers in Livestock Genomics, 2:43. doi: 10.3389/fgene.2011.00043.
• 2012:
  Zhi-Liang Hu et al. Animal QTLdb: an improved database tool for livestock animal QTL data dissemination in the post-genome era. Nucl. Acids Res. (2013) 41 (D1): D871-D879.
• 2012:
  Terje Raudsepp et al. Genome-Wide Association Study Implicates Testis-Sperm Specific FKBP6 as a Susceptibility Locus for Impaired Acrosome Reaction in Stallions. PLoS Genet 8(12): e1003139.
• 2012:
  Petersen JL et al. Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS Genet 9(1): e1003211. doi:10.1371/journal.pgen.1003211.
• 2013:
  Petersen JL et al. Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS ONE 8(1): e54997. doi:10.1371/journal.pone.0054997.
• 2013:
  Bouabid Badaoui et al. Pig immune response to general stimulus and to porcine reproductive and respiratory syndrome virus infection: a meta-analysis approach. BMC Genomics 2013, 14:220; doi:10.1186/ 1471-2164-14-220.
• 2013:
  Lifan Zhang et al. Genome-wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay and Targhee Sheep. PLoS ONE, 2013 Jun 10;8(6):e65942. doi: 10.1371.
• 2013:
  Hu Z-L. et al. Chapter 24. Standard genetic nomenclature. In: The Genetics of Cattle, Edition 2. Ed. Garrick, D.J. and Ruvinsky A.,CAB International, Wallingford, Oxon OX10 8DE, UK (2014)
• 2013:
  McCoy AM et al. Evidence of Positive Selection for a Glycogen Synthase (GYS1) Mutation in Domestic Horse Populations. Journal of Heredity, 2013. doi: 10.1093/jhered/est075.
• 2013:
  Yniv Palti et al. A resource of single-nucleotide polymorphisms for rainbow trout generated by RAD sequencing of doubled haploids. Molecular Ecology Resources, Volume 14, Issue 3, pages 588-596, May 2014.
• 2014:
  Luyang Sun et al. Identification and Analysis of Genome-Wide SNPs Provide Insight into Signatures of Selection and Domestication in Channel Catfish (Ictalurus punctatus). PLoS One. 2014 Oct 14;9(10):e109666. doi: 10.1371/journal.pone.0109666.
• 2014:
  ALI ALI et al. Characterization of the rainbow trout spleen transcriptome andidentification of immune-related genes. Front. Genet., 14 October 2014 | doi: 10.3389/fgene.2014.00348.
• 2014:
  Laercio R. et al. The genetic architecture of climatic adaptation of tropical cattle. PLoS One. 2014 Nov 24;9(11):e113284. doi: 10.1371.
• 2014:
  Carrie J. et al. SERPINB11 Mutation Associated with Novel Hoof Specific Phenotype in Connemara Ponies. PLoS Genet. 2015 Apr; 11(4): e1005122.
• 2014:
  Mohamed Salem et al. Transcriptome assembly, gene annotation and tissue gene expression atlas of the rainbow trout. PLoS One. 2015 Mar 20;10(3):e0121778. doi: 10.1371/journal.pone.0121778.
• 2015:
  Holl HM et al. Generation of a de novo transcriptome from equine lamellar tissue. BMC Genomics. 2015 Oct 3;16(1):739.
• 2015:
  Michelle R. et al. Genome-wide association identifies SLC2A9 and NLN gene regions as associated with entropion in domestic sheep. PLoS One. 2015 Jun 22;10(6):e0128909. doi: 10.1371/journal.pone.0128909.
• 2015:
  Petersen JL et al. The American Quarter Horse: Population structure and relationship to the Thoroughbred. Journal of Heredity. 105:148-162.
• 2015:
  AM McCoy et al. Identification and Validation of Risk Loci for Osteochondrosis in Standardbreds. BMC Genomics, 201617:41, DOI: 10.1186/s12864-016-2385-z.
• 2015:
  Michelle R. et al. Ovine leukocyte profiles do not associate with variation in the prion gene, but are breed dependent. Anim Genet. 2016 Feb;47(1):136-7. doi: 10.1111/age.12381.
