Article
Biotechnology & Applied Microbiology
Quanlin Li, Zhongyi Duan, Congjiao Sun, Jiangxia Zheng, Guiyun Xu, Ning Yang
Summary: The genetic architecture underlying the crystal ultrastructure of eggshell quality has been investigated, showing a significant correlation between eggshell quality and total integral intensity and degree of crystal orientation. Key genes regulating total integral intensity are located in the GGA1 region and involved in regulating cytosolic calcium ion concentration.
Article
Plant Sciences
Fenglei Sun, Jun Ma, Weijun Shi, Yanlong Yang
Summary: In this study, a genome-wide association study (GWAS) was conducted on 8 traits of 150 cotton germplasms using resequencing data. The results showed that 18 SNPs were significantly correlated with cotton yield traits under drought conditions, while 8 SNPs were significantly correlated with the traits related to yield. Transcriptome data analysis identified four highly expressed genes after drought stress. qRT-PCR confirmed that these genes had the same expression pattern in samples with extreme drought tolerance. This study provides a theoretical basis for genetic analysis and breeding improvement of cotton yield traits under drought stress.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Shiyu Liao, Ju Yan, Hongkun Xing, Yuan Tu, Hu Zhao, Gongwei Wang
Summary: The study identified significant association loci for vascular bundle variations in rice, with key loci such as Ghd7 and NAL1 influencing the vascular bundles in different parts of the plant. These findings could be valuable for improving the vascular bundle system in rice breeding.
Article
Biology
Michelle C. Ward, Nicholas E. Banovich, Abhishek Sarkar, Matthew Stephens, Yoav Gilad
Summary: In this study, an in vitro model was established using induced pluripotent stem cell-derived cardiomyocytes from 15 individuals to investigate inter-individual differences in response to hypoxia. The research identified dynamic genetic effects on gene expression associated with complex traits and disease, which can be uncovered under stress conditions.
Article
Gastroenterology & Hepatology
Connor A. Emdin, Mary Haas, Veeral Ajmera, Tracey G. Simon, Julian Homburger, Cynthia Neben, Lan Jiang, Wei-Qi Wei, Qiping Feng, Alicia Zhou, Joshua Denny, Kathleen Corey, Rohit Loomba, Sekar Kathiresan, Amit Khera
Summary: This study identified 12 independent genetic variants, including 7 newly identified ones, that confer risk for cirrhosis. A polygenic score based on these variants can identify a subset of the population at substantially increased risk, particularly those susceptible to the hepatotoxic effects of excess alcohol consumption or obesity.
Article
Plant Sciences
Wenjun Wang, Xianjin Qiu, Ziqi Wang, Tianyi Xie, Wenqiang Sun, Jianlong Xu, Fan Zhang, Sibin Yu
Summary: Whole grain rice is recommended for its nutritional and health benefits compared to polished or white rice. The genetic basis of color variation in whole grain rice was studied using a genome-wide association analysis. Multiple loci were identified for grain color, including some previously known genes. An analysis excluding pigmented rice revealed additional loci associated with grain color. Differential expression analysis and metabolic analysis identified potential candidate genes involved in the flavonoid metabolic pathway related to pericarp color. These findings contribute to the improvement of appearance and commercial quality of whole grain rice through genomic breeding.
Article
Plant Sciences
Agnieszka Deja-Muylle, Davy Opdenacker, Boris Parizot, Hans Motte, Guillaume Lobet, Veronique Storme, Pieter Clauw, Maria Njo, Tom Beeckman
Summary: Root system architecture (RSA) directly affects nutrient uptake efficiency and plant growth. Using natural variation, this study conducted a detailed in vitro analysis of 241 Arabidopsis thaliana accessions, revealing a high variability in RSA traits among different accessions and their correlation with natural habitat conditions. The study also found a high consistency in the spatial distribution of roots between in vitro and ex vitro conditions, with a larger root area in the lower zone favoring drought tolerance. Genome-wide association studies (GWAS) based on collected RSA phenotype data identified multiple known genes associated with RSA traits and potential candidate genes involved in adaptation to natural habitats.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
David R. Blair, Thomas J. Hoffmann, Joseph T. Shieh
Summary: This study investigates the relationship between the severity of rare genetic diseases and common genetic variations using biobank-scale clinical and genetic data. The study develops a model-based approach to infer quantitative traits capturing disease-related phenotypic variability and identifies common genetic variations that predict the diagnosis and outcomes of Mendelian diseases.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Haiyang Duan, Jianxin Li, Yan Sun, Xuehang Xiong, Li Sun, Wenlong Li, Jionghao Gao, Na Li, Junli Zhang, Jiangkuan Cui, Zhiyuan Fu, Xuehai Zhang, Jihua Tang
