Jicai Jiang
Big Data Analytics, Genomics
Works (57)
Updated: December 19th, 2024 05:03
2024 article
A compendium of genetic regulatory effects across pig tissues
Teng, J., Gao, Y., Yin, H., Bai, Z., Liu, S., Zeng, H., … Fang, L. (2024, January 4). NATURE GENETICS, Vol. 1.
TL;DR:
The pilot phase of PigGTEx, re-analyzing 5,457 published RNA-seq samples, presents a pan-tissue catalog of molecular quantitative trait loci and cross-species comparisons identify traits with shared genetic regulation in humans.
(via Semantic Scholar)
open access via www.nature.com (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: February 12, 2024
2024 journal article
Capturing resilience from phenotypic deviations: a case study using feed consumption and whole genome data in pigs
BMC GENOMICS, 25(1).
author keywords: Whole genome sequence; Resilience; Swine; Feed consumption; Environmental variance; LnVar
Sources: Web Of Science, NC State University Libraries
Added: December 2, 2024
2024 journal article
Effects of germplasm exchange strategies on genetic gain, homozygosity, and genetic diversity in dairy stud populations: A simulation study
JOURNAL OF DAIRY SCIENCE, 107(12), 11149–11163.
author keywords: inbreeding; genetic progress; Holstein
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: September 1, 2024
2024 journal article
MAGE: metafounders-assisted genomic estimation of breeding value, a novel additive-dominance single-step model in crossbreeding systems
BIOINFORMATICS, 40(2).
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: April 15, 2024
2024 journal article
MPH: fast REML for large-scale genome partitioning of quantitative genetic variation
BIOINFORMATICS, 40(5).
Ed(s): R. Schwartz
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: May 1, 2024
2024 article
The effect of temperature-humidity index in different pregnancy stages on litter traits in Taiwan Landrace sows
Lin, K.-H., Flowers, B., Jiang, J., Knauer, M., & Lin, E.-C. (2024, May 5). JOURNAL OF ANIMAL SCIENCE, Vol. 102, pp. 20–20.
author keywords: Landrace; litter traits; pregnancy stages,temperature-humidity index; Taiwan
Sources: Web Of Science, NC State University Libraries
Added: May 20, 2024
2024 article
Trio-binning Assemblies of the Duroc and Landrace swine breeds
Ackerson, L. K., Kuhn, K., Gondro, C., Jiang, J., Maltecca, C., Rohrer, G. A., … Huang, W. (2024, September 14). JOURNAL OF ANIMAL SCIENCE, Vol. 102, pp. 523–523.
author keywords: swine; pangenome; assembly
Sources: Web Of Science, NC State University Libraries
Added: September 30, 2024
2024 article
Trio-binning Assemblies of the Duroc and Landrace swine breeds
Ackerson, L. K., Kuhn, K., Gondro, C., Jiang, J., Maltecca, C., Rohrer, G. A., … Huang, W. (2024, September). JOURNAL OF ANIMAL SCIENCE, Vol. 102, pp. 523–523.
author keywords: swine; pangenome; assembly
Sources: Web Of Science, NC State University Libraries
Added: September 30, 2024
2023 journal article
123 Benchmarking of Artificial Neural Network Models for Genomic Prediction of Quantitative Traits in Pigs
Journal of Animal Science, 101(Supplement_3), 17–18.
author keywords: artificial neural network; genomic prediction; swine
TL;DR:
It is found ANN with up to three layers could not improve genomic predictions compared with routine linear methods for pig quantitative traits, and hyper-parameter tuning is critical for improving the genomic prediction accuracy in pigs.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: December 11, 2023
2023 journal article
A Million-Cow Genome-Wide Association Study of Three Fertility Traits in US Holstein Cows
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 24(13).
author keywords: GWAS; fertility; daughter pregnancy rate; cow conception rate; heifer conception rate; SNP; Holstein cow
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: June 24, 2023
2023 journal article
Genome-wide association analysis of heifer livability and early first calving in Holstein cattle
BMC GENOMICS, 24(1).
author keywords: Dairy Cattle; Heifer; Fertility; Disease; GWAS; TWAS
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: November 6, 2023
2023 journal article
Inbreeding depression for producer-recorded udder, metabolic, and reproductive diseases in US dairy cattle
Journal of Dairy Science, 107(5), 3032–3046.