• 2015:
  Rafet Al-Tobasei et al. Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout. PLoS ONE 11(2): e0148940. doi:10.1371/journal.pone.0148940.
• 2015:
  Petersen JL et al. Genome-wide SNP data shows little different iation between the Appaloosa and other American stock horse breeds. Animal Genetics. 46:585-586.
• 2016:
  Zhenqiang Xu et al. Combination analysis of Genome-wide association and transcriptome sequencing of residual feed intake in quality chickens. BMC Genomics. 2016 Aug 9;17:594. doi: 10.1186/s12864-016-2861-5.
• 2016:
  Staiger EA et al. Loci impacting polymorphic gait in the Tennessee Walking Horse. Journal of Animal Science (2016) doi: 10.2527/jas.2015-9936.
• 2016:
  Francesca Bertolini et al. Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks. Anim Genet. doi:10.1111/age.12522.
• 2016:
  Mohammed Al et al. Application of Genomic Estimation Methods of Inbreeding and Population Structure in an Arabian Horse Herd. J Hered (2017) 108 (4): 361-368.
• 2016:
  Mohammed A. et al. Genome-Wide Scans Reveal a Quantitative Trait Locus for Withers Height in Horses Near the ANKRD1 Gene. Journal of Equine Veterinary Science, Jan 2018, 60(67-73). DOI.10.1016/j.jevs.2017.05.008.
• 2017:
  Saria Almarzook et al. Genetic diversity of Syrian Arabian horses. Animal Genetics, 48(4): 486-489.
• 2017:
  Xiuling Li et al. Identification of positive selection in pigs by comparing linkage disequilibrium variances. Animal Genetics, 48(5), 600-605.
• 2017:
  Wei-Feng Peng et al. A genome-wide association study reveals candidate genes for the supernumerary nipple phenotype in sheep (Ovis aries). Anim Genet. 2017 Oct;48(5):570-579.
• 2017:
  Snelling W.M. et al. Linkage disequilibrium among commonly genotyped SNP and variants detected from bull sequence. Anim Genet, 48: 516–522.
• 2017:
  AJ Cross et al. Genome wide association of changes in swine feeding behavior due to heat stress. Genet Sel Evol. 2018 Mar 25;50(1):11.
• 2017:
  C. Kumar et al. Population structure, genetic diversity, and selection signatures within seven indigenous Pakistani goat populations. Anim Genet. 2018 Dec;49(6):592-604.
• 2017:
  Mohammed Al et al. Whole Genome Detection of Sequence and Structural Polymorphisms in Six Diverse Horses. BioRxiv, doi: https://doi.org/10.1101/545111.
• 2017:
  Xiaohong He et al. Genome-wide association analysis reveals the common genetic locus for both the typical and atypical polycerate phenotype in Tibetan sheep. Anim Genet. 2018 Apr;49(2):142-143.
• 2017:
  A. Niggeler et al. A genome-wide significant association on chromosome 2 for footrot resistance/susceptibility in Swiss White Alpine sheep. Animal Genetics, 2017 Oct; 48(6):.
• 2017:
  J. H. et al. Regulatory gene network from a genome-wide association study for sow lifetime productivity traits. Anim Genet. 2018 Jun;49(3):254-258.
• 2017:
  Yuan Wang et al. Genome-wide association study for reproductive traits in a Large White pig population. Animal Genetics, 49(2):127-131.
• 2017:
  S. Ishihara et al. Genetic relationships among Vietnamese local pigs investigated using genome-wide SNP markers. Animal Genetics, Jan. 15, 2018, DOI: 10.1111/age.12633.
• 2017:
  Onzima RB et al. Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds. Journal of Animal Genetics, 49(1):59-70. doi:10.1111/age.12631.
• 2017:
  Nicole Dürig et al. Two MC1R loss-of-function alleles in cream-coloured Australian Cattle Dogs and white Huskies. Animal Genetics, 2018 Aug;49(4):284-290.
• 2017:
  Orla M. et al. An independent validation study of loci associated with nematode resistance in sheep. Animal Genetics, 49: 265-268.
• 2017:
  Anina Bauer et al. A splice site variant in the SUV39H2 gene in Greyhounds with nasal parakeratosis. Anim Genet. 2018 Apr;49(2):137-140.doi: 10.1111/age.12643. Epub 2018 Feb 9.
