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Research Output 1989 2019

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2019

A large-scale genome-wide association study in U.S. Holstein cattle

Jiang, J., Ma, L., Prakapenka, D., VanRaden, P. M., Cole, J. B. & Da, Y., Jan 1 2019, In : Frontiers in Genetics. 10, MAY, 412.

Research output: Contribution to journalArticle

Open Access
Genome-Wide Association Study
Single Nucleotide Polymorphism
Milk Proteins
Fertility
Fats
1 Citation (Scopus)

Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls

Jiang, J., Cole, J. B., Freebern, E., Da, Y., VanRaden, P. M. & Ma, L., Dec 1 2019, In : Communications Biology. 2, 1, 212.

Research output: Contribution to journalArticle

Open Access
agronomic traits
bulls
Holstein
Genes
cattle
4 Citations (Scopus)

Genome changes due to artificial selection in U.S. Holstein cattle

Ma, L., Sonstegard, T. S., Cole, J. B., Vantassell, C. P., Wiggans, G. R., Crooker, B. A., Tan, C., Prakapenka, D., Liu, G. E. & Da, Y., Feb 11 2019, In : BMC Genomics. 20, 1, 128.

Research output: Contribution to journalArticle

Open Access
Fertility
Genome
Immunity
Single Nucleotide Polymorphism
Genetic Selection
3 Citations (Scopus)

Symposium review: Genetics, genome-wide association study, and genetic improvement of dairy fertility traits

Ma, L., Cole, J. B., Da, Y. & VanRaden, P. M., Apr 1 2019, In : Journal of Dairy Science. 102, 4, p. 3735-3743 9 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
genetic improvement
dairy cattle
Fertility
dairies
2017
4 Citations (Scopus)

Genome-wide association study and accuracy of genomic prediction for teat number in Duroc pigs using genotyping-by-sequencing

Tan, C., Wu, Z., Ren, J., Huang, Z., Liu, D., He, X., Prakapenka, D., Zhang, R., Li, N., Da, Y. & Hu, X., Mar 29 2017, In : Genetics Selection Evolution. 49, 1, 35.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Duroc
teats
pig
genotyping
2016

Genetic composition of captive panda population

Yang, J., Shen, F., Hou, R. & Da, Y., Oct 3 2016, In : BMC genetics. 17, 1, 133.

Research output: Contribution to journalArticle

Population
Breeding
Ecosystem
Gene Pool
Inbreeding
6 Citations (Scopus)

Genomic inbreeding and relatedness in wild panda populations

Garbe, J. R., Prakapenka, D., Tan, C. & Da, Y., Aug 1 2016, In : PloS one. 11, 8, e0160496.

Research output: Contribution to journalArticle

Inbreeding
inbreeding
Ecosystem
Conservation
Genes
2015
66 Citations (Scopus)

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis

Ma, L., O'Connell, J. R., VanRaden, P. M., Shen, B., Padhi, A., Sun, C., Bickhart, D. M., Cole, J. B., Null, D. J., Liu, G. E., Da, Y. & Wiggans, G. R., Nov 1 2015, In : PLoS genetics. 11, 11, e1005387.

Research output: Contribution to journalArticle

Pedigree
pedigree
Genetic Recombination
recombination
cattle
8 Citations (Scopus)
Haplotypes
Single Nucleotide Polymorphism
Alleles
Genome
Genetic Models
2014
11 Citations (Scopus)

A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens

Feng, C., Gao, Y., Dorshorst, B., Song, C., Gu, X., Li, Q., Li, J., Liu, T., Rubin, C. J., Zhao, Y., Wang, Y., Fei, J., Li, H., Chen, K., Qu, H., Shu, D., Ashwell, C., Da, Y., Andersson, L., Hu, X. & 1 others, Li, N., Aug 28 2014, In : PLoS genetics. 10, 8, e1004576.

Research output: Contribution to journalArticle

Feathers
feather
feathers
Chickens
mutation
3 Citations (Scopus)
heritability
rainbow
Oncorhynchus mykiss
genomics
dominance (genetics)
13 Citations (Scopus)

GVCBLUP: A computer package for genomic prediction and variance component estimation of additive and dominance effects

Wang, C., Prakapenka, D., Wang, S., Pulugurta, S., Runesha, H. B. & Da, Y., Aug 9 2014, In : BMC bioinformatics. 15, 1, 270.

