Article
Agronomy
Jiaowen Pan, Ximeng Zhou, Naveed Ahmad, Kun Zhang, Ronghua Tang, Huiling Zhao, Jing Jiang, Mengdi Tian, Changsheng Li, Aiqin Li, Xianying Zhang, Liangqiong He, Jing Ma, Xiaojie Li, Ruizheng Tian, Changle Ma, Manish K. Pandey, Rajeev K. Varshney, Xingjun Wang, Chuanzhi Zhao
Summary: The candidate gene AhLBA1, which controls the lateral branch angle of peanut, was fine-mapped to a specific physical region on chromosome 15 using BSA-seq and QTL mapping. Genes related to hormone metabolism and regulation were found in this region, suggesting their potential role in determining the lateral branch angle of peanut.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Deyin Zhang, Xiaoxue Zhang, Fadi Li, Teng Liu, Zhihong Hu, Ning Gao, Lvfeng Yuan, Xiaolong Li, Yuan Zhao, Liming Zhao, Yukun Zhang, Dan Xu, Qizhi Song, Jiangbo Cheng, Weimin Wang
Summary: This study identified important candidate genes affecting the increase in rib number in sheep through whole-genome resequencing and analysis. Genes such as CPOX, KCNH1, and CPQ were found to have a combined effect on rib number, providing valuable molecular markers for sheep breeding in relation to rib number.
Article
Biochemistry & Molecular Biology
Wenyu Zhang, Guy R. Reeves, Diethard Tautz
Summary: Through gene disruption assays and an automated phenotyping system, it was found that most candidate genes have an effect on pupal length phenotype in Drosophila, and genes below the GWA significance threshold also showed comparable effect sizes to GWA candidate genes.
Article
Veterinary Sciences
Xinmiao He, Ming Tian, Wentao Wang, Yanzhong Feng, Zhongqiu Li, Jiahui Wang, Yan Song, Jinfeng Zhang, Di Liu
Summary: Min pigs from northeast China have good meat quality, strong disease- and cold-resistance characters, and unique villi hair traits. The study of villi hair traits is significant for understanding cold resistance and animal welfare. In this study, a population of Large White x Min pigs was used to investigate the association between copy number variations (CNVs) and villi hair appearance. Important villi hair-related genes were identified, providing a reference for the breeding of cold-resistant pigs.
VETERINARY SCIENCES
(2023)
Article
Plant Sciences
Vinay Sharma, Sunil S. Gangurde, Spurthi N. Nayak, Anjan S. Gowda, B. S. Sukanth, Supriya S. S. Mahadevaiah, Surendra S. Manohar, Rakeshkumar S. Choudhary, T. Anitha, Sachin S. Malavalli, S. N. Srikanth, Prasad Bajaj, Shailendra Sharma, Rajeev K. Varshney, Putta Latha, Pasupuleti Janila, Ramesh S. Bhat, Manish K. Pandey
Summary: Rising temperatures in semi-arid environments hinder groundnut productivity and quality. Understanding the molecular mechanisms of heat stress tolerance will help address yield losses. QTL analysis identified three QTL clusters that harbor most of the major QTLs for heat tolerant traits, and several candidate genes with potential roles in seed development, plant architecture regulation, yield, plant growth and flowering time regulation, and photosynthesis were also identified. These findings provide a platform for further mapping, gene discovery, and marker development for genomics-assisted breeding of heat-tolerant groundnut varieties.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Lovepreet Singh, Rajat Pruthi, Sandeep Chapagain, Prasanta K. Subudhi
Summary: Alkalinity stress is a major obstacle to rice production, and understanding the mechanisms of alkalinity tolerance is limited. A genome-wide association study was conducted to identify tolerant genotypes and candidate genes for alkalinity tolerance in rice seedlings. Principal component analysis revealed the traits with the highest contributions to tolerance, and clustering analysis grouped the genotypes into different subgroups. Several significant SNPs associated with alkalinity tolerance were identified, as well as novel QTLs and candidate genes. These genomic and genetic resources are valuable for investigating alkalinity tolerance mechanisms and improving tolerance in rice.