author keywords: dairy cattle; inbreeding depression; age of inbreeding; health traits
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries, Crossref
Added: December 5, 2023
2023 journal article
Investigation of lncRNA in <i>Bos taurus</i> Mammary Tissue during Dry and Lactation Periods
GENES, 14(9).
author keywords: Bos taurus; lncRNA; mammary
TL;DR:
Findings indicate that there are crucial relationships between the lncRNAs found in mammary tissue and the development of the tissue, to meet both the animal’s needs and their own production needs; these relationships should be further investigated to ensure that the authors continue to breed the most resilient, efficient dairy cattle.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: September 13, 2023
2023 journal article
SLEMM: million-scale genomic predictions with window-based SNP weighting
BIOINFORMATICS, 39(3).
Ed(s): R. Schwartz
MeSH headings : Female; Animals; Cattle; Polymorphism, Single Nucleotide; Bayes Theorem; Genome; Genomics / methods; Genotype; Phenotype; Models, Genetic
TL;DR:
Extensive analyses on seven public datasets showed that SLEMM with SNP weighting had overall the best predictive ability among a variety of genomic prediction methods including GCTA's empirical BLUP, BayesR, KAML, and LDAK’s BOLT andBayesR models.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: March 10, 2023
2023 dataset
Simulated Sequence Genotypes
Source: ORCID
Added: October 25, 2023
2023 dataset
sequence-genotypes.zip
Source: ORCID
Added: October 25, 2023
2022 article
Editorial: Bridging (Epi-) Genomics and Environmental Changes: The Livestock Research
Duan, J. E., Jiang, J., & He, Y. (2022, July 5). FRONTIERS IN GENETICS, Vol. 13.
author keywords: genomics; epigenomics; complex traits; environmental factors; climate changes; GWAS
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 1, 2022
2022 journal article
Exploring methods to summarize gut microbiota composition for microbiability estimation and phenotypic prediction in swine
JOURNAL OF ANIMAL SCIENCE, 100(9).
Contributors: Y. He n, F. Tiezzi n, n , J. Howard, Y. Huang, K. Gray*, J. Choi *, C. Maltecca n
author keywords: Gut microbiota; microbial similarity matrix; microbiability; prediction; swine
MeSH headings : Animals; Body Composition / genetics; Gastrointestinal Microbiome; Male; Phenotype; RNA, Ribosomal, 16S / genetics; Swine
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: July 2, 2022
2022 journal article
Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle
JOURNAL OF DAIRY SCIENCE, 105(11), 8956–8971.
Contributors: E. Lozada-Soto n, F. Tiezzi *, n , J. Cole *, P. VanRaden * & C. Maltecca n
author keywords: dairy cattle; runs of homozygosity; inbreeding; genetic diversity
MeSH headings : Cattle / genetics; Animals; Inbreeding; Polymorphism, Single Nucleotide; Physical Conditioning, Animal; Genome; Genomics; Homozygote; Genotype
TL;DR:
This study characterized the genomic landscape of autozygosity and assessed trends in genetic diversity in 5 breeds of US dairy cattle and identified ROH islands in each breed, revealing selection patterns for milk production, productive life, health, and reproduction in most breeds.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: September 22, 2022
2022 journal article
Investigation of rumen long noncoding RNA before and after weaning in cattle
BMC GENOMICS, 23(1).
MeSH headings : Animals; Cattle / genetics; Female; Genome; Phenotype; RNA, Long Noncoding / genetics; RNA, Long Noncoding / metabolism; Rumen / metabolism; Weaning
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 1, 2022
2022 article
The Addition of Epistatic Genetic Effects Increases Genomic Prediction Accuracy for Reproduction and Production Traits in Duroc Pigs Using Genomic Models
Cheng, J., Tiezzi, F., Howard, J., Maltecca, C., & Jiang, J. (2022, January 6).
Source: ORCID
Added: February 1, 2022
2022 article
Transcriptome Analysis of Chicken Reveals the Impact of Herpesvirus of Turkeys on Bursa RNA Expression in Marek's Disease Virus Infections
Wang, J., Hicks, J., Jiang, J., & Liu, H.-C. (2022, October). JOURNAL OF ANIMAL SCIENCE, Vol. 100, pp. 215–215.
author keywords: chicken RNA-seq MDV
TL;DR:
The result of differential gene expression showed that 14 days post infection might be the point in time when HVT worked and better understand host-pathogen interaction in the bursa and elucidate the mechanism how HVT contribute to resist MDV.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: June 26, 2023
2022 journal article
Use of Host Feeding Behavior and Gut Microbiome Data in Estimating Variance Components and Predicting Growth and Body Composition Traits in Swine
GENES, 13(5).
