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Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters.

Zenger KR, Khatkar MS, Jones DB, Khalilisamani N, Jerry DR, Raadsma HW.

Front Genet. 2019 Jan 23;9:693. doi: 10.3389/fgene.2018.00693. eCollection 2018. Review.


Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus): a dietary-specialist species distributed across heterogeneous environments.

Kjeldsen SR, Raadsma HW, Leigh KA, Tobey JR, Phalen D, Krockenberger A, Ellis WA, Hynes E, Higgins DP, Zenger KR.

Heredity (Edinb). 2019 May;122(5):525-544. doi: 10.1038/s41437-018-0144-4. Epub 2018 Sep 12.


De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome.

Huerlimann R, Wade NM, Gordon L, Montenegro JD, Goodall J, McWilliam S, Tinning M, Siemering K, Giardina E, Donovan D, Sellars MJ, Cowley JA, Condon K, Coman GJ, Khatkar MS, Raadsma HW, Maes GE, Zenger KR, Jerry DR.

Sci Rep. 2018 Sep 10;8(1):13553. doi: 10.1038/s41598-018-31148-4.


The State of "Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization.

Guppy JL, Jones DB, Jerry DR, Wade NM, Raadsma HW, Huerlimann R, Zenger KR.

Front Genet. 2018 Aug 3;9:282. doi: 10.3389/fgene.2018.00282. eCollection 2018. Review.


A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei.

Jones DB, Jerry DR, Khatkar MS, Raadsma HW, Steen HV, Prochaska J, Forêt S, Zenger KR.

Sci Rep. 2017 Sep 4;7(1):10360. doi: 10.1038/s41598-017-10515-7.


Identification of key contributors in complex population structures.

Neuditschko M, Raadsma HW, Khatkar MS, Jonas E, Steinig EJ, Flury C, Signer-Hasler H, Frischknecht M, von Niederhäusern R, Leeb T, Rieder S.

PLoS One. 2017 May 16;12(5):e0177638. doi: 10.1371/journal.pone.0177638. eCollection 2017.


Use of diagnostic reports to estimate prevalence and distribution of skeletal lesions in young Thoroughbreds.

Axling JM, Castle K, Velie BD, Tammen I, Thomson PC, Hamilton NA, Raadsma HW, Lindgren G, Jeffcott LB, Nicholas FW.

Vet J. 2016 Aug;214:72-6. doi: 10.1016/j.tvjl.2016.03.022. Epub 2016 Mar 31.


A Meta-Assembly of Selection Signatures in Cattle.

Randhawa IA, Khatkar MS, Thomson PC, Raadsma HW.

PLoS One. 2016 Apr 5;11(4):e0153013. doi: 10.1371/journal.pone.0153013. eCollection 2016.


Targeted Analysis Reveals an Important Role of JAK-STAT-SOCS Genes for Milk Production Traits in Australian Dairy Cattle.

Arun SJ, Thomson PC, Sheehy PA, Khatkar MS, Raadsma HW, Williamson P.

Front Genet. 2015 Dec 15;6:342. doi: 10.3389/fgene.2015.00342. eCollection 2015.


netview p: a network visualization tool to unravel complex population structure using genome-wide SNPs.

Steinig EJ, Neuditschko M, Khatkar MS, Raadsma HW, Zenger KR.

Mol Ecol Resour. 2016 Jan;16(1):216-27. doi: 10.1111/1755-0998.12442. Epub 2015 Jul 24.


Composite Selection Signals for Complex Traits Exemplified Through Bovine Stature Using Multibreed Cohorts of European and African Bos taurus.

Randhawa IA, Khatkar MS, Thomson PC, Raadsma HW.

G3 (Bethesda). 2015 Apr 30;5(7):1391-401. doi: 10.1534/g3.115.017772.


Heritability of epistaxis in the Australian Thoroughbred racehorse population.

Velie BD, Raadsma HW, Wade CM, Knight PK, Hamilton NA.