Research output: Contribution to journalArticle

Variance Components
Nucleotides
Polymorphism
Single Nucleotide Polymorphism
Genomics
42 Citations (Scopus)

Mixed model methods for genomic prediction and variance component estimation of additive and dominance effects using SNP markers

Da, Y., Wang, C., Wang, S. & Hu, G., Jan 30 2014, In : PloS one. 9, 1, e87666.

Research output: Contribution to journalArticle

dominance (genetics)
Breeding
Single Nucleotide Polymorphism
Maximum likelihood estimation
genomics
10 Citations (Scopus)

Quantitative genetics model as the

Wang, C. & Da, Y., Dec 17 2014, In : PLoS One. 9, 12, p. e114484 e114484.

Research output: Contribution to journalArticle

Genetic Models
quantitative genetics
Single Nucleotide Polymorphism
Inbreeding
genomics
2013
67 Citations (Scopus)

Effect of artificial selection on runs of homozygosity in U.S. Holstein cattle

Kim, E. S., Cole, J. B., Huson, H., Wiggans, G. R., Van Tassel, C. P., Crooker, B. A., Liu, G., Da, Y. & Sonstegard, T. S., Nov 14 2013, In : PloS one. 8, 11, e80813.

Research output: Contribution to journalArticle

artificial selection
homozygosity
Holstein
Genes
Genome
2012
29 Citations (Scopus)

A genome-wide scan of selective sweeps in two broiler chicken lines divergently selected for abdominal fat content

Zhang, H., Wang, S. Z., Wang, Z. P., Da, Y., Wang, N., Hu, X. X., Zhang, Y. D., Wang, Y. X., Leng, L., Tang, Z. Q. & Li, H., Dec 15 2012, In : BMC Genomics. 13, 1, 704.

Research output: Contribution to journalArticle

Abdominal Fat
Chickens
Genome
Breeding
Haplotypes
23 Citations (Scopus)

Effect of sample stratification on dairy GWAS results

Ma, L., Wiggans, G. R., Wang, S., Sonstegard, T. S., Yang, J., Crooker, B. A., Cole, J. B., Van Tassell, C. P., Lawlor, T. J. & Da, Y., Oct 6 2012, In : BMC Genomics. 13, 1, 536.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Genetic Selection
Single Nucleotide Polymorphism
Artificial Insemination
Pedigree
64 Citations (Scopus)

Genome-wide association study identified a narrow chromosome 1 region associated with chicken growth traits

Xie, L., Luo, C., Zhang, C., Zhang, R., Tang, J., Nie, Q., Ma, L., Hu, X., Li, N., Da, Y. & Zhang, X., Feb 16 2012, In : PloS one. 7, 2, e30910.

Research output: Contribution to journalArticle

Chromosomes, Human, Pair 1
Genome-Wide Association Study
growth traits
Chromosomes
Single Nucleotide Polymorphism
24 Citations (Scopus)

Selection signature analysis implicates the PC1/PCSK1 region for chicken abdominal fat content

Zhang, H., Hu, X., Wang, Z., Zhang, Y., Wang, S., Wang, N., Ma, L., Leng, L., Wang, S., Wang, Q., Wang, Y., Tang, Z., Li, N., Da, Y. & Li, H., Jul 11 2012, In : PLoS One. 7, 7, e40736.

Research output: Contribution to journalArticle

Abdominal Fat
abdominal fat
Chickens
Haplotypes
Genes
38 Citations (Scopus)

SNPEVG: A graphical tool for GWAS graphing with mouse clicks

Wang, S., Dvorkin, D. & Da, Y., Nov 30 2012, In : BMC Bioinformatics. 13, 1, 319.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Nucleotides
Polymorphism
Single Nucleotide Polymorphism
Mouse
2011
171 Citations (Scopus)

Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows

Cole, J. B., Wiggans, G. R., Ma, L., Sonstegard, T. S., Lawlor, T. J., Crooker, B. A., Van Tassell, C. P., Yang, J., Wang, S., Matukumalli, L. K. & Da, Y., Aug 11 2011, In : BMC Genomics. 12, 408.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Reproduction
Stillbirth
Genome
Health
81 Citations (Scopus)

Genome-wide association study of body weight in chicken F2 resource population

Gu, X., Feng, C., Ma, L., Song, C., Wang, Y., Da, Y., Li, H., Chen, K., Ye, S., Ge, C., Hu, X. & Li, N., Jul 19 2011, In : PloS one. 6, 7, e21872.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Single Nucleotide Polymorphism
Chickens
Genes
Body Weight
2010
57 Citations (Scopus)

Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham Heart Study data

Ma, L., Yang, J., Runesha, H. B., Tanaka, T., Ferrucci, L., Bandinelli, S. & Da, Y., Apr 6 2010, In : BMC medical genetics. 11, 1, 55.