Summary: By scoring three leaf angle-related traits on 492 maize inbred lines, we found that leaf angle-related traits were normally distributed and showed significant variation among environments and genotypes. A genome-wide association study identified 85 significant SNPs and 32 non-redundant QTLs that explained 4.80%-24.09% of the phenotypic variation. Meta-analysis identified 47 meta-QTLs and 816 genes, as well as co-located QTLs discovered by both GWAS and meta-analysis.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Jinyang Liu, Yun Lin, Jingbin Chen, Qiang Yan, Chenchen Xue, Ranran Wu, Xin Chen, Xingxing Yuan
Summary: In this study, a large number of genetic resources and extensive genomic data were used to systematically investigate the quantitative trait nucleotides (QTNs) and QTN-by-environment interactions (QEIs) for seed length, width, and weight in mungbean. Genes and candidate genes associated with these traits were identified, providing a reliable approach and solid foundation for identifying seed size-related genes and further molecular biology research.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Shengnan Song, Liangxiao Zhang, Yan Zhao, Chen Sheng, Wangyi Zhou, Senouwa Segla Koffi Dossou, Linhai Wang, Jun You, Rong Zhou, Xin Wei, Xiurong Zhang
Summary: This study identified the genetic variants associated with primary metabolite content variation in sesame using metabolomics analysis and genome-wide association study. Several candidate causative genes were identified, including SiDSEL, SiCAC3, and SiKASI, which are responsible for multiple traits and fatty acid content variation. Overexpression of SiCAC3 in transgenic plants and yeast showed its potential as a target gene for improving unsaturated fatty acid levels in crops. This research provides valuable genetic resources for enhancing sesame seed quality and understanding primary metabolism in oilseed crops.
Article
Plant Sciences
Jianhui Ma, Jingjie Ren, Xuqing Yuan, Meng Yuan, Daijing Zhang, Chunxi Li, Qingdong Zeng, Jianhui Wu, Dejun Han, Lina Jiang
Summary: This study provides important information on the genetic basis of grain calcium content in wheat, contributing to efforts to improve the nutrient quality of wheat.
PLANT CELL REPORTS
(2023)
Article
Neurosciences
Alexey A. Shadrin, Tobias Kaufmann, Dennis van der Meer, Clare E. Palmer, Carolina Makowski, Robert Loughnan, Terry L. Jernigan, Tyler M. Seibert, Donald J. Hagler, Olav B. Smeland, Ehsan Motazedi, Yunhan Chu, Aihua Lin, Weiqiu Cheng, Guy Hindley, Wesley K. Thompson, Chun C. Fan, Dominic Holland, Lars T. Westlye, Oleksandr Frei, Ole A. Andreassen, Anders M. Dale
Summary: The study shows that brain morphology is highly heritable, with only a small portion explained by genetic variants discovered so far. By applying the MOSTest method, researchers identified 780 unique genetic loci associated with cortical morphology in the UK Biobank, with robust replication in the Adolescent Brain Cognitive Development study. Functional analyses implicated pathways involved in neurogenesis and cell differentiation, highlighting the advantage of the MOSTest approach in enhancing research power.
Article
Biotechnology & Applied Microbiology
Dan Xu, Wei Zhu, Youhao Wu, Shuo Wei, Gang Shu, Yaofu Tian, Xiaohui Du, Jigao Tang, Yulong Feng, Gemin Wu, Xue Han, Xiaoling Zhao
Summary: The genetic diversity, relationships, and population structures of Guizhou indigenous chicken breeds were analyzed in this study. The results showed higher genetic diversity in Guizhou chicken breeds compared to commercial chicken breeds. The population structure analysis reflected the breeding history and geographical distribution of Guizhou indigenous chickens. Selective sweep analysis revealed candidate genes associated with specific phenotypic characteristics and economic traits. The study provides important genetic information for further research, conservation, and breeding of Guizhou indigenous chickens.
Article
Agriculture, Dairy & Animal Science
Y. D. Li, X. Liu, Z. W. Li, W. J. Wang, Y. M. Li, Z. P. Cao, P. Luan, F. Xiao, H. H. Gao, H. S. Guo, N. Wang, H. Li, S. Z. Wang
Summary: This study aimed to dissect the genetic basis of bone traits in chickens through a combination of genome-wide association study and selection signature analysis, identifying candidate genes and significant variants. A total of 21 positional candidate genes regulating chicken bone growth and development were identified, providing insights into the genetic architecture of chicken bone traits and offering a molecular basis for applying genomics in practical chicken breeding.
Article
Biotechnology & Applied Microbiology
Weiwei Fu, Rui Wang, Naiyi Xu, Jinxin Wang, Ran Li, Hojjat Asadollahpour Nanaei, Qinghua Nie, Xin Zhao, Jianlin Han, Ning Yang, Yu Jiang
Summary: Galbase is an easily accessible repository that integrates public chicken multi-omics data, providing new opportunities for in-depth functional genomic studies on chicken and identification of genetic variations responsible for chicken complex traits.