Article
Agriculture, Dairy & Animal Science
Gai-ge Ji, Ming Zhang, Yi-fan Liu, Yan-ju Shan, Yun-jie Tu, Xiao-jun Ju, Jian-min Zou, Jing-ting Shu, Jun-feng Wu, Jin-fang Xie
Summary: Significant differences in gene expression were found between the back and thigh skin of chickens, with genes involved in cell proliferation, differentiation, apoptosis, adhesion, and transport processes. Functionally, the differentially expressed genes were mapped into ECM-receptor interaction, peroxisome, focal adhesion, Hedgehog, and PPAR signaling pathways. Signaling pathways related to feathers morphogenesis and development occupied important positions in the protein-protein interaction network analysis.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2021)
Article
Genetics & Heredity
Yuhan Xie, Wei Jiang, Weilai Dong, Hongyu Li, Sheng Chih Jin, Martina Brueckner, Hongyu Zhao
Summary: De novo variants (DNVs) with deleterious effects have been used to identify risk genes for early-onset diseases like congenital heart disease (CHD). However, the statistical power of current methods is limited for large cohorts. In this study, we developed a Markov Random Field model that leverages information from protein-protein interaction networks to increase the power of identifying risk genes. By applying our method to CHD data, we identified several candidate genes and discovered potential functional gene clusters for CHD.
Article
Biochemistry & Molecular Biology
Chen Cao, Jianhua Wang, Devin Kwok, Feifei Cui, Zilong Zhang, Da Zhao, Mulin Jun Li, Quan Zou
Summary: webTWAS is a new resource that combines comprehensive disease GWAS datasets with information on potential causal genes, allowing researchers to explore gene-disease associations. With data from 1298 high-quality GWAS summary statistics, a total of 235,064 gene-disease associations can be accessed, and custom TWAS analyses can be run on a user-friendly web server.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Xiurong Zhao, Changsheng Nie, Jinxin Zhang, Xinghua Li, Tao Zhu, Zi Guan, Yu Chen, Liang Wang, Xue Ze Lv, Weifang Yang, Yaxiong Jia, Zhonghua Ning, Haiying Li, Changqing Qu, Huie Wang, Lujiang Qu
Summary: This study utilized genome-wide association study to identify 148 SNPs associated with egg number traits and 32 candidate genes related to hormone regulation, follicle development, and reproductive system development. The study also highlighted a genomic region on GGA5 as a potential candidate region underlying egg number traits.
Article
Biotechnology & Applied Microbiology
Junmin He, Bingru Zhao, Xixia Huang, Xuefeng Fu, Guifen Liu, Yuezhen Tian, Cuiling Wu, Jingyi Mao, Jing Liu, Shuangbao Gun, Kechuan Tian
Summary: This study identified differentially expressed genes during the development of hair follicles in Merino sheep and identified key genes affecting hair follicle morphogenesis through network analysis. These findings are important for understanding fleece evolution in animals and provide a theoretical basis for breeding fine wool sheep.
Article
Agronomy
Salman Naveed, Sachin Rustgi
Summary: This study used TRV-VIGS technology to functionally characterize two candidate genes in cotton, and found that Gohir.D05G103700 gene is a positive regulator of the indeterminate growth habit, while Gohir.D12G153600 gene does not affect the habit. The study demonstrates that TRV-VIGS technology can be used for rapid analysis of cotton genes and provides potential for breeding cotton plants suited for specific regions.
Article
Multidisciplinary Sciences
Ning Zhang, Xueqing Huang
Summary: The leaf angle of maize is a critical trait that influences plant architecture and crop yields. Through genetic mapping, this study identified eight QTL related to leaf angle, providing valuable insights into the genetic mechanism behind leaf angle formation and facilitating the development of novel maize varieties with ideal plant architecture.