Contributors: Y. He n, F. Tiezzi n, n , J. Howard, Y. Huang, K. Gray*, J. Choi, C. Maltecca n
author keywords: feeding behavior; gut microbiome composition; prediction; growth; breeds; swine
MeSH headings : Animals; Body Composition / genetics; Feeding Behavior; Gastrointestinal Microbiome / genetics; Male; Phenotype; RNA, Ribosomal, 16S / genetics; Swine
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: April 27, 2022
2021 journal article
A Large-Scale Genome-Wide Association Study of Epistasis Effects of Production Traits and Daughter Pregnancy Rate in US Holstein Cattle
GENES, 12(7).
author keywords: epistasis; GWAS; milk production; fertility
MeSH headings : Animals; Cattle; Epistasis, Genetic / genetics; Female; Fertility / genetics; Gene Expression / genetics; Gene Expression Profiling / methods; Gene Expression Regulation / genetics; Genome-Wide Association Study / methods; Genotype; Lactation / genetics; Milk / chemistry; Milk / metabolism; Phenotype; Polymorphism, Single Nucleotide / genetics; Pregnancy; Pregnancy Rate; Transcriptome / genetics
TL;DR:
Genome-wide association study using 76,109 SNPs and 294,079 first-lactation Holstein cows was conducted for testing pairwise epistasis effects of five production traits and three fertility traits, indicating new understanding about the genetic mechanism underlying quantitative traits in Holstein cattle.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 2, 2021
2021 journal article
Effect of Temperature and Maternal Age on Recombination Rate in Cattle
FRONTIERS IN GENETICS, 12.
Contributors: B. Shen*, E. Freebern*, n , C. Maltecca n , J. Cole *, G. Liu *, L. Ma *
author keywords: recombination; maternal age; temperature; cattle; genetics
TL;DR:
The maternal age and temperature effects on recombination rate are characterized and the adaptation of meiotic recombination to environmental stimuli in cattle is suggested and provided first-hand information regarding the plastic nature of meiosis recombination in a mammalian species.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 16, 2021
2021 article
On the Use of Z-Scores for Fine-Mapping with Related Individuals
Jiang, J. (2021, October 13). (Vol. 10). Vol. 10.
TL;DR:
It is shown in theory and simulation what modifications are necessary to extend the use of summary statistics to related individuals and that though existing summary-statistics-based fine-mapping methods can be adapted for related individuals, they appear to have no computational advantage over individual-data-based methods.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2020 journal article
Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle
Genome Research, 30(5), 790–801.
Contributors: L. Fang *, W. Cai *, S. Liu *, O. Canela-Xandri *, Y. Gao *, * , K. Rawlik *, B. Li *
MeSH headings : Animals; Cattle / genetics; Cattle / growth & development; Cattle / physiology; DNA Methylation; Female; Genes; Milk; Organ Specificity; RNA-Seq; Reproduction; Transcriptome
TL;DR:
These findings provided novel insights into the genetic and biological mechanisms underlying complex traits in cattle, and the transcriptome atlas can serve as a primary source for biological interpretation, functional validation, studies of adaptive evolution, and genomic improvement in livestock.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2020 journal article
Evidence for recombination variability in purebred swine populations
Journal of Animal Breeding and Genetics, 138(2), 259–273.
Contributors: E. Lozada-Soto n, C. Maltecca n , H. Wackel n, W. Flowers n , K. Gray, Y. He n, Y. Huang, n , F. Tiezzi n
author keywords: genetic variance; recombination rate; selection; swine
MeSH headings : Animals; Female; Genome; Genomics; Male; Phenotype; Recombination, Genetic; Swine
TL;DR:
Evidence of variability for recombination in purebred swine populations is provided, with differences found for sex, breed, sex-breed interaction, and age effects for genome-wide recombination rate and RO at one or more chromosomes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 26, 2020
2020 journal article
GWAS and fine-mapping of livability and six disease traits in Holstein cattle
BMC GENOMICS, 21(1).