Article
Biochemistry & Molecular Biology
Ming Li, Congjiao Sun, Naiyi Xu, Peipei Bian, Xiaomeng Tian, Xihong Wang, Yuzhe Wang, Xinzheng Jia, Rasmus Heller, Mingshan Wang, Fei Wang, Xuelei Dai, Rongsong Luo, Yingwei Guo, Xiangnan Wang, Peng Yang, Dexiang Hu, Zhenyu Liu, Weiwei Fu, Shunjin Zhang, Xiaochang Li, Chaoliang Wen, Fangren Lan, Amam Zonaed Siddiki, Chatmongkon Suwannapoom, Xin Zhao, Qinghua Nie, Xiaoxiang Hu, Yu Jiang, Ning Yang
Summary: The gene numbers and evolutionary rates of birds are lower than those of mammals, but birds have a large species number and morphological diversity. To understand avian evolution, it is necessary to study the complete avian genome. A chicken pan-genome was constructed from 20 de novo assembled genomes, revealing novel protein-coding genes and long noncoding RNAs not found in previous databases. These hidden genes were found to be shared by all chicken genomes, including many housekeeping genes, and were enriched in immune pathways. Comparative genomics showed that these novel genes have higher substitution rates than known genes, updating our knowledge about evolutionary rates in birds. This study provides a framework for constructing a better chicken genome, contributing to the understanding of avian evolution and improvement of poultry breeding.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Agriculture, Dairy & Animal Science
Jianbo Li, Xiuan Zhang, Xiqiong Wang, Congjiao Sun, Jiangxia Zheng, Junying Li, Guoqiang Yi, Ning Yang
Summary: This study established a comprehensive m6A methylation profile of chicken embryonic gonads using MeRIP-seq and identified YTHDC2 as a key regulator in sex differentiation. The results demonstrate that m6A methylation plays an important role in chicken gonad differentiation, providing a better understanding of the epigenetic factors involved in chicken sex determination and differentiation.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
Article
Cell Biology
Jianbo Li, Congjiao Sun, Jiangxia Zheng, Junying Li, Guoqiang Yi, Ning Yang
Summary: This study provides a comprehensive profile of four representative stages of chicken gonadal development at the transcriptional and chromatin levels. The findings suggest that candidate genes involved in morphogenesis, meiosis, and subcellular structure formation may contribute to asymmetric gonadal development. Further analysis reveals that chromatin accessibility and transcriptional activity of these candidate genes may be regulated by nearby open chromatin regions, acting as potential cis-regulatory elements.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Shuang Gu, Chaoliang Wen, Junying Li, Honghong Liu, Qiang Huang, Jiangxia Zheng, Congjiao Sun, Ning Yang
Summary: This study selected four different breeds of chickens to investigate the temporal expression patterns of key regulatory genes during embryonic muscle development, providing a foundation for understanding the regulation mechanisms. The highest expression level of Myomaker, a crucial gene for myoblast fusion, occurred from embryonic days 13 to 15, with Cornish breed showing the highest expression level. The MYOD gene may play an important role after hatching. Histomorphology analysis suggested that the myofibers were largely complete by embryonic day 17 due to increased expression of MSTN and decreased expression of Myomaker.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Jiaming Jin, Qianqian Zhou, Fangren Lan, Junying Li, Ning Yang, Congjiao Sun
Summary: The internal quality of eggs is crucial for human consumption and embryonic development. The composition and differences in microbiota between egg yolks and whites, as well as the migration of microbes from egg white to yolk during incubation, have been explored in this study.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Qianqian Zhou, Fangren Lan, Shuang Gu, Guangqi Li, Guiqin Wu, Yiyuan Yan, Xiaochang Li, Jiaming Jin, Chaoliang Wen, Congjiao Sun, Ning Yang
Summary: In this study, the researchers investigated the effects of host genetics and gut microbiota on feed efficiency in laying hens. They found that genetic factors and gut microbiota both play important roles in determining feed efficiency, with RFI having the highest microbial influence. They also identified three microbial genera that were negatively correlated with RFI and positively contributed to improving feed efficiency.
Article
Genetics & Heredity
Xiuan Zhang, Jianbo Li, Xiqiong Wang, Yuchen Jie, Congjiao Sun, Jiangxia Zheng, Junying Li, Ning Yang, Sirui Chen
Summary: In this study, a sex-reversed chicken flock was created by injecting an aromatase inhibitor, fadrozole, and high-resolution profiles of gene expression and chromatin accessibility in embryonic gonads were constructed. The results showed that fadrozole affected the transcriptional activities of genes related to sex determination and differentiation and regulated the expression of genes related to gonadal development through nearby open chromatin regions. After sexual maturity, the sex-reversed chickens were found to be infertile, and promising genes related to spermatogenesis and infertility were identified through RNA-seq. This study provides important insights into the molecular basis of sex differentiation and infertility in sex-reversed chickens and lays a foundation for further research on bird sex development.
