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Articles by Yanjun Zan
The genome and GeneBank genomics of allotetraploid Nicotiana tabacum provide insights into genome evolution and complex trait regulation - Nature Genetics
Abstract Nicotiana tabacum is an allotetraploid hybrid of Nicotiana sylvestris and Nicotiana tomentosiformis and a model organism in genetics. However, features of subgenome evolution, expression coordination, genetic diversity and complex traits regulation of N. tabacum remain unresolved. Here we present chromosome-scale assemblies for all three species, and genotype and phenotypic data for 5,196 N. tabacum germplasms.
Author Correction: Origin and de novo domestication of sweet orange - Nature Genetics
Correction to: Nature Genetics https://doi.org/10.1038/s41588-025-02122-4, published online 5 March 2025. In the version of the Supplementary Information initially published with this article, the photograph shown in position 49 of Supplementary Fig. 25 was incorrect and has now been amended in the Supplementary Information file accompanying the article online.
Origin and de novo domestication of sweet orange - Nature Genetics
Abstract Sweet orange is cultivated worldwide but suffers from various devastating diseases because of its monogenetic background. The elucidation of the origin of a crop facilitates the domestication of new crops that may better cope with new challenges. Here we collected and sequenced 226 citrus accessions and assembled telomere-to-telomere phased diploid genomes of sweet orange and sour orange.
Natural genetic and transcriptomic variation in photosynthesis associated pathways contribute to adaptive traits variation in worldwide Arabidopsis thaliana population
Abstract Photosynthesis is the most important reaction underlying carbon fixation. Despite its potential in boosting carbon assimilation, nature variations underlying genes in photosynthesis pathway and their role in adaptive traits variation remains elusive.
Dual-trait genomic analysis in highly stratified Arabidopsis thaliana populations using genome-wide association summary statistics - Heredity
Abstract Genome-wide association study (GWAS) is a powerful tool to identify genomic loci underlying complex traits. However, the application in natural populations comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a GWAS dataset of Arabidopsis thaliana. We demonstrate the efficiency of dual-phenotype analysis to uncover hidden genetic loci masked by population structure via a series of simulations.
Complex genetic architecture underlying the plasticity of tobacco leaf width provides insight into across-environment genomic prediction
Abstract Phenotypic plasticity is the property of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant for future agriculture under changing climate. Here, we investigated the genetic basis of leaf width plasticity in a tobacco MAGIC population across four different environments.
The pan-genome and local adaptation of Arabidopsis thaliana - Nature Communications
Abstract Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation.
Dual-trait pleiotropic analysis in highly stratified natural populations using genome-wide association summary statistics
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The allotetraploid Nicotiana tabacum genome and GenBank genomics highlight the genomic features, genetic diversity and regulation of morphological, metabolic and disease-resistance traits
New Results doi: https://doi.org/10.1101/2023.02.21.529366 Abstract Nicotiana tabacum is a model organism in plant molecular and pathogenic research and has significant potential in the production of biofuels and active pharmaceutical compounds in synthetic biology. Because of the large allotetraploid genome of tobacco, its genomic features, genetic diversity and genetic regulation of many complex traits remain unknown. In this study, we present a nearly complete chromosome-scale assembly of N.
GenBank genomics highlight the genomic features, genetic diversity and regulation of morphological, metabolic and disease-resistance traits in Nicotiana tabacum
New Results doi: https://doi.org/10.1101/2023.02.21.529366 Abstract Nicotiana tabacum is a model organism in plant molecular and pathogenic research, and has significant potential in producing biofuels and active pharmaceutical compounds in synthetic biology. Challenged by the large allotetraploid genome, the genomic features, genetic diversity and genetic regulation of many complex traits remain unknown. In this study, we present the nearly complete chromosome-scale assembly of N.
Publisher Correction: Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis - Genome Biology
Publisher Correction Open Access Published: 15 July 2021 Zhi-Qiang Chen1, Yanjun Zan1, Pascal Milesi2, Linghua Zhou1, Jun Chen2,3, Lili Li2, BinBin Cui4, Shihui Niu5, Johan Westin6,7, Bo Karlsson8, 1, Martin Lascoux2 & Harry X.
Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis
Zhi-Qiang Chen1, Yanjun Zan1, Pascal Milesi2, Linghua Zhou1, Jun Chen2,3, Lili Li2, BinBin Cui4, Shihui Niu5, Johan Westin6,7, Bo Karlsson8, 1, Martin Lascoux2 & Harry X. Wu ORCID: orcid.org/0000-0002-7072-47041,5,9 Genome Biology volume 22, Article number: 179 (2021) Cite this article Abstract Background Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits.
A complex multi-locus, multi-allelic genetic architecture underlying the long-term selection-response in the Virginia body weight line of chickens
A complex multi-locus, multi-allelic genetic architecture underlying the long-term selection-response in the Virginia body weight line of chickens Yanjun Zan, Zheya Sheng, Lars Ronnegard, Christa F Honaker, Paul B Siegel, Orjan Carlborg bioRxiv 098160; doi: https://doi.org/10.1101/098160
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