Vet J. 2014 Nov;202(2):274-8. doi: 10.1016/j.tvjl.2014.06.010. Epub 2014 Jun 16.


Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep.

Randhawa IA, Khatkar MS, Thomson PC, Raadsma HW.

BMC Genet. 2014 Mar 17;15:34. doi: 10.1186/1471-2156-15-34.


A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection.

Jones DB, Jerry DR, Khatkar MS, Raadsma HW, Zenger KR.

BMC Genomics. 2013 Nov 20;14:810. doi: 10.1186/1471-2164-14-810.


Genetic correlations among canine hip dysplasia radiographic traits in a cohort of Australian German Shepherd Dogs, and implications for the design of a more effective genetic control program.

Wilson BJ, Nicholas FW, James JW, Wade CM, Raadsma HW, Thomson PC.

PLoS One. 2013 Nov 7;8(11):e78929. doi: 10.1371/journal.pone.0078929. eCollection 2013.


QTL and association analysis for skin and fibre pigmentation in sheep provides evidence of a major causative mutation and epistatic effects.

Raadsma HW, Jonas E, Fleet MR, Fullard K, Gongora J, Cavanagh CR, Tammen I, Thomson PC.

Anim Genet. 2013 Aug;44(5):547-59. doi: 10.1111/age.12033. Epub 2013 Mar 4.


Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16.

Hamilton NA, Tammen I, Raadsma HW.

PLoS One. 2013;8(2):e55434. doi: 10.1371/journal.pone.0055434. Epub 2013 Feb 8.


Comparative transcriptome analyses reveal conserved and distinct mechanisms in ovine and bovine lactation.

Singh M, Thomson PC, Sheehy PA, Raadsma HW.

Funct Integr Genomics. 2013 Mar;13(1):115-31. doi: 10.1007/s10142-012-0307-y. Epub 2013 Jan 17.


NetView: a high-definition network-visualization approach to detect fine-scale population structures from genome-wide patterns of variation.

Neuditschko M, Khatkar MS, Raadsma HW.

PLoS One. 2012;7(10):e48375. doi: 10.1371/journal.pone.0048375. Epub 2012 Oct 31.


Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle.

Khatkar MS, Moser G, Hayes BJ, Raadsma HW.

BMC Genomics. 2012 Oct 8;13:538. doi: 10.1186/1471-2164-13-538.


Heritability and phenotypic variation of canine hip dysplasia radiographic traits in a cohort of Australian German shepherd dogs.

Wilson BJ, Nicholas FW, James JW, Wade CM, Tammen I, Raadsma HW, Castle K, Thomson PC.

PLoS One. 2012;7(6):e39620. doi: 10.1371/journal.pone.0039620. Epub 2012 Jun 27.


Identification of a null allele in genetic tests for bovine leukocyte adhesion deficiency in Pakistani Bos indicus × Bos taurus cattle.

Nasreen F, Malik NA, Qureshi JA, Raadsma HW, Tammen I.

Mol Cell Probes. 2012 Dec;26(6):259-62. doi: 10.1016/j.mcp.2012.01.004. Epub 2012 Feb 22.


Resistance to liver fluke infection in the natural sheep host is correlated with a type-1 cytokine response.

Pleasance J, Wiedosari E, Raadsma HW, Meeusen E, Piedrafita D.

Parasite Immunol. 2011 Sep;33(9):495-505. doi: 10.1111/j.1365-3024.2011.01305.x.


Mapping quantitative trait loci (QTL) in sheep. IV. Analysis of lactation persistency and extended lactation traits in sheep.

Jonas E, Thomson PC, Hall EJ, McGill D, Lam MK, Raadsma HW.

Genet Sel Evol. 2011 Jun 21;43:22. doi: 10.1186/1297-9686-43-22.


Symmetry of hip dysplasia traits in the German Shepherd Dog in Australia.

Wilson BJ, Nicholas FW, James JW, Wade CM, Tammen I, Raadsma HW, Castle K, Thomson PC.