Research output: Contribution to journalArticle

Genome-Wide Association Study
HDL Cholesterol
Single Nucleotide Polymorphism
Cholesterol
Genes
9 Citations (Scopus)

Identification of quantitative trait loci for shank length and growth at different development stages in chicken

Gao, Y., Du, Z. Q., Feng, C. G., Deng, X. M., Li, N., Da, Y. & Hu, X. X., Feb 1 2010, In : Animal Genetics. 41, 1, p. 101-104 4 p.

Research output: Contribution to journalArticle

Quantitative Trait Loci
Chickens
quantitative trait loci
chickens
Growth
11 Citations (Scopus)

Multi-locus test conditional on confirmed effects leads to increased power in genome-wide association studies

Ma, L., Han, S., Yang, J. & Da, Y., Dec 3 2010, In : PloS one. 5, 11, e15006.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Single Nucleotide Polymorphism
Genes
loci
testing
2009
6 Citations (Scopus)

Role of selection and inbreeding on the incidence of cutaneous malignant melanoma in Sinclair swine

Gomez-Raya, L., Amoss, M. S., Da, Y., Beattie, C. W., Ash, O. & Rauw, W. M., Jun 1 2009, In : Journal of Animal Breeding and Genetics. 126, 3, p. 242-249 8 p.

Research output: Contribution to journalArticle

Inbreeding
melanoma
inbreeding
Swine
incidence
62 Citations (Scopus)

The value of avian genomics to the conservation of wildlife

Romanov, M. N., Tuttle, E. M., Houck, M. L., Modi, W. S., Chemnick, L. G., Korody, M. L., Mork, E. M. S., Otten, C. A., Renner, T., Jones, K. C., Dandekar, S., Papp, J. C., Da, Y., Green, E. D., Magrini, V., Hickenbotham, M. T., Glasscock, J., McGrath, S., Mardis, E. R. & Ryder, O. A., Jul 14 2009, In : BMC Genomics. 10, SUPPL. 2, S10.

Research output: Contribution to journalArticle

Sparrows
Genomics
Chromosomes
Genome
Genetic Techniques
2008
68 Citations (Scopus)
Epistasis
Single nucleotide Polymorphism
Genome-Wide Association Study
Nucleotides
Polymorphism
2006
17 Citations (Scopus)

A genome scan for quantitative trait loci associated with body weight at different developmental stages in chickens

Gao, Y., Hu, X. X., Du, Z. Q., Deng, X. M., Huang, Y. H., Fei, J., Feng, J. D., Liu, Z. L., Da, Y. & Li, N., Jun 1 2006, In : Animal Genetics. 37, 3, p. 276-278 3 p.

Research output: Contribution to journalArticle

Quantitative Trait Loci
Chickens
quantitative trait loci
Body Weight
developmental stages
40 Citations (Scopus)

Detection of SNP epistasis effects of quantitative traits using an extended Kempthorne model

Mao, Y., London, N. R., Ma, L., Dvorkin, D. & Da, Y., Dec 13 2006, In : Physiological Genomics. 28, 1, p. 46-52 7 p.

Research output: Contribution to journalArticle

Single Nucleotide Polymorphism
Linkage Disequilibrium
Sample Size
Genetic Epistasis
Genetic Models
13 Citations (Scopus)

Single nucleotide polymorphisms in the chicken Lmbr1 gene are associated with chicken polydactyly

Huang, Y. Q., Deng, X. M., Du, Z. Q., Qiu, X., Du, X., Chen, W., Morisson, M., Leroux, S., Ponce de León, F. A., Da, Y. & Li, N., Jun 7 2006, In : Gene. 374, 1-2, p. 10-18 9 p.