• 2017:
  Qiong Wang et al. Genome-wide association study confirms that sex chromosome harbors a region responsible for rumplessness in Hongshan chicken. Anim Genet. 2018 Aug;49(4):326-328.
• 2017:
  Zewdu Edea et al. Genetic diversity and population structure of Ethiopian sheep populations revealed by high-density SNP markers. Front Genet. 2017 Dec 22;8:218.
• 2017:
  Anina Bauer et al. MKLN1 splicing defect in dogs with lethal acrodermatitis. PLoS Genet. 2018 Mar 22;14(3):e1007264. doi: 10.1371/journal.pgen.1007264.
• 2017:
  Ali Ali et al. Integrated analysis of lncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fillet quality traits. Nature, Scientific Reports (Open published on Aug. 14, 2018).
• 2018:
  Eberth J.E. et al. Multiple Alleles of ACAN Associated with Chondrodysplastic Dwarfism in Miniature Horses. Animal Genetics, 2018 Jul 30. doi: 10.1111/age.12682.
• 2018:
  Shunyan Jiang et al. Genome-wide association analysis reveals novel loci for hypoxia adaptability in Tibetan chicken. Anim Genet. 2018 Aug;49(4):337-339.
• 2018:
  Gao G. et al. A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing. Frontiers in Genetics, 9: 147. DOI 10.3389/fgene.2018.00147.
• 2018:
  Lei Gao et al. Genome-wide association study reveals novel genes for the ear size in sheep (Ovis aries). Anim Genet. 2018 Aug;49(4):345-348.
• 2018:
  Song-Song Xu et al. Genome-wide association analyses provide novel insights into different genetic mechanisms for litter size among sheep breeds. Front Genet. 2018 Apr 10;9:118.
• 2018:
  Muhammed Walugembe et al. Detection of selection signatures among Brazilian, Sri Lankan, and Egyptian chicken populations under different environmental conditions. Front Genet. 2018; 9: 737.
• 2018:
  Annette M. et al. Identification and Validation of Genetic Variants Predictive of Gait in Standardbred Horses. PLoS Genet. 2019 May 28;15(5): e1008146.
• 2018:
  Abulgasim Ahbara et al. Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. Frontier in Genetics, doi: 10.3389/fgene.2018.00699.
• 2018:
  Shijie Lyu et al. Reducing the interval of a growth QTL on chromosome 4 in laying hens. Anim Genet. 2018 Oct;49(5):467-471.
• 2018:
  Martijn F.L. et al. Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome. PLoS Genet 14(9): e1007661.
• 2018:
  Ahmed R. et al. Natural Selection Footprints among African Chicken Breeds and Village Ecotypes. Front Genet. 2019; 10: 376.
• 2018:
  Salvatore Mastrangelo et al. Genome-wide association study reveals the locus responsible for microtia in Valle del Belice sheep breed. Animal Genetics. 49:636-640.
• 2018:
  Li X. et al. Genome-wide association study identifies variants in the CAPN9 gene associated with umbilical hernia in pigs. Anim Genet, 50(2): 162-165.
• 2018:
  Salvatore Mastrangelo et al. Conservation status and historical relatedness of Italian cattle breeds. Genetics Selection Evolution. 50:35.
• 2018:
  Carrai M. et al. Umbilical tissue as a sampling technique for DNA testing in neonate dogs. Anim Genet. 2018 Oct;49(5):499-500.
• 2018:
  Milena Gallana et al. Genome-wide association study and heritability estimate for ectopic ureters in Entlebucher mountain dogs. Anim Genet. 2018 Dec;49(6):645-650.
• 2018:
  Alonso I. et al. Genomic differentiation among varieties of Iberian pig. SPANISH JOURNAL OF AGRICULTURAL RESEARCH. 18 (1), e0401, 9 pages (2020).
• 2018:
  Cesarani A. et al. Genome-wide variability and selection signatures in Italian island cattle breeds. Animal Genetics, 49(5), 371-383.
• 2018:
  Hofstetter S et al. A non-coding regulatory variant in the 5’-region of the MITF gene is associated with white spotted coat in Brown Swiss cattle. Anim Genet. 2019 Feb;50(1):27-32.