Contributors: E. Freebern*, D. Santos *, L. Fang *, * , K. Parker Gaddis *, G. Liu *, P. Vanraden *, C. Maltecca n , J. Cole *, L. Ma *
author keywords: GWAS; Fine mapping; Health trait; Gene expression; Dairy cattle
MeSH headings : Animals; Cattle; Cattle Diseases / diagnosis; Cattle Diseases / genetics; Chromosome Mapping; Dairying; Genetic Predisposition to Disease; Genome-Wide Association Study; Genomics; Phenotype; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Quantitative Trait, Heritable; Transcriptome
TL;DR:
The genetic basis of seven health traits in dairy cattle is investigated and potential candidate genes associated with cattle health are identified using genome-wide association studies, fine mapping, and analyses of multitissue transcriptome data.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: March 10, 2020
2019 journal article
A large-scale genome-wide association study in U.S. Holstein cattle
Frontiers in Genetics, 10(MAY).
Contributors: * , L. Ma *, D. Prakapenka *, P. VanRaden *, J. Cole * & Y. Da *
author keywords: GWAS; dairy cattle; milk production; fertility; somatic cell score
TL;DR:
A large-scale GWAS using 294,079 first-lactation Holstein cows identified new additive and dominance effects on five production traits, three fertility traits, and somatic cell score and found DGAT1 antagonism was an extreme antagonistic pleiotropy between fat yield and milk and protein yields among all SNPs in this study.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: February 1, 2022
2019 journal article
Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits
Epigenetics, 14(3), 260–276.
Contributors: L. Fang *, Y. Zhou *, S. Liu *, * , D. Bickhart *, D. Null *, B. Li *, S. Schroeder *
author keywords: Sperm DNA methylation; epigenome evolution; large-scale GWAS; cattle complex traits; human complex traits
MeSH headings : Animals; Cattle; DNA Methylation; Epigenome; Evolution, Molecular; Genome-Wide Association Study; Histones / metabolism; Humans; Male; Mice; Multifactorial Inheritance / genetics; Mutation Rate; Promoter Regions, Genetic; Spermatozoa / physiology
TL;DR:
Comparing sperm DNA methylomes and large-scale genome-wide association study (GWAS) signals between human and cattle aimed at examining the DNA methylome evolution and its associations with complex phenotypes in mammals demonstrated important roles of epigenome evolution in shaping the genetic architecture underlyingcomplex phenotypes.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2019 journal article
Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls
Communications Biology, 2(1).
MeSH headings : Agriculture; Animals; Bayes Theorem; Cattle / genetics; Chromosome Mapping; Genome-Wide Association Study; Quantitative Trait Loci; Reproduction / genetics
TL;DR:
The analysis of sequence variants from over 27,000 Holstein bulls associated with 35 traits for production, reproduction, and body conformation enhanced the understanding of the genetic basis of cattle complex traits and demonstrated the utility of BFMAP.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: February 1, 2022
2019 journal article
Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle
Communications Biology, 2(1).
MeSH headings : Animals; Cattle; Chromosome Mapping; Computational Biology / methods; Epigenesis, Genetic; Female; Genome-Wide Association Study; Gestational Age; Male; Methylation; Molecular Sequence Annotation; Paternal Inheritance; Phenotype; Pregnancy; Quantitative Trait Loci; Spermatozoa / metabolism; Transcription Factors / metabolism
TL;DR:
The findings support that the paternal genome and epigenome can impact gestation length potentially through regulation of the embryonic development and reveal that gestation length shares genetic and epigenetic architecture in sperm with calving ability, body depth, and conception rate.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2019 journal article
Integrating Signals from Sperm Methylome Analysis and Genome-Wide Association Study for a Better Understanding of Male Fertility in Cattle
Epigenomes, 3(2), 10.
author keywords: sperm DNA methylation; male fertility; large-scale GWAS; cattle complex traits
TL;DR:
This initial effort supported a hypothesis that sperm DNA methylation may contribute to male fertility in cattle and revealed the usefulness of functional annotations in enhancing biological interpretation and genomic prediction for complex traits and diseases.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2018 journal article
Characterization of recombination features and the genetic basis in multiple cattle breeds
BMC Genomics, 19(1).
