Zebin Zhang

Zebin Zhang


Visa sidan på svenska
Works at Department of Zoology
Visiting address Svante Arrheniusväg 18b
Room D547
Postal address Zoologiska institutionen: Populationsgenetik 106 91 Stockholm

About me

I'm a bioinformatics analyst and molecular biologist. I'm currently analyzing RAD-seq data from interspecific yeast hybrids to understand how hybrid genomes are assembled and selected under environmental stress, testing predictions of quantitative genetics. I'm also interested in the adaptive value of ploidy variation, and in detecting signatures of domestication in the genome.



13.   Wang Q, Jia Y, Wang Y, Jiang Z, Zhou X, Zhang Z, Nie C, Li J, Yang N, Qu L (2019) Landscape and evolution of cis- and trans-regulatory divergence in chicken genome between two contrasted breeds analyzed in three tissues at one day age. BMC Genomics (in press)

12.   Zhang Z*, Bendixsen DP*, Janzen T, Nolte AW, Greig D, Stelkens R (2019) Recombining Your Way Out of Trouble: The Genetic Architecture of Hybrid Fitness under Environmental Stress, Molecular Biology and Evolution, msz211

11.   Gu H, Qi X, Jia Y, Zhang Z, Nie C, Li X, Li J, Jiang Z, Wang Q, Qu L (2019) Inheritance patterns of the transcriptome in hybrid chickens and their parents revealed by expression analysis. Scientific reports 9(1),5750


10.   Zhang Z, Jia Y, Almeida P, Mank JE, van Tuinen M, Wang Q, Jiang Z, Chen Y, Zhan K, Hou S, Zhou Z, Li H, Yang F, He Y, Ning Z, Yang Z, Qu L (2018) Whole-genome resequencing reveals signatures of selection and timing of duck domestication, GigaScience, 7:1-11

9.     Zhang Z, Jia Y, Chen Y, Wang L, Lv X, Yang F, He Y, Qu L (2018) Genomic variation in three Pekin duck populations developed in different countries revealed by whole genomic data. Animal genetics, 49(2), 132-136


8.     Li X, Nie C, Zhang Z, Wang Q, Shao P, Zhao Q, Chen Y, Wang D, Li Y, Jiao W, Li L, Qin S, He L, Jia Y, Ning Z, Qu L (2017) Evaluation of genetic resistance to Salmonella Pullorum in three chicken lines, Poultry Science, 97(3):764–769


7.     Zhang Z, Nie C, Jia Y, Jiang R, Xia H, Lv X, Chen Y, Li J, Li X, Ning Z, Xu G, Chen J, Yang N, Qu L (2016) Parallel evolution of polydactyly traits in Chinese and European chickens. PloS one 11(2): e0149010

6.     Nie C*, Zhang Z*, Zheng J, Sun H, Ning Z, Xu G, Yang N, Qu L (2016) Genome-wide association study revealed genomic regions related to white/red earlobe color trait in the Rhode Island Red chickens. BMC Genetics, 17(1): 115

5.     Huang J, Guo F, Zhang Z, Zhang Y, Wang X, Ju Z, Yang C, Wang C, Hou M, Zhong J (2016) PCK1 is negatively regulated by bta-miR-26a, and a single-nucleotide polymorphism in the 3’ untranslated region is involved in semen quality and longevity of Holstein bulls. Molecular reproduction and development, 83(3), 217-225


4.     Sun H, Jiang R, Xu S, Zhang Z, Xu G, Zheng J, Qu L (2015) Transcriptome responses to heat stress in hypothalamus of a meat-type chicken. Journal of animal science and biotechnology, 6(1), 6

3.     Fu D, Zhang D, Xu G, Li K, Wang Q, Zhang Z, Li J, Chen Y, Jia Y, Qu L (2015) Effects of different rearing systems on meat production traits and meat fiber microstructure of Beijing-you chicken. Animal Science Journal, 86(7): 729-735


2.     Zhang Z, Zhang W, Li R, Li J, Zhong J, Zhao Z, Huang M (2013) Novel splice variants of the bovine PCK1 gene. Genetics and Molecular Research, 12(3): 4028-4035


1.     Wang X, Huang J, Zhao L, Wang C, Ju Z, Li Q, Qi C, Zhang Y, Zhang Z, Zhang W, Hou M, Yuan J, Zhong J (2012) The exon 29 c. 3535A> T in the alpha-2-macroglobulin gene causing aberrant splice variants is associated with mastitis in dairy cattle. Immunogenetics, 64(11): 807-816


A selection from Stockholm University publication database
  • 2020. Zebin Zhang (et al.). Molecular biology and evolution 37 (1), 167-182

    Hybridization between species can either promote or impede adaptation. But we know very little about the genetic basis of hybrid fitness, especially in nondomesticated organisms, and when populations are facing environmental stress. We made genetically variable F2 hybrid populations from two divergent Saccharomyces yeast species. We exposed populations to ten toxins and sequenced the most resilient hybrids on low coverage using ddRADseq to investigate four aspects of their genomes: 1) hybridity, 2) interspecific heterozygosity, 3) epistasis (positive or negative associations between nonhomologous chromosomes), and 4) ploidy. We used linear mixed-effect models and simulations to measure to which extent hybrid genome composition was contingent on the environment. Genomes grown in different environments varied in every aspect of hybridness measured, revealing strong genotype–environment interactions. We also found selection against heterozygosity or directional selection for one of the parental alleles, with larger fitness of genomes carrying more homozygous allelic combinations in an otherwise hybrid genomic background. In addition, individual chromosomes and chromosomal interactions showed significant species biases and pervasive aneuploidies. Against our expectations, we observed multiple beneficial, opposite-species chromosome associations, confirmed by epistasis- and selection-free computer simulations, which is surprising given the large divergence of parental genomes (∼15%). Together, these results suggest that successful, stress-resilient hybrid genomes can be assembled from the best features of both parents without paying high costs of negative epistasis. This illustrates the importance of measuring genetic trait architecture in an environmental context when determining the evolutionary potential of genetically diverse hybrid populations.

  • 2019. Hongchang Gu (et al.). Scientific Reports 9

    Although many phenotypic traits of chickens have been well documented, the genetic patterns of gene expression levels in chickens remain to be determined. In the present study, we crossed two chicken breeds, White Leghorn (WL) and Cornish (Cor), which have been selected for egg and meat production, respectively, for a few hundred years. We evaluated transcriptome abundance in the brain, muscle, and liver from the day-old progenies of pure-bred WL and Cor, and the hybrids of these two breeds, by RNA-Seq in order to determine the inheritance patterns of gene expression. Comparison among expression levels in the different groups revealed that most of the genes showed conserved expression patterns in all three examined tissues and that brain had the highest number of conserved genes, which indicates that conserved genes are predominantly important compared to others. On the basis of allelic expression analysis, in addition to the conserved genes, we identified the extensive presence of additive, dominant (Cor dominant and WL dominant), over-dominant, and under-dominant genes in all three tissues in hybrids. Our study is the first to provide an overview of inheritance patterns of the transcriptome in layers and broilers, and we also provide insights into the genetics of chickens at the gene expression level.

Show all publications by Zebin Zhang at Stockholm University

Last updated: February 13, 2020

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