• 2018:
  Brian W. et al. Validation of SNP associations with bovine ovulation and twinning rate. Anim Genet. 2019 Jun;50(3):259-261.
• 2018:
  A. M. et al. Genome-wide association studies for milk production traits in Valle del Belice sheep using repeated measures. Anim Genet. 2019 Jun;50(3):311-314.
• 2018:
  Z.Edea; H.Dadi; et al. Genomic-wide scan Reveals Divergent Selection Among Taurine and Zebu Cattle Populations from Different Regions. Anim Genet. 2018 Dec;49(6):550-563.
• 2018:
  Rosalia Di et al. Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep. PLoS ONE 14(4): e0215204.
• 2018:
  Oget C. et al. Genetic diversity analysis of French goat populations reveals soft selective sweeps involved in their adaptation. Animal Genetics, Volume 50, Issue 1.
• 2018:
  Roberta Davoli et al. Genome-wide association study identifies markers associated with meat ultimate pH in Duroc pigs. Anim Genet. 2019, 50(2):154-156.
• 2018:
  AM McCoy et al. SNP‐based heritability and genetic architecture of tarsal osteochondrosis in North American Standardbred horses. Animal Genetics, 50(1); https://doi.org/10.1111/age.12738.
• 2018:
  Mirte Bosse et al. Deleterious alleles in the context of domestication, inbreeding and selection. Evolutionary Applications Volume 12, Issue 1.
• 2018:
  Ranran Liu et al. Effects of genomic selection for intramuscular fat content in breast muscle in Chinese local chickens. Animal GeneticsVolume 50, Issue 1.
• 2018:
  Zhi-Liang Hu et al. Building a Livestock Genetic and Genomic Information Knowledgebase Through Integrative Developments of Animal QTLdb and CorrDB. Nucleic Acids Research, Database Issue, 47(D1): D701-D710, January 9, 2019.
• 2018:
  Martijn F.L. et al. Loss of function mutations in essential genes cause embryonic lethality in pigs. PLoS genetics 15(3).
• 2018:
  Samantha K et al. Robust remapping of equine SNP array coordinates to EquCab3. Anim Genet. 2019 Feb;50(1):114-115.
• 2018:
  Haile Berihulay et al. Genetic diversity and population structure in multiple Chinese goat populations using SNP panel. Anim Genet. 2019 Jun;50(3):242-249.
• 2018:
  Salvatore Mastrangelo et al. Genome-wide analysis identify the potential causative genes explaining the phenotypic variability in Pinzirita sheep. Animal Genetics 50: 189-190.
• 2019:
  Falomir-Lockhart AH et al. Polledness in Argentinean Creole Cattle, five centuries surviving. Anim Genet. 2019 Aug;50(4):381-385.
• 2019:
  Rabiul Islam1 et al. Genome-wide association analysis reveals the genetic locus for high reproduction trait in Chinese Arbas Cashmere goat. Genes Genomics. 2020 Aug;42(8):893-899.
• 2019:
  Samantha K et al. Exploration of fine-scale recombination rate variation in the domestic horse. Genome Res. 2019. 29: 1744-1752.
• 2019:
  Grilz-Seger G et al. Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size. Anim Genet. 2019 Aug;50(4):334-346.
• 2019:
  Huang H et al. Genome-wide association study identifies energy metabolism genes for resistance to ketosis in Chinese Holstein cattle. Anim Genet. 2019 Aug;50(4):376-380.
• 2019:
  Hao Li et al. Genome-wide association study of milk production traits in a crossbred dairy sheep population using three statistical models. Animal Genetics, DOI: 10.1111/age.12956.
• 2019:
  C. Jia et al. Genome-wide association study-mediated identification of genetic loci associated with growth traits at weaning in polled yak. Animal Genetics, 2019, 51(2): 300-305.
• 2019:
  Guangtu Gao et al. A New Single Nucleotide Polymorphism Database for North American Atlantic Salmon Generated Through Whole Genome Resequencing. Frontiers in Genetics. 11:85. DOI: 10.3389/fgene.2020.00085.
• 2020:
  Juber Herrera-Uribe et al. Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure. Frontiers in Genetics. Epigenomics and Epigenetics. 20 August 2020.