Research output: Contribution to journalArticle

Polydactyly
Single Nucleotide Polymorphism
Chickens
Open Reading Frames
Genes
2005
6 Citations (Scopus)
Genomics
Sheep
Industry
Genome
Education
7 Citations (Scopus)

Statistical power for detecting epistasis QTL effects under the F-2 design

Mao, Y. & Da, Y., Mar 1 2005, In : Genetics Selection Evolution. 37, 2, p. 129-150 22 p.

Research output: Contribution to journalArticle

epistasis
Quantitative Trait Loci
dominance (genetics)
quantitative trait loci
Sample Size
2004
181 Citations (Scopus)

Detection of quantitative trait loci affecting milk production, health, and reproductive traits in Holstein cattle

Ashwell, M. S., Heyen, D. W., Sonstegard, T. S., Van Tassell, C. P., Da, Y., VanRaden, P. M., Ron, M., Weller, J. I. & Lewin, H. A., Jan 1 2004, In : Journal of Dairy Science. 87, 2, p. 468-475 8 p.

Research output: Contribution to journalArticle

Quantitative Trait Loci
Reproductive Health
reproductive traits
Pregnancy Rate
quantitative trait loci
2003
27 Citations (Scopus)

Allelic variation and genetic linkage of avian microsatellites in a new turkey population for genetic mapping

Reed, K. M., Chaves, L. D., Garbe, J. R., Da, Y. & Harry, D. E., Dec 1 2003, In : Cytogenetic and Genome Research. 102, 1-4, p. 331-339 9 p.

Research output: Contribution to journalArticle

Genetic Linkage
Population Genetics
Microsatellite Repeats
Chickens
Quail
4 Citations (Scopus)

A software tool for the graphical visualization of large and complex populations.

Garbe, J. R. & Da, Y., Jan 1 2003, In : Yi chuan xue bao = Acta genetica Sinica. 30, 12, p. 1193-1195 3 p.

Research output: Contribution to journalArticle

Pedigree
Software
Population
Zoo Animals
Genealogy and Heraldry
62 Citations (Scopus)

Clinical Characteristics and Inheritance of Idiopathic Epilepsy in Vizslas

Patterson, N., Mickelson, J. R., Da, Y., Roberts, M. C., Mc Vey, A. S., O'Brien, D. P., Johnson, G. S. & Armstrong, P. J., May 1 2003, In : Journal of veterinary internal medicine. 17, 3, p. 319-325 7 p.

Research output: Contribution to journalArticle

epilepsy
seizures
Epilepsy
inheritance (genetics)
Seizures

Linkage analysis for mapping genes of sex-influenced traits

London, N. R., Garbe, J. R., Schmutz, S. M., Abrahamsen, M. S. & Da, Y., Apr 1 2003, In : Mammalian Genome. 14, 4, p. 261-267 7 p.

Research output: Contribution to journalArticle

Chromosome Mapping
Genetic Recombination
Genes
Alleles
2002
3 Citations (Scopus)

Linkage analysis using direct and indirect counting and relative efficiencies for codominant and dominant loci

Da, Y., Garbe, J. R., London, N. & Xu, J., Oct 1 2002, In : Journal of Animal Science. 80, 10, p. 2528-2539 12 p.

Research output: Contribution to journalArticle

Genetic Recombination
linkage (genetics)
loci
Information Storage and Retrieval
gender
2001
13 Citations (Scopus)

Generation and exploration of a dense genetic map in a region of a QTL affecting corpora lutea in a Meishan x Yorkshire cross

Braunschweig, M. H., Paszek, A. A., Weller, J. I., Da, Y., Hawken, R. J., Wheeler, M. B., Schook, L. B. & Alexander, L. J., Sep 11 2001, In : Mammalian Genome. 12, 9, p. 719-723 5 p.

Research output: Contribution to journalArticle

Quantitative Trait Loci
Corpus Luteum
Microsatellite Repeats
Swine
Least-Squares Analysis
2000
9 Citations (Scopus)

Detection and parameter estimation for quantitative trait loci using regression models and multiple markers

Da, Y., VanRaden, P. M. & Schook, L. B., Sep 26 2000, In : Genetics Selection Evolution. 32, 4, p. 357-381 25 p.

Research output: Contribution to journalArticle

Quantitative Trait Loci
quantitative trait loci
recombination
chromosome
Genetic Recombination
1999
176 Citations (Scopus)

A genome scan for QTL influencing milk production and health traits in dairy cattle.