J Anim Breed Genet. 2011 Jun;128(3):230-43. doi: 10.1111/j.1439-0388.2010.00903.x. Epub 2011 Apr 13.


Innate and adaptive resistance of Indonesian Thin Tail sheep to liver fluke: a comparative analysis of Fasciola gigantica and Fasciola hepatica infection.

Pleasance J, Raadsma HW, Estuningsih SE, Widjajanti S, Meeusen E, Piedrafita D.

Vet Parasitol. 2011 Jun 10;178(3-4):264-72. doi: 10.1016/j.vetpar.2011.01.037. Epub 2011 Jan 26.


Racing towards the genes for speed.

Hamilton NA, Raadsma HW.

Vet J. 2011 Oct;190(1):5-6. doi: 10.1016/j.tvjl.2011.01.002. Epub 2011 Feb 9. No abstract available.


Fecundity in adult Haemonchus contortus parasites is correlated with abomasal tissue eosinophils and γδ T cells in resistant Canaria Hair Breed sheep.

González JF, Hernández A, Meeusen EN, Rodríguez F, Molina JM, Jaber JR, Raadsma HW, Piedrafita D.

Vet Parasitol. 2011 Jun 10;178(3-4):286-92. doi: 10.1016/j.vetpar.2011.01.005. Epub 2011 Jan 18.


Deterministic models of breeding scheme designs that incorporate genomic selection.

Pryce JE, Goddard ME, Raadsma HW, Hayes BJ.

J Dairy Sci. 2010 Nov;93(11):5455-66. doi: 10.3168/jds.2010-3256.


Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers.

Moser G, Khatkar MS, Hayes BJ, Raadsma HW.

Genet Sel Evol. 2010 Oct 16;42:37. doi: 10.1186/1297-9686-42-37.


Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL.

Cavanagh CR, Jonas E, Hobbs M, Thomson PC, Tammen I, Raadsma HW.

Genet Sel Evol. 2010 Sep 16;42:36. doi: 10.1186/1297-9686-42-36.


Increased production through parasite control: can ancient breeds of sheep teach us new lessons?

Piedrafita D, Raadsma HW, Gonzalez J, Meeusen E.

Trends Parasitol. 2010 Dec;26(12):568-73. doi: 10.1016/ Epub 2010 Sep 15.


The sheep genome reference sequence: a work in progress.

International Sheep Genomics Consortium, Archibald AL, Cockett NE, Dalrymple BP, Faraut T, Kijas JW, Maddox JF, McEwan JC, Hutton Oddy V, Raadsma HW, Wade C, Wang J, Wang W, Xun X.

Anim Genet. 2010 Oct;41(5):449-53. doi: 10.1111/j.1365-2052.2010.02100.x. Review.


Improving animal and human health through understanding liver fluke immunology.

Piedrafita D, Spithill TW, Smith RE, Raadsma HW.

Parasite Immunol. 2010 Aug;32(8):572-81. doi: 10.1111/j.1365-3024.2010.01223.x. Review.


Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates.

Khatkar MS, Hobbs M, Neuditschko M, Sölkner J, Nicholas FW, Raadsma HW.

BMC Bioinformatics. 2010 Apr 7;11:171. doi: 10.1186/1471-2105-11-171.


A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers.

Moser G, Tier B, Crump RE, Khatkar MS, Raadsma HW.

Genet Sel Evol. 2009 Dec 31;41:56. doi: 10.1186/1297-9686-41-56.


The utility of estimated breeding values for inherited disorders of dogs.

Thomson PC, Wilson BJ, Wade CM, Shariflou MR, James JW, Tammen I, Raadsma HW, Nicholas FW.

Vet J. 2010 Mar;183(3):243-4. doi: 10.1016/j.tvjl.2009.12.002. Epub 2009 Dec 29. No abstract available.


Mapping quantitative trait loci (QTL) in sheep. II. Meta-assembly and identification of novel QTL for milk production traits in sheep.