Article
Plant Sciences
Uday Chand Jha, Harsh Nayyar, Ramesh Palakurthi, Rintu Jha, Vinod Valluri, Prasad Bajaj, Annapurna Chitikineni, Narendra P. Singh, Rajeev K. Varshney, Mahendar Thudi
Summary: This study identified key QTLs related to heat stress tolerance in chickpea through genomic region identification and evaluation under heat stress conditions. Candidate genes associated with heat tolerance were also identified, providing valuable information for further molecular breeding efforts.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Dandan Li, Conghao Zhong, Yi Sun, Li Kang, Yunliang Jiang
Summary: By comparing the transcriptomes of granulosa cells between pre-hierarchical and hierarchical follicles in chickens, genes underlying follicle selection were identified. Differential gene, transcript, and lncRNA expression were observed between pre-hierarchical and hierarchical follicles. This study provides important insights into the genetic mechanisms underlying follicle selection in chickens and other poultry species.
FRONTIERS IN GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Jingwei Yuan, Shijun Li, Zheya Sheng, Meikun Zhang, Xuming Liu, Zhengdong Yuan, Ning Yang, Jilan Chen
Summary: High genetic diversity is observed in Tibetan native chickens, with intense inbreeding in the Nyingchi population. Candidate genes in ROH islands are likely to be the drivers of adaptation to high altitude exhibited by the Tibetan native chicken populations.
Article
Nutrition & Dietetics
Bowen Yang, Shimeng Huang, Ning Yang, Aizhi Cao, Lihong Zhao, Jianyun Zhang, Guoxian Zhao, Qiugang Ma
Summary: This study found that bile acids can promote the absorption of fat-soluble vitamins, even under low-fat diets. Through experiments, it was found that bile acids can emulsify fat and promote its hydrolysis, and can improve the digestion and absorption rate of vitamin A. In the experiment, feeding diets supplemented with 60 mg/kg bile acids significantly improved laying performance in laying hens and promoted the growth of follicles in the ovaries. In addition, bile acids can also improve the utilization rate of fat and energy, and enhance the activity of lipase and lipoprotein lipase in the small intestine. Furthermore, the addition of bile acids can increase the vitamin A content in the liver and serum of laying hens, improve serum immune indicators, and antioxidant capacity.
FRONTIERS IN NUTRITION
(2022)
Article
Biotechnology & Applied Microbiology
Jing Yang, Zhiqiong Mao, Xiqiong Wang, Jingjie Zhuang, Sijia Gong, Zhouyang Gao, Guiyun Xu, Ning Yang, Congjiao Sun
Summary: The study comprehensively investigated the regulatory mechanisms of eggshell brownness in different eggshell color and time following oviposition. Results suggest that Pp IX is synthesized de novo and stored in the shell gland, with ALAS1 identified as a key gene regulating Pp IX synthesis. Additionally, three transporters in the Pp IX pathway and three metabolites in shell glands and uterine fluid may influence eggshell browning.
Article
Agriculture, Dairy & Animal Science
Qiang Huang, Chaoliang Wen, Wei Yan, Congjiao Sun, Shuang Gu, Jiangxia Zheng, Ning Yang
Summary: Improving feed efficiency is an important goal in chicken breeding and production. This study found that the development of the gizzard, liver, and cecum is related to the feed efficiency of chickens.
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
Agriculture, Dairy & Animal Science
Xingzheng Li, Jianlou Song, Xuefeng Shi, Mingyi Huang, Lei Liu, Guoqiang Yi, Ning Yang, Guiyun Xu, Jiangxia Zheng
Summary: The study revealed the crucial roles of liver FMO3 and cecal microbes in TMA metabolism in ducks, with the limited oxidation ability of FMO3 explaining the weakening of TMA metabolism in ducks.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
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)
Article
Agriculture, Dairy & Animal Science
Chaoliang Wen, Chunning Mai, Ronglang Cai, Qinli Gou, Boxuan Zhang, Junying Li, Congjiao Sun, Ning Yang
Summary: Duration of fertility (DF) is an important economic trait in poultry production, and its correlation with egg production and breeding efficiency has been analyzed. The heritability of DF traits is low, but improvement of DF is possible through selection. Fertility duration day (FDD) is an effective selection criterion for improving DF, and it can be incorporated into a breeding program to enhance reproductive efficiency.
GENETICS SELECTION EVOLUTION
(2022)