Heyen, D. W., Weller, J. I., Ron, M., Band, M., Beever, J. E., Feldmesser, E., Da, Y., Wiggans, G. R., VanRaden, P. M. & Lewin, H. A., Nov 11 1999, In : Physiological Genomics. 1, 3, p. 165-175 11 p.

Research output: Contribution to journalArticle

Quantitative Trait Loci
Milk
Genome
Fats
Health
3 Citations (Scopus)

Standardization and conversion of marker polymorphism measures

Da, Y., VanRaden, P. M., Ron, M., Beever, J. E., Paszek, A. A., Song, J., Wiggans, G. R., Ma, R., Weller, J. I. & Lewin, H. A., Jan 1 1999, In : Animal Biotechnology. 10, 1-2, p. 25-35 11 p.

Research output: Contribution to journalArticle

Chromosome Mapping
Polymorphism
Genetic Markers
standardization
Standardization
1998

Designs of reference families for the construction of genetic linkage maps

Da, Y., VanRaden, P. M., Li, N., Beattie, C. W., Wu, C. & Schook, L. B., Jan 1 1998, In : Animal Biotechnology. 9, 3, p. 205-228 24 p.

Research output: Contribution to journalArticle

Genetic Linkage
chromosome mapping
linkage (genetics)
Costs and Cost Analysis
loci
43 Citations (Scopus)

Detection of Putative Loci Affecting Conformational Type Traits in an Elite Population of United States Holsteins Using Microsatellite Markers

Ashwell, M. S., Da, Y., Vanraden, P. M., Rexroad, C. E. & Miller, R. H., Jan 1 1998, In : Journal of Dairy Science. 81, 4, p. 1120-1125 6 p.

Research output: Contribution to journalArticle

body conformation
Quantitative Trait Loci
Microsatellite Repeats
Animal Mammary Glands
microsatellite repeats
36 Citations (Scopus)

Detection of Putative Loci Affecting Milk Production and Composition, Health, and Type Traits in a United States Holstein Population

Ashwell, M. S., Da, Y., Van Tassell, C. P., Vanraden, P. M., Miller, R. H. & Rexroad, C. E., Jan 1 1998, In : Journal of Dairy Science. 81, 12, p. 3309-3314 6 p.

Research output: Contribution to journalArticle

body conformation
milk composition
milk production
Milk
Holstein
42 Citations (Scopus)

Reduced bovine leukaemia virus proviral load in genetically resistant cattle

Mirsky, M. L., Olmstead, C., Da, Y. & Lewin, H. A., Aug 1 1998, In : Animal Genetics. 29, 4, p. 245-252 8 p.

Research output: Contribution to journalArticle

Bovine Leukemia Virus
Bovine leukemia virus
viral load
Lymphocytosis
B-lymphocytes
1997
73 Citations (Scopus)

Detection of loci affecting milk production and health traits in an elite US Holstein population using microsatellite markers

Ashwell, M. S., Rexroad, C. E., Miller, R. H., VanRaden, P. M. & Da, Y., Jan 1 1997, In : Animal Genetics. 28, 3, p. 216-222 7 p.

Research output: Contribution to journalArticle

Quantitative Trait Loci
Microsatellite Repeats
quantitative trait loci
milk production
Milk
101 Citations (Scopus)

Exclusion probabilities of 22 bovine microsatellite markers in fluorescent multiplexes for semiautomated parentage testing

Heyen, D. W., Beever, J. E., Da, Y., Evert, R. E., Green, C., Bates, S. R. E., Ziegle, J. S. & Lewin, H. A., Jan 1 1997, In : Animal Genetics. 28, 1, p. 21-27 7 p.

Research output: Contribution to journalArticle

parentage
Microsatellite Repeats
microsatellite repeats
Genotype
cattle
1996
107 Citations (Scopus)

A male linkage map of the cattle (Bobs taurus) genome

Ma, R. Z., Beever, J. E., Da, Y., Green, C. A., Russ, I., Park, C., Heyen, D. W., Everts, R. E., Fisher, S. R., Overton, K. M., Teale, A. J., Kemp, S. J., Hines, H. C., Guérin, G. & Lewin, H. A., Jan 1 1996, In : Journal of Heredity. 87, 4, p. 261-271 11 p.

Research output: Contribution to journalArticle

Genome
Blood Group Antigens
Microsatellite Repeats
Chromosomes
Gene Order