EPIGENETICS & CHROMATIN
(2023)
Article
Biology
Junxiao Ren, Zhengzheng Hu, Quanlin Li, Shuang Gu, Fangren Lan, Xiqiong Wang, Jianbo Li, Junying Li, Liwa Shao, Ning Yang, Congjiao Sun
Summary: Chicken embryonic diapause is a state of temporary arrest of embryonic development triggered by cold stress-induced IRF1 expression, mediated by the PKC-NF-kappa B signaling pathway. This is in contrast to mammalian diapause which is mTOR-dependent. The study characterized the dynamic transcriptomic and phosphoproteomic profiles of chicken embryos in different diapause states and identified key regulators of diapause.
Review
Biochemistry & Molecular Biology
Xiuan Zhang, Jianbo Li, Sirui Chen, Ning Yang, Jiangxia Zheng
Summary: Sex determination and differentiation in birds involves genetic factors controlling the sex determination program, while sex differentiation is influenced by hormones and can be reversed when disturbed. The regulatory mechanism of avian cell autonomous sex identity and sex development is still not clearly understood and requires further exploration. However, avian sex research findings have provided theoretical bases for gender control technologies in poultry production, which are being improved through interdisciplinary cooperation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Chaoliang Wen, Qinli Gou, Shuang Gu, Qiang Huang, Congjiao Sun, Jiangxia Zheng, Ning Yang
Summary: This study investigated the composition of microbial communities in chicken muscle tissue and their relationship with meat quality. The results showed that the microbial composition in muscle tissue can affect the fat content, and there is also a correlation between fat content in different muscle tissues. These findings provide important insights for improving meat quality in chickens.
Article
Agriculture, Dairy & Animal Science
Yiming Yuan, Gang Zheng, Zhen You, Lulu Wang, Ziyi Wang, Congjiao Sun, Changjun Liu, Xianyao Li, Peng Zhao, Yongqiang Wang, Ning Yang, Ling Lian
Summary: This study used whole genome bisulfite sequencing (WGBS) and RNA-seq to identify genes playing important roles in the tumor transformation of Marek's disease (MD). 8 genes, including CD4 and HMGB1, were found to be negatively correlated with methylation and showed high expression in the MDV-infected group. Overexpression of CD4 and HMGB1 significantly promoted MDCC-MSB-1 cell proliferation, suggesting their potential promoting roles in MD tumorigenesis.
Article
Multidisciplinary Sciences
Zhangyuan Pan, Ying Wang, Mingshan Wang, Yuzhe Wang, Xiaoning Zhu, Shenwen Gu, Conghao Zhong, Liqi An, Mingzhu Shan, Joana Damas, Michelle M. Halstead, Dailu Guan, Nares Trakooljul, Klaus Wimmers, Ye Bi, Shang Wu, Mary E. Delany, Xuechen Bai, Hans H. Cheng, Congjiao Sun, Ning Yang, Xiaoxiang Hu, Harris A. Lewin, Lingzhao Fang, Huaijun Zhou
Summary: This study identified and characterized regulatory elements in the chicken genome by integrating genome-wide sequencing datasets from 23 adult tissues. It annotated 1.57 million regulatory elements, predicted enhancer-gene pairs, and super-enhancers. These findings have significant implications for understanding gene regulation in chicken domestication, selection, and complex trait regulation.
Article
Biotechnology & Applied Microbiology
Xinwei Jiang, Boxuan Zhang, Fangren Lan, Conghao Zhong, Jiaming Jin, Xiaochang Li, Qianqian Zhou, Junying Li, Ning Yang, Chaoliang Wen, Congjiao Sun
Summary: Blood biochemical indicators are regulated by both host genetics and gut microbiota, and their interrelationships can affect growth traits in chickens. The heritability and microbiability of these indicators vary, and several candidate genes and microbial species have been identified as potentially involved in their regulation.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Ziyi Wang, Yiming Yuan, Gang Zheng, Meng Sun, Qinyuan Wang, Junfeng Wu, Junying Li, Congjiao Sun, Yongqiang Wang, Ning Yang, Ling Lian
Summary: This study reveals the distribution of ALVE in 11 chicken breeds, including the identification of 23 novel ALVEs in Chinese domestic breeds. Most of these insertion sites are located in intergenic regions and introns.
JOURNAL OF ANIMAL SCIENCE
(2023)