Contributors: B. Shen*, * , E. Seroussi *, G. Liu * & L. Ma *
author keywords: Recombination; Dairy cattle; Breed; Sex; GWAS; Pedigree
MeSH headings : Animals; Breeding; Cattle; Chromosome Mapping; Female; Genome-Wide Association Study; Genotype; Male; Meiosis; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Recombination, Genetic
TL;DR:
This work constructed breed- and sex-specific genome-wide recombination maps for multiple cattle breeds, provided a comprehensive characterization and comparison of recombination patterns between breeds, and expanded the understanding of the breed-level variations in recombination features within an important livestock species.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2018 journal article
Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins
Journal of Dairy Science, 101(10), 9089–9107.
Contributors: J. Weller *, D. Bickhart *, G. Wiggans *, M. Tooker *, . J.R. O'Connell, * , M. Ron *, P. VanRaden *
author keywords: genomic selection; a posteriori granddaughter design; quantitative trait nucleotide; concordance
MeSH headings : Animals; Cattle / genetics; Chromosome Mapping; Female; Genotype; Male; Milk; Nucleotides; Phenotype; Polymorphism, Single Nucleotide; Pregnancy; Pregnancy Rate; Quantitative Trait Loci
TL;DR:
The only polymorphism found likely to improve predictive power for genomic evaluation of dairy cattle was on chromosome 15; that polymorphism had a frequency of 0.45 for the allele with economically positive effects on all production traits.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: February 1, 2022
2018 article
Fast Bayesian fine-mapping of 35 production, reproduction and body conformation traits in dairy cattle
Jiang, J., Cole, J. B., Da, Y., VanRaden, P. M., & Ma, L. (2018, September 26). (Vol. 9). Vol. 9.
TL;DR:
The utility of a fast Bayesian approach for fine-mapping and functional enrichment analysis is demonstrated, candidate causative genes and variants are identified, and the genetic basis of complex traits in dairy cattle is enhanced.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2017 journal article
Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals
BMC Genomics, 18(1).
Contributors: X. Feng *, * , A. Padhi*, C. Ning *, J. Fu*, A. Wang *, R. Mrode *, J. Liu *
author keywords: Domestic animals; Segmental duplications; Copy number; Duplicated genes
MeSH headings : Animals; Animals, Domestic / genetics; Animals, Domestic / immunology; Chickens; Chromosome Mapping / methods; Evolution, Molecular; Glucuronosyltransferase / genetics; Goats; Horses; Interferon-alpha / genetics; Rabbits; Segmental Duplications, Genomic; Sheep
TL;DR:
The mapped genome-wide SDs of horse, rabbit, goat, sheep and chicken are mapped and the existing SD maps of cattle and pig genomes are enhanced based on the most updated genome assemblies to provide insights into livestock genome evolution and offer rich genomic sources for livestock genomic research.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2017 journal article
Construction of PRDM9 allele-specific recombination maps in cattle using large-scale pedigree analysis and genome-wide single sperm genomics
DNA Research, 25(2), 183–194.
Contributors: Y. Zhou *, B. Shen*, * , A. Padhi*, K. Park*, A. Oswalt, C. Sattler, B. Telugu *
MeSH headings : Alleles; Animals; Cattle; Genomics; Histone-Lysine N-Methyltransferase / genetics; Histone-Lysine N-Methyltransferase / metabolism; Male; Meiosis; Pedigree; Recombination, Genetic; Sequence Analysis, DNA; Spermatozoa / metabolism; Zinc Fingers
TL;DR:
The study comprehensively surveyed the bovine PRDM9 alleles, generated allele-specific recombination maps, and expanded the understanding of the role ofPRDM9 on genome distribution of recombination.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: February 1, 2022
2017 journal article
Dissection of additive, dominance, and imprinting effects for production and reproduction traits in Holstein cattle
BMC Genomics, 18(1).