Raadsma HW, Jonas E, McGill D, Hobbs M, Lam MK, Thomson PC.

Genet Sel Evol. 2009 Oct 22;41:45. doi: 10.1186/1297-9686-41-45.


The influence of extracellular matrix and prolactin on global gene expression profiles of primary bovine mammary epithelial cells in vitro.

Riley LG, Gardiner-Garden M, Thomson PC, Wynn PC, Williamson P, Raadsma HW, Sheehy PA.

Anim Genet. 2010 Feb;41(1):55-63. doi: 10.1111/j.1365-2052.2009.01964.x. Epub 2009 Sep 29.


A functional genomics approach to evaluate candidate genes located in a QTL interval for milk production traits on BTA6.

Sheehy PA, Riley LG, Raadsma HW, Williamson P, Wynn PC.

Anim Genet. 2009 Aug;40(4):492-8. doi: 10.1111/j.1365-2052.2009.01862.x. Epub 2009 Mar 18.


Mapping quantitative trait loci (QTL) in sheep. I. A new male framework linkage map and QTL for growth rate and body weight.

Raadsma HW, Thomson PC, Zenger KR, Cavanagh C, Lam MK, Jonas E, Jones M, Attard G, Palmer D, Nicholas FW.

Genet Sel Evol. 2009 Apr 24;41:34. doi: 10.1186/1297-9686-41-34.


The effect of footrot on weight gain in sheep.

Nieuwhof GJ, Bishop SC, Hill WG, Raadsma HW.

Animal. 2008 Oct;2(10):1427-36. doi: 10.1017/S1751731108002619.


Predicting genetic merit for mastitis and fertility in dairy cattle using genome wide selection and high density SNP screens.

Raadsma HW, Moser G, Crump RE, Khatkar MS, Zenger KR, Cavanagh JAL, Hawken RJ, Hobbs M, Barris W, Solkner J, Nicholas FW, Tier B.

Dev Biol (Basel). 2008;132:219-223. doi: 10.1159/000317163.


Host responses during experimental infection with Fasciola gigantica and Fasciola hepatica in Merino sheep II. Development of a predictive index for Fasciola gigantica worm burden.

Raadsma HW, Kingsford NM, Suharyanta, Spithill TW, Piedrafita D.

Vet Parasitol. 2008 Jul 4;154(3-4):250-61. doi: 10.1016/j.vetpar.2008.03.018. Epub 2008 Apr 4.


Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel.

Khatkar MS, Nicholas FW, Collins AR, Zenger KR, Cavanagh JA, Barris W, Schnabel RD, Taylor JF, Raadsma HW.

BMC Genomics. 2008 Apr 24;9:187. doi: 10.1186/1471-2164-9-187.


Comparative experimental Haemonchus contortus infection of two sheep breeds native to the Canary Islands.

González JF, Hernández A, Molina JM, Fernández A, Raadsma HW, Meeusen EN, Piedrafita D.

Vet Parasitol. 2008 May 31;153(3-4):374-8. doi: 10.1016/j.vetpar.2008.02.019. Epub 2008 Mar 4.


Bulldog dwarfism in Dexter cattle is caused by mutations in ACAN.

Cavanagh JA, Tammen I, Windsor PA, Bateman JF, Savarirayan R, Nicholas FW, Raadsma HW.

Mamm Genome. 2007 Nov;18(11):808-14. Epub 2007 Oct 22.


Effect of myostatin F94L on carcass yield in cattle.

Sellick GS, Pitchford WS, Morris CA, Cullen NG, Crawford AM, Raadsma HW, Bottema CD.

Anim Genet. 2007 Oct;38(5):440-6. Epub 2007 Jul 6.


A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle.

Khatkar MS, Zenger KR, Hobbs M, Hawken RJ, Cavanagh JA, Barris W, McClintock AE, McClintock S, Thomson PC, Tier B, Nicholas FW, Raadsma HW.

Genetics. 2007 Jun;176(2):763-72. Epub 2007 Apr 15.


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