Contributors: * , B. Shen*, . J.R. O'Connell, P. VanRaden, J. Cole & L. Ma *
author keywords: Variance decomposition; Additive; Dominance; Imprinting; Cattle; Dairy traits; Qtl
MeSH headings : Animals; Cattle / genetics; Cattle / physiology; Genome-Wide Association Study; Genomic Imprinting; Genotype; Phenotype; Polymorphism, Single Nucleotide; Quantitative Trait Loci / genetics; Reproduction / genetics
TL;DR:
It is suggested that non-additive effects contributed a non-negligible amount to the total genetic variance of complex traits in cattle, and detection of QTLs with non- additive effect is possible in GWAS using a large dataset.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2017 journal article
Ruminant-specific multiple duplication events of PRDM9 before speciation
BMC Evolutionary Biology, 17(1).
author keywords: Speciation genetics; Genetic incompatibility; PRDM9; Gene duplication; Positive selection; Molecular evolution; Ruminants
MeSH headings : Amino Acid Sequence; Animals; Biological Evolution; Evolution, Molecular; Gene Conversion; Gene Duplication; Genetic Speciation; Histone-Lysine N-Methyltransferase / chemistry; Histone-Lysine N-Methyltransferase / genetics; Meiosis; Phylogeny; Recombination, Genetic; Ruminants / classification; Ruminants / genetics
TL;DR:
Evidence of ruminant-specific multiple gene duplication events, and an intra-chromosomal X-linked duplication, which resulted in two additional copies of PRDM9 in ruminants are demonstrated, supporting the notion of well-established Red Queen hypothesis.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2016 journal article
Effect of sex, age and genetics on crossover interference in cattle
Scientific Reports, 6.
MeSH headings : Aging / genetics; Aging / physiology; Animals; Breeding; Cattle / genetics; Cattle / physiology; Chromosomes, Mammalian / genetics; Crossing Over, Genetic; Female; Genome-Wide Association Study; Male; Polymorphism, Single Nucleotide / genetics; Sex Characteristics
TL;DR:
Large-scale analysis of Holstein and Jersey cattle with genotype data provided a comprehensive description of crossover interference across chromosome, sex and age groups, identified associated candidate genes, and produced useful insights into the mechanism ofrossover interference.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2016 journal article
Identification of copy number variations in Xiang and Kele pigs
PLoS ONE, 11(2).
MeSH headings : Animals; China; Gene Dosage; Litter Size / genetics; Polymorphism, Single Nucleotide; Swine / genetics
TL;DR:
The results provide meaningful information about genomic variation, which may be useful in future assessments of the associations between CNVs and important phenotypes in Xiang and Kele pigs to ultimately help protect these rare breeds.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2016 journal article
The impact of variable degrees of freedom and scale parameters in Bayesian methods for genomic prediction in Chinese Simmental beef cattle
PLoS ONE, 11(5).
MeSH headings : Animals; Bayes Theorem; Cattle / genetics; Female; Genomics / methods; Male; Models, Statistical; Polymorphism, Single Nucleotide; Quantitative Trait Loci / genetics
TL;DR:
The modified methods with distribution assumed to the two hyperparameters were beneficial for improving the predictive accuracy and the predictive accuracies of the modified methods were slightly higher than those of their counterparts especially for traits with low heritability and a small number of QTLs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: ORCID
Added: February 1, 2022
2015 journal article
Differential expression of genes in milk of dairy cattle during lactation
Animal Genetics, 47(2), 174–180.
Contributors: J. Yang *, * , X. Liu*, H. Wang *, G. Guo, Q. Zhang *, L. Jiang *
author keywords: differentially expressed genes; milk fat globules; milk production traits; RNA sequencing
MeSH headings : Animals; Cattle / genetics; Chromosome Mapping; Dairying; Female; Gene Expression; Glycolipids / genetics; Glycoproteins / genetics; Lactation / genetics; Lipid Droplets; Milk; Molecular Sequence Annotation; Quantitative Trait Loci; Sequence Analysis, RNA
TL;DR:
Gene Ontology enrichment and pathway analysis revealed that these differentially expressed genes were enriched in biological processes involved in mammary gland development, protein and lipid metabolism process, signal transduction, cellular process, differentiation and immune function.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2015 journal article
Improved detection and characterization of copy number variations among diverse pig breeds by array CGH
G3: Genes, Genomes, Genetics, 5(6), 1253–1261.
Contributors: J. Wang *, * , H. Wang *, H. Kang *, Q. Zhang * & J. Liu *
author keywords: genomic variation; copy number variations; array CGH; pigs
MeSH headings : Animals; Breeding; Chromosomes, Mammalian / genetics; Cluster Analysis; Comparative Genomic Hybridization / methods; DNA Copy Number Variations / genetics; Genome; Phylogeny; Real-Time Polymerase Chain Reaction; Sus scrofa / genetics
TL;DR:
CNVs detected in diverse populations herein are essentially complementary to the CNV map in the Pig genome, which would be helpful for understanding the pig genome variants and investigating the associations between various phenotypes and CNVs.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2015 journal article
Joint prediction of multiple quantitative traits using a Bayesian multivariate antedependence model
Heredity, 115(1), 29–36.
MeSH headings : Algorithms; Animals; Bayes Theorem; Computer Simulation; Female; Linear Models; Male; Mice; Models, Genetic; Phenotype; Quantitative Trait Loci
TL;DR:
A novel multivariate antedependence-based method for joint prediction of multiple quantitative traits using a Bayesian algorithm via modeling a linear relationship of effect vector between each pair of adjacent markers that is more accurate and robust than corresponding traditional counterparts (Bayes A and multi-trait Bayes A).
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2014 journal article
Enhancing genome-wide copy number variation identification by high density array CGH using diverse resources of pig breeds
PLoS ONE, 9(1).
Contributors: J. Wang *, * , H. Wang *, H. Kang *, Q. Zhang * & J. Liu *
MeSH headings : Animals; Breeding / methods; China; Comparative Genomic Hybridization / methods; DNA Copy Number Variations / genetics; Genome / genetics; Real-Time Polymerase Chain Reaction / veterinary; Species Specificity; Sus scrofa / genetics
TL;DR:
The results are essential complementary to the CNV map in the pig genome, which will provide abundant genetic markers to investigate association studies between various phenotypes and CNVs in pigs.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2014 journal article
Global copy number analyses by next generation sequencing provide insight into pig genome variation
BMC Genomics, 15(1).
author keywords: Copy number variations (CNVs); Segmental duplications (SDs); Next generation sequencing (NGS); Pigs
MeSH headings : Animals; Comparative Genomic Hybridization; DNA Copy Number Variations; Gene Dosage; Genome; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; Sus scrofa / genetics
TL;DR:
These studies lay out one way for characterization of CNVs in the pig genome, provide insight into the pig genomes variation and prompt CNV mechanisms studies when using pigs as biomedical models for human diseases.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
9. Industry, Innovation and Infrastructure
(OpenAlex)
Source: ORCID
Added: February 1, 2022
2014 journal article
Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits
BMC Genomics, 15(1).
Contributors: L. Jiang *, X. Liu*, J. Yang *, H. Wang *, * , L. Liu *, S. He *, X. Ding *, J. Liu *, Q. Zhang *
author keywords: Genetic variants; Milk production traits; Targeted resequencing
MeSH headings : Animals; Cattle; Genetic Loci; Genome; Genome-Wide Association Study; Genotype; High-Throughput Nucleotide Sequencing; Lactation / genetics; Milk / metabolism; Polymorphism, Single Nucleotide; RNA, Messenger / metabolism; Sequence Analysis, DNA
Source: ORCID
Added: February 1, 2022
2013 journal article
Genome-Wide Detection of Selective Signature in Chinese Holstein
PLoS ONE, 8(3).
Contributors: D. Pan*, S. Zhang *, * , L. Jiang *, Q. Zhang * & J. Liu *
MeSH headings : Animals; Cattle / genetics; Female; Genome; Genome-Wide Association Study; Genomics; Haplotypes; Homozygote; Male; Molecular Sequence Annotation; Selection, Genetic
TL;DR:
Results showed that some functional genes associated with milk production traits, as reflected by GO terms, could be clustered in core regions, which provided promising evidence for the exploitability of the core regions identified by EHH tests.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2013 journal article
Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins
BMC Genomics, 14(1).
Contributors: L. Jiang *, * , J. Yang *, X. Liu*, J. Wang *, H. Wang *, X. Ding *, J. Liu *, Q. Zhang *
author keywords: Copy number variations; Cattle; BovineHD beadChip; Genome variation; Quantitative real time PCR
MeSH headings : Animals; Cattle; China; Chromosomes, Mammalian / genetics; Comparative Genomic Hybridization; DNA Copy Number Variations; Female; Genome; Genomic Structural Variation; Genomics / methods; Genotype; Male; Molecular Sequence Annotation; Polymorphism, Single Nucleotide; X Chromosome / genetics
TL;DR:
This study demonstrates the high density SNP array can significantly improve the accuracy and sensitivity of CNV calling and integration of different platforms can enhance the detection of genomic structure variants.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2013 journal article
Identification of Genome-Wide Copy Number Variations among Diverse Pig Breeds Using SNP Genotyping Arrays
PLoS ONE, 8(7).
MeSH headings : Animals; Breeding; DNA Copy Number Variations / genetics; Genome / genetics; Genotyping Techniques / methods; Polymorphism, Single Nucleotide / genetics; Real-Time Polymerase Chain Reaction; Reproducibility of Results; Sus scrofa / genetics
TL;DR:
CNVs detected in diverse populations herein are essential complementary to the CNV map in the pig genome, which provide an important resource for studies of genomic variation and the association between various economically important traits and CNVs.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2012 journal article
A genome-wide detection of copy number variations using SNP genotyping arrays in swine
BMC Genomics, 13(1).
Contributors: J. Wang *, * , W. Fu *, L. Jiang *, X. Ding *, J. Liu *, Q. Zhang *
author keywords: Copy number variations; Genetic variation; SNP arrays; Quantitative real time PCR; Pig
MeSH headings : Animals; Chromosomes, Mammalian / genetics; Crosses, Genetic; DNA Copy Number Variations / genetics; Female; Genetics, Population; Genome / genetics; Genotyping Techniques / methods; Male; Polymorphism, Single Nucleotide / genetics; Real-Time Polymerase Chain Reaction; Reproducibility of Results; Sample Size; Sus scrofa / genetics
TL;DR:
A genome-wide CNV detection based on the Porcine SNP60 genotyping data of 474 pigs from three pure breed populations and one Duroc × Erhualian crossbred population is performed to provide a comprehensive map of copy number variation in the pig genome.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2012 journal article
Differential gene expression profiling of porcine epithelial cells infected with three enterotoxigenic Escherichia coli strains
BMC Genomics, 13(1).
Contributors: C. Zhou*, Z. Liu*, * , Y. Yu* & Q. Zhang *
MeSH headings : Animals; Chemokine CCL20 / genetics; Chemokine CXCL2 / genetics; Enterotoxigenic Escherichia coli / pathogenicity; Epithelial Cells / metabolism; Epithelial Cells / microbiology; Gene Expression Profiling; Interleukin-6 / genetics; Interleukin-8 / genetics; Intestines / cytology; Swine; Transcriptome / genetics; Tumor Necrosis Factor-alpha / genetics
TL;DR:
The genes induced by ETECs with F4 versus F18 fimbriae suggest why ETEC with F 4 may be more virulent compared to F18 which seems to elicit milder effects.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2012 journal article
Genome-Wide Identification of Copy Number Variations in Chinese Holstein
PLoS ONE, 7(11).
Contributors: L. Jiang *, * , J. Wang *, X. Ding *, J. Liu * & Q. Zhang *
MeSH headings : Algorithms; Animals; Cattle / genetics; China; DNA Copy Number Variations; Gene Dosage; Genomics; Polymerase Chain Reaction
TL;DR:
An account of CNV regions in the cattle genome in Chinese Holstein population is reported and this resource is an important resource for investigation of genome structure and genomic variation underlying traits of interest in cattle.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
2011 journal article
Snat: A SNP annotation tool for bovine by integrating various sources of genomic information
BMC Genetics, 12.
Contributors: * , L. Jiang *, B. Zhou *, W. Fu *, J. Liu * & Q. Zhang *
MeSH headings : Animals; Cattle / genetics; Databases, Genetic; Genome; Genome-Wide Association Study; Genomics / methods; Genotype; Internet; Molecular Sequence Annotation; Polymorphism, Single Nucleotide; Software
TL;DR:
Snat is one of first tools focusing on SNP annotation for livestock with convenient and powerful platform to aid functional analyses and accurate evaluation on genes/variants related to SNPs, and facilitates follow-up replication studies in the post-GWAS era.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2022
Employment
Updated: December 9th, 2019 15:21
2019 - present
North Carolina State University Raleigh, NC, US
Assistant Professor
Department of Animal Science
2018 - 2019
University of Maryland School of Medicine Baltimore, MD, US
Post-Doc Fellow
Department of Medicine
Education
Updated: December 9th, 2019 15:22
2014 - 2018
University of Maryland College Park, MD, US
PhD
Department of Animal and Avian Sciences
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